From max.taubert at gmail.com  Sun May  1 15:48:13 2011
From: max.taubert at gmail.com (Max T.)
Date: Sun, 1 May 2011 15:48:13 +0200
Subject: [FieldTrip] Plotting Dipoles
Message-ID: <BANLkTi=OF9LkP4a+oj+AkE1q_8Zub6A==g@mail.gmail.com>

Dear all,

I'd like to visualize the results of ft_dipolefitting, sadly I've got
no individual MRIs. Is there any function like ft_sourceplot that can
handle ft_dipolefitting-results, maybe using a template brain? Besides
this, is there any function that can transform my Unit
Sphere-coordinates into Talairach space? And is it possible to apply
the 'adaptive spatial filter' if I dont want to use a Beamformer?

Thanks in advance
Max Taubert


From m.severens at maartenskliniek.nl  Mon May  2 13:57:17 2011
From: m.severens at maartenskliniek.nl (Severens, Marianne)
Date: Mon, 2 May 2011 13:57:17 +0200
Subject: [FieldTrip] adding lines in multiplot TFR
Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl>

Dear fieldtrippers

I have a question regarding the ft_multiplotTFR. Is it possible to add something to one (or more) of the subplots of the multiplot? My time axis of the TFR consists of several phases and I would like to add the transistion of one phase to the next in the plots with for example a vertical line.
I've tried to find the axes of the individual subplots, but these don't seem to exist. Has someone already tried something like this?

Thanks in advance
Best Marianne Severens

Disclaimer
Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan.

Sint Maartenskliniek
Hengstdal 3
6522 JV NIJMEGEN
Telefoon 024-3659 911
Telefax 024-3659 204
KvK nummer 41055111



From jm.horschig at donders.ru.nl  Mon May  2 14:10:11 2011
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 02 May 2011 14:10:11 +0200
Subject: [FieldTrip] adding lines in multiplot TFR
In-Reply-To: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl>
References: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl>
Message-ID: <4DBE9F23.8070600@donders.ru.nl>

Hi Marianne,

Adding vertical lines to annotate, for example, events is not possible 
using ft_multiplot_XXX afaik. A similar feature is added in 
ft_databrowser, which however does only work for two-dimensional data 
(amplitude x time). One way around would be to filter your data in the 
desired frequency range and then use ft_databrowser. The function, 
however, still lacks some functionality and compatibility. Should you 
encounter any strange problems, feel free to contact me and we (the FT 
developer team) will try to improve the databrowser according to your 
experiences and wishes.

Another, slightly less elegant way to answer your question is the 
following: Rutger from your group changed a fieldtrip method for his 
personal purposes. Unselfishly, he called the function rutgerplot_TFR. 
In this function, he added horizontal lines to annotate specific 
frequency bands. You can maybe ask him to re-write this hack to add 
vertical lines to annotate the events you are interested in.

Hope this helps!
Best,
Jörn

On 5/2/2011 1:57 PM, Severens, Marianne wrote:
> Dear fieldtrippers
>
> I have a question regarding the ft_multiplotTFR. Is it possible to add something to one (or more) of the subplots of the multiplot? My time axis of the TFR consists of several phases and I would like to add the transistion of one phase to the next in the plots with for example a vertical line.
> I've tried to find the axes of the individual subplots, but these don't seem to exist. Has someone already tried something like this?
>
> Thanks in advance
> Best Marianne Severens
>
> Disclaimer
> Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan.
>
> Sint Maartenskliniek
> Hengstdal 3
> 6522 JV NIJMEGEN
> Telefoon 024-3659 911
> Telefax 024-3659 204
> KvK nummer 41055111
>
> _______________________________________________
> 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

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
Kapitelweg 29
NL-6525 EN Nijmegen
The Netherlands



From m.severens at maartenskliniek.nl  Mon May  2 14:34:56 2011
From: m.severens at maartenskliniek.nl (Severens, Marianne)
Date: Mon, 2 May 2011 14:34:56 +0200
Subject: [FieldTrip] adding lines in multiplot TFR
In-Reply-To: <4DBE9F23.8070600@donders.ru.nl>
References: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl>,
	<4DBE9F23.8070600@donders.ru.nl>
Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B71@smkexch02.maartenskliniek.nl>

Hi Jörn

Thanks for your quick reply! The plots need to be TFR plots, with several frequency bins, so I think the databrowser is not really appropriate for this. I'll try to modify Rutger's solution to make the lines vertical!

Best, Marianne

________________________________________
From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Jörn M. Horschig [jm.horschig at donders.ru.nl]
Sent: Monday, May 02, 2011 2:10 PM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] adding lines in multiplot TFR

Hi Marianne,

Adding vertical lines to annotate, for example, events is not possible
using ft_multiplot_XXX afaik. A similar feature is added in
ft_databrowser, which however does only work for two-dimensional data
(amplitude x time). One way around would be to filter your data in the
desired frequency range and then use ft_databrowser. The function,
however, still lacks some functionality and compatibility. Should you
encounter any strange problems, feel free to contact me and we (the FT
developer team) will try to improve the databrowser according to your
experiences and wishes.

Another, slightly less elegant way to answer your question is the
following: Rutger from your group changed a fieldtrip method for his
personal purposes. Unselfishly, he called the function rutgerplot_TFR.
In this function, he added horizontal lines to annotate specific
frequency bands. You can maybe ask him to re-write this hack to add
vertical lines to annotate the events you are interested in.

Hope this helps!
Best,
Jörn

On 5/2/2011 1:57 PM, Severens, Marianne wrote:
> Dear fieldtrippers
>
> I have a question regarding the ft_multiplotTFR. Is it possible to add something to one (or more) of the subplots of the multiplot? My time axis of the TFR consists of several phases and I would like to add the transistion of one phase to the next in the plots with for example a vertical line.
> I've tried to find the axes of the individual subplots, but these don't seem to exist. Has someone already tried something like this?
>
> Thanks in advance
> Best Marianne Severens
>
> Disclaimer
> Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan.
>
> Sint Maartenskliniek
> Hengstdal 3
> 6522 JV NIJMEGEN
> Telefoon 024-3659 911
> Telefax 024-3659 204
> KvK nummer 41055111
>
> _______________________________________________
> 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

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
Kapitelweg 29
NL-6525 EN Nijmegen
The Netherlands

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Disclaimer
Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan.

Sint Maartenskliniek
Hengstdal 3
6522 JV NIJMEGEN
Telefoon 024-3659 911
Telefax 024-3659 204
KvK nummer 41055111



From andrecravo at gmail.com  Mon May  2 14:38:37 2011
From: andrecravo at gmail.com (Andre Cravo)
Date: Mon, 2 May 2011 09:38:37 -0300
Subject: [FieldTrip] QuikCap 128 NSL layout
In-Reply-To: <BANLkTikzborhgcxnenJa4bkyo9opT=b+Zw@mail.gmail.com>
References: <BANLkTikzborhgcxnenJa4bkyo9opT=b+Zw@mail.gmail.com>
Message-ID: <BANLkTi=kv6uMi02noTc4L-c9kMz4d=Pd3A@mail.gmail.com>

Hello,

I am collecting EEG data from a SynAmps RT 128 channels. I am using a
QuikCap NSL, which although has 128 electrodes, does not follow standard
10-20 localisation.

I'm trying to create a layout to visualise my data using the template
fiducials of the cap. My script currently looks something like this:

cfg =[];
cfg.elecfile='QuikCap_128_NSL.sfp'
cfg.rotate=0;
cfg.projection='polar'
lay=ft_prepare_layout(cfg);
ft_layoutplot(cfg)

However, the electrodes seems to be shifted towards the back of the head.
The layout I get can be seen in the FieldTrip_Layout figure attached. I have
tried to realign the electrodes (using ft_electroderealign), but I get
similar results.

Has anyone ever had a similar problem?

Please find attached the 'QuikCap_128_NSL.sfp' file with the fiducials and a
.png figure of the electrode positions taken from NeuroScan's website.

Thanks in advance for the help.

Andre Cravo
---
University of Sao Paulo-Brazil
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From cmuehl at gmail.com  Mon May  2 17:48:42 2011
From: cmuehl at gmail.com (Christian Muehl)
Date: Mon, 2 May 2011 17:48:42 +0200
Subject: [FieldTrip] Call for Papers: Affective BCI Workshop, Memphis, USA
Message-ID: <BANLkTim5Ft8xhWVKYxYzb85ZPEbUpRDqQA@mail.gmail.com>

** Call for Papers **

2nd Workshop on Affective Brain-Computer Interfaces (aBCI)
Workshop at ACII 2011

Apologies for multiple postings


http://hmi.ewi.utwente.nl/abci2011

http://www.acii2011.org


The second workshop on affective brain-computer interfaces will
explore the advantages and limitations of using neurophysiological
signals as a modality for the automatic recognition of affective and
cognitive states, and the possibilities of using this information
about the user state in innovative and adaptive applications. The goal
is to bring researchers from the communities of brain computer
interfacing, affective computing, neuroergonomics, affective and
cognitive neuroscience together to present state-of-the-art progress
and visions on the various overlaps between those disciplines.

Recent research in brain-computer interfaces (BCI) shows that brain
activity can be used as an active/voluntary, or passive/involuntary
control modality in man-machine interaction. While active BCI
paradigms have received a lot of attention in recent years, research
on passive approaches to BCI still desperately needs concerted
activity. However, it has been shown more than once that brain
activations can carry information about the affective and cognitive
state of a subject, and that the interaction between humans and
machines can be aided by the recognition of those user states. To
achieve robust passive BCIs, efforts from applied and basic sciences
have to be combined. On the one hand, applied fields such as affective
computing aim at the development of applications that adapt to changes
in the user states and thereby enrich the interaction, leading to a
more natural and effective usability. On the other hand, basic
research in neuroscience advances our understanding of the neural
processes associated with emotions. Furthermore, similar advancements
are being made for more cognitive mental states, for example,
attention, fatigue, and work load, which strongly interact with
affective states.


Topics of interest include, but are not limited to:

* emotion elicitation and data collection for affective BCI
* detection of affective and cognitive states with BCI and other modalities
* adaptive interfaces and affective BCI


Invited Talk:
'Brain Dynamics of Affective Engagement' by Scott Makeig, SCCN,
University of California at San Diego, USA


The workshop will be held in conjunction with the 4th International
conference on Affective Computing and Intelligent Interaction
(ACII2011) at the FedEx Institute of Technology at the University of
Memphis, TN.


Submission Instructions

* The papers should feature original empirical work, theoretical work,
or a well defendable but arguable position of the authors (i.e., not
submitted, in submission, or submitted to another conference or
journal while in review).

* Papers will be published in the proceedings of ACII 2011 by Springer.
Papers should not exceed 10 pages and should be formatted according to
the Springer LNCS formatting guidelines
http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0.

* Papers must be submitted as PDF through the EasyChair conference
system, which can be accessed through the workshop web site and the
ACII conference website.

* For further information, contact abci at cs.utwente.nl


Important Dates:
15th of June:    Workshop papers due
1st   of July:   Notification of Acceptance
18th of July:    Camera-ready papers due
9th of October:  Workshop


Programme Chairs:
* Anton Nijholt, Universiteit Twente, The Netherlands
* Brendan Allison, TU Graz, Austria
* Stephen Dunne, Starlab Barcelona, Spain
* Dirk Heylen, University of Twente, The Netherlands


Local Organizer:
* Christian Mühl, University of Twente, The Netherlands

Programme Committee:
* Egon L. van den Broek, University of Twente, The Netherlands
* Touradj Ebrahimi, EPFL, Lausanne, Switzerland
* Peter Desain, Radboud University Nijmegen, The Netherlands
* Jan B.F. van Erp, TNO Human Factors, Soesterberg, The Netherlands
* Stephen Fairclough, John Moores University, Liverpool, UK
* Gary Garcia Molina, Philips Research, Eindhoven, The Netherlands
* Audrey Girouard, Queen's University, Kingston, Canada
* Jonghwa Kim, University of Augsburg, Germany
* Brent Lance, Army Research Laboratory/TNB, Aberdeen Proving Ground, USA
* Robert Leeb, University of Lausanne, Switzerland
* Scott Makeig, University of California at San Diego, USA
* Femke Nijboer, University of Twente, The Netherlands
* Ioannis Patras, Queen Mary University, London, UK
* Thierry Pun, University of Geneva, Switzerland
* Tanja Schultz, Karlsruhe Institute of Technology (KIT), Germany
* Olga Sourina, NanYang Technological University, Singapore
* Thomas J. Sullivan, NeuroSky, San Jose, USA
* Thorsten Zander, Graz University of Technology, Austria



From r.oostenveld at donders.ru.nl  Tue May  3 10:20:05 2011
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Tue, 3 May 2011 10:20:05 +0200
Subject: [FieldTrip] changed channel names for EGI data format from 'e' to
	'E'
Message-ID: <4522B5B9-579C-4AFF-A2CF-449420DAFFAF@donders.ru.nl>

Dear fieldtrip users working on EGI data,

The EGI system does not have well described channel names, but most software deals with it by prefixing the EGI channel names with an 'E', e.g. E1, E2 ... E256

It turned out that there were some inconsistent definitions  whether it should be a lowercase 'e' or an uppercase 'E'. After consulting with some EGI experts (Joseph Dien, Catherine Poulsen, Ingrid Nieuwenhuis), I have just changed fieldtrip to use an uppercase 'E' consistently throughout the code. The EGI layouts (*.sfp files) also use this uppercase definition.

The consequence is that string comparisons between channels like 'e1' and 'E1' might fail and that in the analysis (e.g. grandaveraging data with mixed case labels)  the identical channels are not recognized/matched to each other. If you encounter problems like these, you should fix them by converting the channel labels for data that you have stored on disk in *.mat files to uppercase. That can be easily done with the "upper" function in MATLAB for example like this:

data.label = upper(data.label);
timelock.label = upper(timelock.label);
freq.label = upper(freq.label);
freq.labelcmb = upper(freq.labelcmb);

Sorry for the inconvenience that this causes, hopefully in the future with the consistent definition of the channel labels we won't have problems like this any more.

best regards,
Robert


From annajafarpour at gmail.com  Tue May  3 19:40:20 2011
From: annajafarpour at gmail.com (Anna Jafarpour)
Date: Tue, 3 May 2011 18:40:20 +0100
Subject: [FieldTrip] tf online tutorial is missed
Message-ID: <BANLkTikVw7QKMNXX5Gw2hhxmnyS4Ez9FBQ@mail.gmail.com>

Hello all,

In the Fieldtrip online documentation, the tutorial about tf analysis is
missed. Where else can I find a copy of the tutorial?

Best,
Anna
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From eelke.spaak at donders.ru.nl  Tue May  3 19:55:44 2011
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Tue, 3 May 2011 19:55:44 +0200
Subject: [FieldTrip] tf online tutorial is missed
In-Reply-To: <BANLkTikVw7QKMNXX5Gw2hhxmnyS4Ez9FBQ@mail.gmail.com>
References: <BANLkTikVw7QKMNXX5Gw2hhxmnyS4Ez9FBQ@mail.gmail.com>
Message-ID: <BANLkTimerHtEWZE7bWXSR9He1u1Ji9SGgg@mail.gmail.com>

Hello Anna,

To be honest, I have no idea what happened, or why the time-frequency
tutorial page was suddenly blank. However, I seem to have fixed the
issue by clearing the page's contents, and re-adding it. I'll look
into the issue further; but for now, your problem is solved.

Best,
Eelke

2011/5/3 Anna Jafarpour <annajafarpour at gmail.com>:
> Hello all,
>
> In the Fieldtrip online documentation, the tutorial about tf analysis is
> missed. Where else can I find a copy of the tutorial?
>
> Best,
> Anna
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>


From annajafarpour at gmail.com  Tue May  3 20:04:57 2011
From: annajafarpour at gmail.com (Anna Jafarpour)
Date: Tue, 3 May 2011 19:04:57 +0100
Subject: [FieldTrip] tf online tutorial is missed
In-Reply-To: <BANLkTimerHtEWZE7bWXSR9He1u1Ji9SGgg@mail.gmail.com>
References: <BANLkTikVw7QKMNXX5Gw2hhxmnyS4Ez9FBQ@mail.gmail.com>
	<BANLkTimerHtEWZE7bWXSR9He1u1Ji9SGgg@mail.gmail.com>
Message-ID: <BANLkTi=uds7xSDoN6hyM3q-kn=7xhnNOFg@mail.gmail.com>

Thank you :)

On Tue, May 3, 2011 at 6:55 PM, Eelke Spaak <eelke.spaak at donders.ru.nl>wrote:

> Hello Anna,
>
> To be honest, I have no idea what happened, or why the time-frequency
> tutorial page was suddenly blank. However, I seem to have fixed the
> issue by clearing the page's contents, and re-adding it. I'll look
> into the issue further; but for now, your problem is solved.
>
> Best,
> Eelke
>
> 2011/5/3 Anna Jafarpour <annajafarpour at gmail.com>:
> > Hello all,
> >
> > In the Fieldtrip online documentation, the tutorial about tf analysis is
> > missed. Where else can I find a copy of the tutorial?
> >
> > Best,
> > Anna
> >
> > _______________________________________________
> > 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
>
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From annajafarpour at gmail.com  Tue May  3 21:10:48 2011
From: annajafarpour at gmail.com (Anna Jafarpour)
Date: Tue, 3 May 2011 20:10:48 +0100
Subject: [FieldTrip] trial selection
Message-ID: <BANLkTi=ZGwRT7o8_aHLfrzYN1sYMj9O_4Q@mail.gmail.com>

Dear All,

I am sorry if this is an FAQ; the online FAQ is not accessible.

Is there any function for selecting trials according to the trialinfo? Or is
there any function for copying specific trials (with its configuration) into
a new variable?

Best,
Anna
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From a.stolk at fcdonders.ru.nl  Tue May  3 21:39:15 2011
From: a.stolk at fcdonders.ru.nl (Stolk, A.)
Date: Tue, 3 May 2011 21:39:15 +0200 (CEST)
Subject: [FieldTrip] trial selection
In-Reply-To: <BANLkTi=ZGwRT7o8_aHLfrzYN1sYMj9O_4Q@mail.gmail.com>
Message-ID: <1167814753.23605.1304451555946.JavaMail.root@sculptor.zimbra.ru.nl>



Hi Anna, 



Have a look at the help of ft_redefinetrial. Possibly the configuration option cfg.trials is the one you're looking for. 



Yours, 

Arjen 



  
----- "Anna Jafarpour" <annajafarpour at gmail.com> schreef: 
> Van: "Anna Jafarpour" <annajafarpour at gmail.com> 
> Aan: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl> 
> Verzonden: Dinsdag 3 mei 2011 21:10:48 
> Onderwerp: [FieldTrip] trial selection 
> 
> Dear All, 
> I am sorry if this is an FAQ; the online FAQ is not accessible. 
> Is there any function for selecting trials according to the trialinfo? Or is there any function for copying specific trials (with its configuration) into a new variable? 
> 
> Best, 
> Anna 
> 
> _______________________________________________ 
> fieldtrip mailing list 
> fieldtrip at donders.ru.nl 
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From inbalots at gmail.com  Wed May  4 14:25:30 2011
From: inbalots at gmail.com (Inbal Lots)
Date: Wed, 4 May 2011 15:25:30 +0300
Subject: [FieldTrip] Question about trl
Message-ID: <BANLkTik_y8P_PpEPSfUp-1Rp1r=U5NNoWA@mail.gmail.com>

Hello
my name is Inbal and I wanted to ask about trl.
Say I define trl myself, as following:
trl = [1000 , 1600 , -100];
Lets assume that the sampling rate is 1000Hz
trl defines, as far as I understand, the onset at sample #1000, the data
start of the data to analyze , before onset, at sample #900 and the end of
the data to analyze at sample # 1500. Is that so?

Thanks
Inbal
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From stan.vanpelt at fcdonders.ru.nl  Wed May  4 14:56:59 2011
From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt)
Date: Wed, 4 May 2011 14:56:59 +0200 (CEST)
Subject: [FieldTrip] Question about trl
In-Reply-To: <244f01cc0a5a$2d05a1e0$8710e5a0$@vanpelt@fcdonders.ru.nl>
Message-ID: <915523278.28822.1304513819890.JavaMail.root@sculptor.zimbra.ru.nl>

Hello Inbal, 




That is not quite correct. Say you define a trial as cfg.trl=[1000 1600 -100], then “-100” is the offset (in samples) of your time axis. So, for this trial, you will get a dataset of 600 samples (or also ms in your example case) length (=1600-1000), of which sample 101 will be defined as t=0s (-100 meaning that the 1 st sample of your trial is -100 samples from t=0). 



So, the third column in cfg.trl doesn’t affect which part of the data will de used to define the trial (samples 1000 to 1600 will always be read from your data), but only affects the position of t=0 on the time-axis of your trial (data.time). 



Best, 

Stan 



Stan van Pelt, PhD 

Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen 

Kapittelweg 29, 6525 EN Nijmegen, Netherlands 

E-mail: stan.vanpelt at donders.ru.nl 

Website: www.ru.nl/donders/ 

Phone: (+31) (0)24 36 68495 

Fax: (+31) (0)24 36 10989 




> 

From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Inbal Lots 
> Sent: Wednesday, May 04, 2011 2:26 PM 
> To: fieldtrip at donders.ru.nl 
> Subject: [FieldTrip] Question about trl 




Hello 
> my name is Inbal and I wanted to ask about trl. 
> Say I define trl myself, as following: 
> trl = [1000 , 1600 , -100]; 
> Lets assume that the sampling rate is 1000Hz 
> trl defines, as far as I understand, the onset at sample #1000, the data start of the data to analyze , before onset, at sample #900 and the end of the data to analyze at sample # 1500. Is that so? 
> 
> Thanks 
> Inbal
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From akiko at nyu.edu  Wed May  4 15:17:49 2011
From: akiko at nyu.edu (Akiko Ikkai)
Date: Wed, 04 May 2011 09:17:49 -0400
Subject: [FieldTrip] overlaying beamformer results to native/normalized space
Message-ID: <5990a22b3c17f9.4dc119bd@mail.nyu.edu>

I sent a below message to the list last night, but it was bounced back. I'm trying from another email account. My apologies if this was duplicate... 



I'm trying to run beamformer analysis on my MEG data, using DICS, and having difficulty visualizing meaningful results. 

I was able to align MRI image to MEG sensors; after segmentation, ft_prepare_singleshell and  ft_prepare_leadfield, plotting ft_data.grad and volume model confirms that they align reasonably. However, using data.grad, grid, and vol to run ft_sourceanalysis, and ft_sourceinterpolate with MRI (in ctf coordinate system and aligned to MEG sensors) somehow distorts the alignment, and the new volume model does not resemble the original. 

I'm assuming that, after ft_sourceinterpolate, if I segment source_interpolated.anatomy and run ft_prepare_singleshell and ft_prepare_leadfield, it should align with MEG sensors, just as the initial volume model aligned with MEG sensors... or am I making too much of an assumption here? 

Because of the misalignment, output data of ft_sourceinterpolate with "anatomy" and "avg.pow" does not agree with topoplot (run ft_freqanalysis on the same dataset).

If anyone could explain why this alignment distortion might be happening during ft_sourceanalysis and/or ft_sourceinterpolate, I'd really appreciate it.

Thanks in advance, Akiko   

-- 
Akiko Ikkai, Ph.D. 
Postdoctoral Fellow
Department of Psychological and Brain Sciences
Johns Hopkins University
Ames Hall, 3400 N. Charles St.
Baltimore, MD 21218


From ting.ac at gmail.com  Wed May  4 15:56:57 2011
From: ting.ac at gmail.com (Allison Connolly)
Date: Wed, 4 May 2011 08:56:57 -0500
Subject: [FieldTrip] error using spm_slice_vol
Message-ID: <BANLkTi=gv_XKymTL2RcXMb=XrCFaJj_t9Q@mail.gmail.com>

Hi all,

I am trying to segment an mri volume using. When I call
ft_read_mri('filename'), I get an error that says:

??? Error using ==> spm_slice_vol at 28
spm_slice_vol.c not compiled - see spm_MAKE.sh

Error in ==> spm_read_vols at 35
    Y(:,:,p,i) = spm_slice_vol(V(i),spm_matrix([0 0 p]),V(i).dim(1:2),0);

Error in ==> ft_read_mri at 97
  img = spm_read_vols(hdr);

I tried installing the most up to date version of fieldtrip and I still get
the same error. Can someone help me?

-Allison
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From annajafarpour at gmail.com  Wed May  4 16:03:18 2011
From: annajafarpour at gmail.com (Anna Jafarpour)
Date: Wed, 4 May 2011 15:03:18 +0100
Subject: [FieldTrip] Multivariate analysis of MEG data
Message-ID: <BANLkTik8=p6CQoDKxQJv3Wt7851vH3UBgA@mail.gmail.com>

Hi,

I am trying to run an SVM on a data (2 X  60 rpt 274 chan 1 freq 41 timep)
using Fieltrip 20110420.
But it gives an error and looks for ft_mv_standardizer. I cannot find this
function anywhere (I set-pathed the multivariate folder as well). What is
the problem?

Best,
Anna
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From r.oostenveld at donders.ru.nl  Wed May  4 22:24:40 2011
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Wed, 4 May 2011 22:24:40 +0200
Subject: [FieldTrip] tf online tutorial is missed
In-Reply-To: <BANLkTi=uds7xSDoN6hyM3q-kn=7xhnNOFg@mail.gmail.com>
References: <BANLkTikVw7QKMNXX5Gw2hhxmnyS4Ez9FBQ@mail.gmail.com>
	<BANLkTimerHtEWZE7bWXSR9He1u1Ji9SGgg@mail.gmail.com>
	<BANLkTi=uds7xSDoN6hyM3q-kn=7xhnNOFg@mail.gmail.com>
Message-ID: <B14C15A3-82C6-4283-965A-8EC84DF705B1@donders.ru.nl>

Dear wiki visitors,

There were some issues on the fieldtrip wiki with pages suddenly displaying as empty. It turned out that it was due to a full hard-disk in our webserver. The problem has been resolved and now everything should work smoothly again.

best regards,
Robert 



On 3 May 2011, at 20:04, Anna Jafarpour wrote:

> Thank you :)
> 
> On Tue, May 3, 2011 at 6:55 PM, Eelke Spaak <eelke.spaak at donders.ru.nl> wrote:
> Hello Anna,
> 
> To be honest, I have no idea what happened, or why the time-frequency
> tutorial page was suddenly blank. However, I seem to have fixed the
> issue by clearing the page's contents, and re-adding it. I'll look
> into the issue further; but for now, your problem is solved.
> 
> Best,
> Eelke
> 
> 2011/5/3 Anna Jafarpour <annajafarpour at gmail.com>:
> > Hello all,
> >
> > In the Fieldtrip online documentation, the tutorial about tf analysis is
> > missed. Where else can I find a copy of the tutorial?
> >
> > Best,
> > Anna
> >
> > _______________________________________________
> > 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
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From ekanal at cmu.edu  Thu May  5 00:05:54 2011
From: ekanal at cmu.edu (Kanal Eliezer)
Date: Wed, 4 May 2011 18:05:54 -0400
Subject: [FieldTrip] ft_channelselection fails with negation and regex
	matching
Message-ID: <710C0AC3-5C40-4746-96FC-FBB2D5D1979F@cmu.edu>

Hello fieldtrip -

We have a Elekta Neuromag 306 scanner, and I'm trying to select only the gradiometers. The magnetometers are labeled 'MEGxxx1', where x can be any number, and the gradiometers are either 'MEGxxx2' or 'MEGxxx3'. However, using ft_channelselection results in the following error:

~~~~
>> ft_channelselection({'all','-STI*','-MEG*1'}, cfg.hdr.label)
??? Matrix index is out of range for deletion.

Error in ==> ft_channelselection at 287
channel([
~~~~

This error is somewhat complex, as I was able to determine that ft_channelselection recursively calls itself a number of times while running, and I was unable to figure out what is causing this problem. Any help would be appreciated. Thanks!

Eliezer Kanal


--------------------
Eliezer Kanal, Ph.D.
Postdoctoral Fellow
Center for the Neural Basis of Cognition
Carnegie Mellon University
4400 Fifth Ave, Suite 110A
Pittsburgh PA 15213
P: 412-268-4115
F: 412-268-5060




From a.stolk at fcdonders.ru.nl  Thu May  5 09:54:53 2011
From: a.stolk at fcdonders.ru.nl (Stolk, A.)
Date: Thu, 5 May 2011 09:54:53 +0200 (CEST)
Subject: [FieldTrip] ft_channelselection fails with negation and
	regex	matching
In-Reply-To: <710C0AC3-5C40-4746-96FC-FBB2D5D1979F@cmu.edu>
Message-ID: <543079.33508.1304582093866.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Kanal,

I've managed to replicate your bug with MEG data and we will try to sort this out.

Yours,
Arjen
----- "Kanal Eliezer" <ekanal at cmu.edu> schreef:

> Van: "Kanal Eliezer" <ekanal at cmu.edu>
> Aan: "Email FieldTrip project discussion list for the" <fieldtrip at donders.ru.nl>
> Verzonden: Donderdag 5 mei 2011 00:05:54
> Onderwerp: [FieldTrip] ft_channelselection fails with negation and regex	matching
>
> Hello fieldtrip -
> 
> We have a Elekta Neuromag 306 scanner, and I'm trying to select only
> the gradiometers. The magnetometers are labeled 'MEGxxx1', where x can
> be any number, and the gradiometers are either 'MEGxxx2' or 'MEGxxx3'.
> However, using ft_channelselection results in the following error:
> 
> ~~~~
> >> ft_channelselection({'all','-STI*','-MEG*1'}, cfg.hdr.label)
> ??? Matrix index is out of range for deletion.
> 
> Error in ==> ft_channelselection at 287
> channel([
> ~~~~
> 
> This error is somewhat complex, as I was able to determine that
> ft_channelselection recursively calls itself a number of times while
> running, and I was unable to figure out what is causing this problem.
> Any help would be appreciated. Thanks!
> 
> Eliezer Kanal
> 
> 
> --------------------
> Eliezer Kanal, Ph.D.
> Postdoctoral Fellow
> Center for the Neural Basis of Cognition
> Carnegie Mellon University
> 4400 Fifth Ave, Suite 110A
> Pittsburgh PA 15213
> P: 412-268-4115
> F: 412-268-5060
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From julian.keil at gmail.com  Thu May  5 14:15:02 2011
From: julian.keil at gmail.com (Julian Keil)
Date: Thu, 5 May 2011 14:15:02 +0200
Subject: [FieldTrip] cfg.maskparameter in ft_multiplotER
Message-ID: <06AC35D0-BE3D-4B96-B67F-3E1B64DBAE22@gmail.com>

Hi all,

i have a question regarding the mask-option in ft_multiplotER (and singleplotER).
After the montecarlo statistic with holm-correction, I get the following data structure:

stats = 

      prob: [145x679 double]
      mask: [145x679 double]
      stat: [145x679 double]
       ref: [145x679 double]
    dimord: 'chan_time'
     label: {145x1 cell}
      time: [1x679 double]
       cfg: [1x1 struct]

I then use these options to plot the results:

cfg=[];
cfg.interactive='yes';
cfg.layout='4D148.lay';
cfg.zparam='stat'; 
cfg.maskparameter='mask';
figure;ft_multiplotER(cfg,stats);

Unfortunately, I get the error message:

??? Error using ==> ft_multiplotER at 528
data in cfg.maskparameter should be vector with one value per channel

I am a bit confused, as this used to work fine with an older version of fieldtrip (fieldtrip-20110113).
Can anyone explain to me how to handle the mask-option. I already tried to reduce the mask-matrix to a one-value-per channel vector, but this produces the error:

??? Attempt to reference field of non-structure array.

Error in ==> ft_multiplotER at 527
    if min(size(datmask)) ~= 1 || max(size(datmask)) ~= length(data.label)

Maybe I missed some important changes in a recent fieldtrip-update....

Thanks a lot

Julian


Dipl. Psych. Julian Keil

OBOB-Lab
University of Konstanz
Department of Psychology
P.O. Box D25
78457 Konstanz
Germany

Tel: ++49 - (0)7531 - 88 42 50
Fax: ++49 - (0)7531 - 88 28 91
Email: julian.keil at uni-konstanz.de
Homepage: http://www.uni-konstanz.de/obob







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From inieuwenhuis at berkeley.edu  Thu May  5 23:55:32 2011
From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis)
Date: Thu, 05 May 2011 14:55:32 -0700
Subject: [FieldTrip] fieldtrip2eeglab
Message-ID: <4DC31CD4.6070508@berkeley.edu>

Hi,

Does a fieldtrip2eeglab script exist, to transform a Matlab structure 
generated by FieldTrip into a Matlab struct that EEGlab can swallow? I 
know the reverse does exist (eeglab2fieldtrip). I need to get some raw 
data (egi_mff dataformat, which is not implemented in EEGlab yet as far 
as I know) into EEGlab. Or if anyone has written some code that might do 
the trick, that would be very much appreciated as well!

Thanks!
Ingrid

-- 
Ingrid Nieuwenhuis PhD
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305



From Maarten.van-Casteren at mrc-cbu.cam.ac.uk  Fri May  6 14:10:13 2011
From: Maarten.van-Casteren at mrc-cbu.cam.ac.uk (Maarten van-Casteren)
Date: Fri, 6 May 2011 12:10:13 +0000
Subject: [FieldTrip] Problem with user specified trial function
Message-ID: <076BBBEE0241DF4FA4F09E43B8EB0176391359F1@WSR21.mrc-cbsu.local>

Hi,

I've just started to use Fieldtrip and I don't
have much experience with Matlab, so I could
just be making a stupid mistake, but I found
some very strange behavious when I tried to
specify my own trailfunction.

I started from the example given on the tutorial
pages of the wiki. I've indicated the line of interest
with an additional '->'. This is what I used:

for i=1:length(event)
  if strcmp(event(i).type, cfg.trialdef.eventtype)
    % it is a trigger, see whether it has the right value
    if ismember(event(i).value, cfg.trialdef.eventvalue)
      % add this to the trl definition
      begsample     = event(i).sample - cfg.trialdef.prestim*hdr.Fs;
      endsample     = event(i).sample + cfg.trialdef.poststim*hdr.Fs - 1;
      offset        = -cfg.trialdef.prestim*hdr.Fs;
      trigger       = event(i).value; % remember the trigger (=condition) for each trial
->    trl(end+1, :) = [round([begsample endsample offset])  trigger];
    end
  end
end

When I use it like this it will clip all sample and
offset values at 0 - 65536, that is the limits of an
unsigned integer. I had to change the actual line
that appends the trial to this to make it work:

trl(end+1, :) = [double(begsample) double(endsample) double(offset) double(trigger)];

All values are shown by the debugger as doubles
anyway, so why this explicit conversion is needed
is completely beyond me.

Does anyone of you know what is going on?
I already asked one of the local Matlab gurus,
but he was even more amazed than me...

Thanks,

Maarten

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From jm.horschig at donders.ru.nl  Fri May  6 14:31:24 2011
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Fri, 06 May 2011 14:31:24 +0200
Subject: [FieldTrip] Problem with user specified trial function
In-Reply-To: <076BBBEE0241DF4FA4F09E43B8EB0176391359F1@WSR21.mrc-cbsu.local>
References: <076BBBEE0241DF4FA4F09E43B8EB0176391359F1@WSR21.mrc-cbsu.local>
Message-ID: <4DC3EA1C.4080606@donders.ru.nl>

Hi Maarten,

no idea what might go wrong there (for me your code snippet works fine). 
Anyway, you could try to first round cfg.trialdef.prestim*hdr.Fs (same 
for poststim) outside the loop and store them as local variables and 
then continue without having to round in every single iteration for 
every single trial-def, e.g.:

trloff = round(-cfg.trialdef.prestim*hdr.Fs);
trldur = round((cfg.trialdef.poststim+cfg.trialdef.prestim)*hdr.Fs) - 1;
% that's from trialfun_general

I bet this will make a difference, although it should of course not. 
Maybe someone else can confirm the error with your code snippet...

Best,
Jörn



On 5/6/2011 2:10 PM, Maarten van-Casteren wrote:
>
> Hi,
>
> I've just started to use Fieldtrip and I don't
>
> have much experience with Matlab, so I could
>
> just be making a stupid mistake, but I found
>
> some very strange behavious when I tried to
>
> specify my own trailfunction.
>
> I started from the example given on the tutorial
>
> pages of the wiki. I've indicated the line of interest
>
> with an additional '->'. This is what I used:
>
> for i=1:length(event)
>
>   if strcmp(event(i).type, cfg.trialdef.eventtype)
>
>     % it is a trigger, see whether it has the right value
>
>     if ismember(event(i).value, cfg.trialdef.eventvalue)
>
>       % add this to the trl definition
>
>       begsample     = event(i).sample - cfg.trialdef.prestim*hdr.Fs;
>
>       endsample     = event(i).sample + cfg.trialdef.poststim*hdr.Fs - 1;
>
>       offset        = -cfg.trialdef.prestim*hdr.Fs;
>
>       trigger       = event(i).value; % remember the trigger 
> (=condition) for each trial
>
> ->    trl(end+1, :) = [round([begsample endsample offset])  trigger];
>
>     end
>
>   end
>
> end
>
> When I use it like this it will clip all sample and
>
> offset values at 0 -- 65536, that is the limits of an
>
> unsigned integer. I had to change the actual line
>
> that appends the trial to this to make it work:
>
> trl(end+1, :) = [double(begsample) double(endsample) double(offset) 
> double(trigger)];
>
> All values are shown by the debugger as doubles
>
> anyway, so why this explicit conversion is needed
>
> is completely beyond me.
>
> Does anyone of you know what is going on?
>
> I already asked one of the local Matlab gurus,
>
> but he was even more amazed than me...
>
> Thanks,
>
> Maarten
>
>
> _______________________________________________
> 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

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
Kapitelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From fedeletommaso at yahoo.it  Fri May  6 17:28:48 2011
From: fedeletommaso at yahoo.it (tommaso fedele)
Date: Fri, 6 May 2011 16:28:48 +0100 (BST)
Subject: [FieldTrip] FT_analysis of the average vs
	average(FT_analysis(single trials))
Message-ID: <686364.21106.qm@web28608.mail.ukl.yahoo.com>

Hi all, 
I want to test if some component that I observe in the average of my ERP signal 
are phase locked to the stimulus.
In oder to do so I compare
1. TFR_averaged_signal =  ft_freqanalysis(cfg, averaged_signal)
2.  TFR_singletrials_signal =  ft_freqanalysis(cfg, singletrials_signal)

with the first structure TFR_averaged_signal everything is fine, and I get my 
nice TF plot.
with the second I should average through "trials". Is there a function for that? 
Or, is it correct to proceed plotting
the average of  TFR_singletrials_signal.powspctrm through the "trials-matrix 
dimension"?

Thanks
Tommaso
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From r.oostenveld at donders.ru.nl  Mon May  9 12:13:40 2011
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Mon, 9 May 2011 12:13:40 +0200
Subject: [FieldTrip] fieldtrip2eeglab
In-Reply-To: <4DC31CD4.6070508@berkeley.edu>
References: <4DC31CD4.6070508@berkeley.edu>
Message-ID: <45F6D404-F8C3-4339-AE25-25E52C8D2598@donders.ru.nl>

Hi Ingrid,

I searched my hard disk and found the attached file. Note that it is a  
very old file (last modified 2006) and I don't know whether the "EEG"  
structure is still like this, but it may help you get started.

best,
Robert




On 5 May 2011, at 23:55, Ingrid Nieuwenhuis wrote:

> Hi,
>
> Does a fieldtrip2eeglab script exist, to transform a Matlab  
> structure generated by FieldTrip into a Matlab struct that EEGlab  
> can swallow? I know the reverse does exist (eeglab2fieldtrip). I  
> need to get some raw data (egi_mff dataformat, which is not  
> implemented in EEGlab yet as far as I know) into EEGlab. Or if  
> anyone has written some code that might do the trick, that would be  
> very much appreciated as well!
>
> Thanks!
> Ingrid


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From jstout211 at yahoo.com  Mon May  9 22:12:15 2011
From: jstout211 at yahoo.com (Jeff Stout)
Date: Mon, 9 May 2011 13:12:15 -0700 (PDT)
Subject: [FieldTrip] Leadfield calculations result in NaNs
Message-ID: <102170.78349.qm@web113519.mail.gq1.yahoo.com>


Hi, 
I am having trouble generating leadfields for source analysis.  I am using data from a 4D magnetometer system (Magnes 3600), at St. Louis University.
The data is averged time domain data.
  The volume conductor is a single shell model generated from the headshape file(~4000 vert. and 8000 triangles).  I have vizualized the volume conductor, sensors, and "inside" grid and they appear to be in the correct locations relative to each other.  I have performed this analysis using the default source space for 4D ('m') and I have tried it scaling the headshape and sensors into cm to conform with the ctf source space.   Below is part of my code and the warning thrown by matlab.  After the calculation of the leadfields, it is apparent that they are all NaN's, so I am unable to generate source activations.
cfg = [];cfg.headshape = shape;shape.pnt = shape.pnt*100;shape.unit  =
 'cm';[vol,cfg] = ft_prepare_singleshell(cfg)
cfg                 = [];cfg.grad            = avg.grad; cfg.grad.pnt = cfg.grad.pnt*100;cfg.grad.unit  = 'cm';cfg.vol             = vol;cfg.sourceunits = 'cm';cfg.coordsys   = 'ctf';cfg.reducerank      ='no';  cfg.channel         = {'MEG'};cfg.grid.resolution = 2[vol, sens] = ft_prepare_vol_sens(vol, cfg.grad)[grid] = ft_prepare_leadfield(cfg)   
>> [grid] = ft_prepare_leadfield(cfg)using headmodel
 specified in the configurationusing gradiometers specified in the configurationcomputing surface normalsWarning: Matrix is singular, close to singular or badly scaled.   <<<<<<<<<<         Results may be inaccurate. RCOND = NaN. > In forward/private/meg_ini>getcoeffs at 111  In forward/private/meg_ini at 53  In ft_prepare_vol_sens at 275  In fieldtrip-20110507/private/prepare_headmodel at 114  In ft_prepare_leadfield at 150creating dipole grid based on automatic 3D grid with specified resolution3528 dipoles inside, 0 dipoles outside brainmaking tight grid3528 dipoles inside, 0 dipoles outside braincomputing leadfieldcomputing leadfield 1/3528computing leadfield 2/3528computing leadfield 3/3528computing leadfield 4/3528 ......

The leadfield data generated is a matrix of NaN's, which appear to be an issue when evaluating bas and gradbas in the get_coeffs subfunction  [bas,gradbas]=legs(x1,n1,order,scale).
Does anyone know how to resolve this issue? Any help will be greatly appreciated.
Thanks,
Jeff Stout










Open in Google Docs ViewerOpen link in new tabOpen link in new windowOpen link in new incognito windowDownload fileCopy link addressEdit PDF File on PDFescape.com
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From matthew at psych.columbia.edu  Tue May 10 00:37:39 2011
From: matthew at psych.columbia.edu (Matthew Davidson)
Date: Mon, 9 May 2011 18:37:39 -0400
Subject: [FieldTrip] Human neurophysiology analysis tech posting in San Diego
Message-ID: <BANLkTinJNMo3kx+11uyxtMN+0toYKJAeLA@mail.gmail.com>

Human Neurophysiology Analysis Technician – To assist a team of experienced
neurophysiologists conduct language, memory, sleep and developmental studies
in humans with MEG and intracranial recordings. MEG localization will use
structural MRI constraints and functional MRI bias. Intracranial recordings
include microelectrode arrays, unit-recordings, and laminar current source
density analysis. The candidate must have high abstract intelligence in
order to rapidly acquire different techniques, modify them as necessary, and
recognize inconsistent results. Prior expertise with MatLab would be very
useful, and some knowledge of neuroscience is expected. Collaborate with a
large, talented and friendly group of scientists, programmers and
technicians engaged in multimodal brain research. The position is available
starting immediately, with the expectation that you would remain for at
least 2 years, but it is subject to annual review and continuation of grant
funding. Everyone is welcome to apply regardless of gender, ethnicity, or
other irrelevancies. Please contact Eric Halgren, Ph.D., Multimodal Imaging
Laboratory, University of California at San Diego,ehalgren at ucsd.edu
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From jan.schoffelen at donders.ru.nl  Tue May 10 08:36:51 2011
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Tue, 10 May 2011 08:36:51 +0200
Subject: [FieldTrip] Leadfield calculations result in NaNs
In-Reply-To: <102170.78349.qm@web113519.mail.gq1.yahoo.com>
References: <102170.78349.qm@web113519.mail.gq1.yahoo.com>
Message-ID: <AC6FBFD8-3F14-454E-8BBC-0812B13E7DC9@donders.ru.nl>

Dear Jeff,

 From what you describe I don't really know what's going wrong. Are  
you using the headsurface file generated with the polhemus? It could  
be that this causes the problem. For the singleshell model to work,  
you need a triangulated surface. The headsurface file contains only a  
point cloud. Matlab tries to create a triangulation from this point  
cloud, and I could imagine that this triangulation misbehaves here,  
leading some nans here and there (judging from your message this  
happens when the normals to the triangles are computed), which  
eventually cause nans all over the place. For the time being you could  
try to use a different volume conductor model (localspheres), or you  
may want to use a structural MRI for the singleshell creation (if  
available), to verify that the problem is caused by the headsurface  
file and not by fieldtrip.

Best,

Jan-Mathijs

On May 9, 2011, at 10:12 PM, Jeff Stout wrote:

>
> Hi,
>
> I am having trouble generating leadfields for source analysis.  I am  
> using data from a 4D magnetometer system (Magnes 3600), at St. Louis  
> University.
>
> The data is averged time domain data.  The volume conductor is a  
> single shell model generated from the headshape file(~4000 vert. and  
> 8000 triangles).  I have vizualized the volume conductor, sensors,  
> and "inside" grid and they appear to be in the correct locations  
> relative to each other.  I have performed this analysis using the  
> default source space for 4D ('m') and I have tried it scaling the  
> headshape and sensors into cm to conform with the ctf source  
> space.   Below is part of my code and the warning thrown by matlab.   
> After the calculation of the leadfields, it is apparent that they  
> are all NaN's, so I am unable to generate source activations.
>
> cfg = [];
> cfg.headshape = shape;
> shape.pnt = shape.pnt*100;
> shape.unit  = 'cm';
> [vol,cfg] = ft_prepare_singleshell(cfg)
>
> cfg                 = [];
> cfg.grad            = avg.grad;
> cfg.grad.pnt = cfg.grad.pnt*100;
> cfg.grad.unit  = 'cm';
> cfg.vol             = vol;
> cfg.sourceunits = 'cm';
> cfg.coordsys   = 'ctf';
> cfg.reducerank      ='no';
> cfg.channel         = {'MEG'};
> cfg.grid.resolution = 2
> [vol, sens] = ft_prepare_vol_sens(vol, cfg.grad)
> [grid] = ft_prepare_leadfield(cfg)
>
> >> [grid] = ft_prepare_leadfield(cfg)
> using headmodel specified in the configuration
> using gradiometers specified in the configuration
> computing surface normals
> Warning: Matrix is singular, close to singular or badly scaled.    
> <<<<<<<<<<
>          Results may be inaccurate. RCOND = NaN.
> > In forward/private/meg_ini>getcoeffs at 111
>   In forward/private/meg_ini at 53
>   In ft_prepare_vol_sens at 275
>   In fieldtrip-20110507/private/prepare_headmodel at 114
>   In ft_prepare_leadfield at 150
> creating dipole grid based on automatic 3D grid with specified  
> resolution
> 3528 dipoles inside, 0 dipoles outside brain
> making tight grid
> 3528 dipoles inside, 0 dipoles outside brain
> computing leadfield
> computing leadfield 1/3528
> computing leadfield 2/3528
> computing leadfield 3/3528
> computing leadfield 4/3528 ......
>
>
> The leadfield data generated is a matrix of NaN's, which appear to  
> be an issue when evaluating bas and gradbas in the get_coeffs  
> subfunction  [bas,gradbas]=legs(x1,n1,order,scale).
>
> Does anyone know how to resolve this issue? Any help will be greatly  
> appreciated.
>
> Thanks,
> Jeff Stout
>
>
>
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793

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From stefan.debener at uni-oldenburg.de  Tue May 10 09:04:47 2011
From: stefan.debener at uni-oldenburg.de (Stefan Debener)
Date: Tue, 10 May 2011 09:04:47 +0200
Subject: [FieldTrip] Auditory BCI post-doc posting
Message-ID: <4DC8E38F.5050902@uni-oldenburg.de>

Dear all,

We are seeking a scientist/post-doc who is interested in developing an 
auditiry brain computer interface. Please visit:
http://www.hearingresearch.uni-oldenburg.de/52922.html
(job offer #4), and feel free to contact me via email for further 
information.
Thanks much,
Stefan

-- 
Prof. Dr. Stefan Debener
Neuropsychology	Lab
Department of Psychology
University of Oldenburg
D-26111 Oldenburg
Germany

Office: A7 0-038
Phone: +49-441-798-4271
Fax:   +49-441-798-5522
Email: stefan.debener at uni-oldenburg.de



From jan.schoffelen at donders.ru.nl  Wed May 11 08:35:19 2011
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Wed, 11 May 2011 08:35:19 +0200
Subject: [FieldTrip] ft_freqstatistics
Message-ID: <4EE8E6A8-5C67-45A6-A6CE-7D6FFA5C3D64@donders.ru.nl>

Dear all,

I just committed to the svn-repository a revamped version of  
ft_freqstatistics, the function which does channel-level statistics on  
frequency domain data. This was a necessary cleaning operation to keep  
the code up-to-date. Important for you to know is that nothing has  
changed in the handling of good old-fashioned (time-frequency) power.  
The new thing is that you don't need to hack your way into the  
function anymore in order to do group level statistics on connectivity  
data. Things should just run fine, but although I extensively tested  
the code (to my best knowledge) on plausible scenarios, please keep  
your eyes open.

Best,

Jan-Mathijs

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793



From ndavid at uke.de  Wed May 11 10:45:32 2011
From: ndavid at uke.de (Nicole David)
Date: Wed, 11 May 2011 10:45:32 +0200
Subject: [FieldTrip] Job Announcement (PhD Position)
In-Reply-To: <03750F99-88BD-42D6-9133-8E4B4814E133@uke.de>
References: <03750F99-88BD-42D6-9133-8E4B4814E133@uke.de>
Message-ID: <BA03A7BF-221C-42C2-8AB2-7A1EF79A8823@uke.de>

Dear FieldTrip list,

I would like to announce an open PhD position with Prof. Andreas Engel  
at the Dept. of Neurophysiology and Pathophysiology, University  
Medical Center Hamburg-Eppendorf.

For details, see below.

Best,
Nicole David
-------------------------------

The Department of Neurophysiology and Pathophysiology at the  
University Medical Center Hamburg-Eppendorf (Director: Prof. Dr.  
Andreas K. Engel) invites applications for a PhD student position. The  
position is available with immediate start. The appointment will be  
for 3 years.

The position is at the intersection of psychology, cognitive  
neuroscience and philosophy. More specifically, experiments  
investigating the sense of agency shall be carried out, using  
neuroscience techniques such as magnetoencephalography (MEG). The  
sense of agency refers to the monitoring of actions and the  
experience, or awareness, of such as self- or other-generated.

Applicants should have experience in analyzing human EEG or MEG  
studies. Programming experience (Matlab) as well as fluent written and  
spoken English is considered mandatory. Applicants will be responsible  
for the management and implementation of research paradigms, data  
acquisition and analysis. Knowledge in theories of action and  
perception, multisensory processing, self-awareness and a basic  
understanding of information processing in the human brain would be  
preferred.

The successful candidate will be member of the European collaborative  
project “Extending Sensorimotor Contingencies to Cognition – eSMCs”  
that has started in January 2011. The main objective of the project is  
to extend the Sensorimotor Contingency Theory as an action-based  
approach to perception and cognition, and to investigate its  
implications in studies of natural and artificial agents. More  
information on the project is to appear at http://eSMCs.eu.  
Information on the Dept. of Neurophysiology and Pathophysiology is  
available at http://www.uke.de/neurophysiologie and at http://www.40hz.de 
.

Please send your application (including a CV) to

Dr. Nicole David or Prof. Dr. Andreas K. Engel
Dept. of Neurophysiology and Pathophysiology
University Medical Center Hamburg-Eppendorf
Martinistrasse 52
20246 Hamburg
Germany

Submission of applications through email (ndavid at uke.de,  
ak.engel at uke.de) is encouraged.

-- 
Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):

Universitätsklinikum Hamburg-Eppendorf
Körperschaft des öffentlichen Rechts
Gerichtsstand: Hamburg

Vorstandsmitglieder:
Prof. Dr. Jörg F. Debatin (Vorsitzender)
Dr. Alexander Kirstein
Joachim Prölß
Prof. Dr. Dr. Uwe Koch-Gromus
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From jan.schoffelen at donders.ru.nl  Wed May 11 10:56:10 2011
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Wed, 11 May 2011 10:56:10 +0200
Subject: [FieldTrip] FT_analysis of the average vs
	average(FT_analysis(single trials))
In-Reply-To: <686364.21106.qm@web28608.mail.ukl.yahoo.com>
References: <686364.21106.qm@web28608.mail.ukl.yahoo.com>
Message-ID: <A8788839-8789-488D-967B-43D82E08B3DD@donders.ru.nl>

Dear Tommaso,

Yes, if you average across the trial-dimension you will obtain the TFR  
you're after.

Best,

JM


On May 6, 2011, at 5:28 PM, tommaso fedele wrote:

> Hi all,
> I want to test if some component that I observe in the average of my  
> ERP signal are phase locked to the stimulus.
> In oder to do so I compare
> 1. TFR_averaged_signal =  ft_freqanalysis(cfg, averaged_signal)
> 2. TFR_singletrials_signal =  ft_freqanalysis(cfg,  
> singletrials_signal)
>
> with the first structure TFR_averaged_signal everything is fine, and  
> I get my nice TF plot.
> with the second I should average through "trials". Is there a  
> function for that? Or, is it correct to proceed plotting
> the average of  TFR_singletrials_signal.powspctrm through the  
> "trials-matrix dimension"?
>
> Thanks
> Tommaso
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793

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From jan.schoffelen at donders.ru.nl  Wed May 11 10:59:06 2011
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Wed, 11 May 2011 10:59:06 +0200
Subject: [FieldTrip] error using spm_slice_vol
In-Reply-To: <BANLkTi=gv_XKymTL2RcXMb=XrCFaJj_t9Q@mail.gmail.com>
References: <BANLkTi=gv_XKymTL2RcXMb=XrCFaJj_t9Q@mail.gmail.com>
Message-ID: <A6AD6C69-2013-428E-8DD9-97C0FB89E291@donders.ru.nl>

Hi Allison,

This looks like an SPM-related error to me, or it is operating system  
related. Can you check which spm-version you are using, in other  
words: is it the fieldtrip/external/spmXXX directory, or do you have  
spm somewhere else on your matlab-path? If it is the former, then it  
is a potential bug which needs fixing by us. Otherwise we cannot help  
it.
What kind of operating system are you using?

Best,

Jan-Mathijs


On May 4, 2011, at 3:56 PM, Allison Connolly wrote:

> Hi all,
>
> I am trying to segment an mri volume using. When I call  
> ft_read_mri('filename'), I get an error that says:
>
> ??? Error using ==> spm_slice_vol at 28
> spm_slice_vol.c not compiled - see spm_MAKE.sh
>
> Error in ==> spm_read_vols at 35
>     Y(:,:,p,i) = spm_slice_vol(V(i),spm_matrix([0 0  
> p]),V(i).dim(1:2),0);
>
> Error in ==> ft_read_mri at 97
>   img = spm_read_vols(hdr);
>
> I tried installing the most up to date version of fieldtrip and I  
> still get the same error. Can someone help me?
>
> -Allison
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793



From jan.schoffelen at donders.ru.nl  Wed May 11 11:02:49 2011
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Wed, 11 May 2011 11:02:49 +0200
Subject: [FieldTrip] overlaying beamformer results to native/normalized
	space
In-Reply-To: <5990a22b3c17f9.4dc119bd@mail.nyu.edu>
References: <5990a22b3c17f9.4dc119bd@mail.nyu.edu>
Message-ID: <F6C2D22E-1708-4097-AF75-4745FFB9367C@donders.ru.nl>

Dear Akiko,

On May 4, 2011, at 3:17 PM, Akiko Ikkai wrote:

> I sent a below message to the list last night, but it was bounced  
> back. I'm trying from another email account. My apologies if this  
> was duplicate...
>
>
>
> I'm trying to run beamformer analysis on my MEG data, using DICS,  
> and having difficulty visualizing meaningful results.
>
> I was able to align MRI image to MEG sensors; after segmentation,  
> ft_prepare_singleshell and  ft_prepare_leadfield, plotting  
> ft_data.grad and volume model confirms that they align reasonably.  
> However, using data.grad, grid, and vol to run ft_sourceanalysis,  
> and ft_sourceinterpolate with MRI (in ctf coordinate system and  
> aligned to MEG sensors) somehow distorts the alignment, and the new  
> volume model does not resemble the original.

So, the problem is that ft_sourceinterpolate does not behave as  
expected?

> I'm assuming that, after ft_sourceinterpolate, if I segment  
> source_interpolated.anatomy and run ft_prepare_singleshell and  
> ft_prepare_leadfield, it should align with MEG sensors, just as the  
> initial volume model aligned with MEG sensors... or am I making too  
> much of an assumption here?

Why would you want to do this?

> Because of the misalignment, output data of ft_sourceinterpolate  
> with "anatomy" and "avg.pow" does not agree with topoplot (run  
> ft_freqanalysis on the same dataset).
> If anyone could explain why this alignment distortion might be  
> happening during ft_sourceanalysis and/or ft_sourceinterpolate, I'd  
> really appreciate it.
>

I am afraid you need to be a bit more specific in order for us to  
understand what may be going wrong here.

Best,

Jan-Mathijs


> Thanks in advance, Akiko
>
> -- 
> Akiko Ikkai, Ph.D.
> Postdoctoral Fellow
> Department of Psychological and Brain Sciences
> Johns Hopkins University
> Ames Hall, 3400 N. Charles St.
> Baltimore, MD 21218
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793

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From ting.ac at gmail.com  Wed May 11 19:30:14 2011
From: ting.ac at gmail.com (Allison Connolly)
Date: Wed, 11 May 2011 12:30:14 -0500
Subject: [FieldTrip] channelcmb with removed channels
Message-ID: <BANLkTik6nbC-GwBXOc5vPVCJo=QC9qOVQw@mail.gmail.com>

I am trying to do beamforming on some MEG data. However, some of the sensors
railed during the recordings, so I want to remove them from the analysis. I
declare the channels I want to use during import with ft_preprocessing by
saying:
cfg.channel                 = {'MEG','-TRIGGER','-RESPONSE',...
    '-UACurrent','-MxA','-MyA','-MzA','-GxxA','-GyxA','-GyyA',...
    '-GzyA','-GzxA','-MxaA','-MyaA','-MzaA','-E1','-E2','-E3','-E4',...
    '-A40','-A57','-A76','-A77','-A79','-A81','-A88','-A89','-A96',...
    '-A100','-A102','-A103','-A108','-A112','-A113','-A114','-A116',...
    '-A120','-A121','-A123','-A124','-A125','-A126','-A127','-A128',...
    '-A129','-A130','-A131','-A124','-A139','-A140','-A141','-A142',...
    '-A144','-A145','-A146','-A147','-A148'};

Then I use ft_freqanalysis to calculate the cross spectral density and
ft_prepare_leadfield to create the brain grid. When I try to run
ft_sourceanalysis, I get this error:
creating dipole grid based on user specified dipole positions
13718 dipoles inside, 144943 dipoles outside brain
???  In an assignment  A(I) = B, a matrix A cannot be resized.

Error in ==> prepare_freq_matrices at 115
    Cf(find(crsspctrmindx)) =
freq.crsspctrm(crsspctrmindx(find(crsspctrmindx)), fbin);

Error in ==> ft_sourceanalysis at 461
    [Cf, Cr, Pr, Ntrials, cfg] = prepare_freq_matrices(cfg, data);


I think it is because I have removed channels. When I try to run
ft_freqanalysis while specifying the channels in cfg.channel, i get this
error:
the input is raw data with 111 channels and 60 trials
??? Error using ==> ft_freqanalysis at 352
*channels in cfg.channelcmb not present in cfg.channel*
*
*I think I need to explicitly define cfg.channelcmb, but I don't know how to
do this if I have removed channels.

-Allison
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From jpoll at ugr.es  Thu May 12 14:10:46 2011
From: jpoll at ugr.es (JOAN PAUL POZUELOS LOPEZ)
Date: Thu, 12 May 2011 14:10:46 +0200
Subject: [FieldTrip] Problems with the Buffer
Message-ID: <FC78BFD4-422B-45CF-BB55-4C449DBB252C@ugr.es>

Hello everyone,

Im new using the matlab for analyzing ERP´s. I have been using the FASTER program (Nolan, Whelan &Reilly, 2010, Journal of Neuroscience Methods) and i have encounter a problem with some files contained in the filedtrip toolbox. The problem its that when it is computing the ICA the process is not finished because theres an error that says: "error - invalid MEX_file 'c: Users\....\Matlab\external\fieldtrip-20110320\realtime\buffer\matlab\buffer.mexw32': could not find the specified module. 

When i check the folder containing the Buffer.mexw32 file, it is in the folder that the Filepath looks. Any suggestions on how to solve this problem?.

Thank you very much for your help

JOAN PAUL POZUELOS LOPEZ
Departamento de Psicología Experimental y Fisiología del Comportamiento
Universidad de Granada
jpoll at ugr.es







From nuria.donamayor at neuro.uni-luebeck.de  Fri May 13 10:42:05 2011
From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso)
Date: Fri, 13 May 2011 10:42:05 +0200
Subject: [FieldTrip] problem reading 4d header
In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de>
References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de>
Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>

Dear fieltrip users,
I am using fieldtrip to analyze my 4D/BTI data on a Linux machine with a 64-bit Matlab version and I am getting an error I don't know how to solve:

hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']);
??? SWITCH expression must be a scalar or string constant.

Error in ==> read_4d_hdr at 60
  switch format

Error in ==> ft_read_header at 153
    orig            = read_4d_hdr(datafile);

If I try to read the same data on my Windows PC with 32-bit Matlab I have no problem reading the header file (but I can't even finish the preprocessing before it runs out of memory, therefore the switch to the Linux machine), so I'm pretty clueless here... Can any of you help me?
Thanks,
Nuria



Nuria Doñamayor Alonso, MSc
Universitätsklinikum Schleswig-Holstein
Campus Lübeck
Klinik für Neurologie
Ratzeburger Allee 160
23538 Lübeck



From paul_c at gmx.de  Fri May 13 11:27:01 2011
From: paul_c at gmx.de (Paul Czienskowski)
Date: Fri, 13 May 2011 11:27:01 +0200
Subject: [FieldTrip] Systematic electrode displacement
Message-ID: <4DCCF965.4050408@gmx.de>

Dear fieldtrippers,

I've got an issue with electrode placement and I hope that someone has 
any idea how to tackle those issues.

For research on my diploma thesis I am fitting simulated data with the 
realistic brain shape I used to simulate the data as well as a icbm 
model (BEM models). I used the electrode system for the icbm152 brain 
provided by Robert Oostenveld and did some manual correction to the 
realistic brains (which were normalised to icbm brain) with the 
ft_electroderealign function.
I simulated the data in a position near the auditory cortex, since this 
is the location where we assume our real ERP.
In my fitted data I encountered strange systematic errors (especially 
some kind of bias on the z-axis), as seen on the 
boxplot_coord_20110407.png file (note that it's both age groups: 1 for 
old and 2 for young, scale is meters). While investigating on the origin 
of this bias, I made a box plot of the distance of the electrodes in the 
icbm model and the electrodes in each of the realistic models 
(dist_electrodes.png). Obviously there already is an bias in the 
electrodes placement. First I assumed this was caused my the manual 
correction of the electrodes I performed. To check this out, I fitted 
the very data with the manually corrected electrodes on the icbm brain. 
Still I found that there was a bias, mainly on the z-axis and - what 
astonished me even more, there was still a bias in the electrodes. This 
is observable in the boxplot_20110512_electrode_locations_matched.png 
(sorry for the German captions), x-Axis is coordinate and y-axis is the 
deviation of the electrode's positions.
Furthermore I simulated and fitted a position near the vertex (though 
still in the brain ;) ). There was not so much of a bias there, 
therefore I assume it's mainly the lateral and maybe posterior electrodes
causing the bias, not that much the superior.

Due to those results I assumed that it's got something to do with the 
automatic projection of the electrodes on the head surface. I had no 
time yet to compare those electrode positions manually (or better 
visually), but this is definitely on my agenda. I wondered, if anyone 
had an idea, how to improve this, for electrode deviations up to ~10 cm 
is way to much, asking me. I already checked if there maybe was any 
confusion in the order of the electrodes, but I just checked the labels 
and this does not support it.

Thanks in advance and best regards,
Paul Czienskowski

-- 
Paul Czienskowski
Björnsonstr. 25
12163 Berlin

Tel.: (+49)(0)30/221609359
Handy: (+49)(0)1788378772
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From yuvharpaz at gmail.com  Fri May 13 13:39:29 2011
From: yuvharpaz at gmail.com (Yuval Harpaz)
Date: Fri, 13 May 2011 14:39:29 +0300
Subject: [FieldTrip] problem reading 4d header
In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>
References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>
Message-ID: <BANLkTikoifrBKypx74pbabzyiHWxfb33+w@mail.gmail.com>

Dear Nuria
Is it exactly the same fieldtrip version?
I hope someone will solve this.
as temporary work around you can read the header on windows and then move to
linux

yuval

On 13 May 2011 11:42, Nuria Donamayor Alonso <
nuria.donamayor at neuro.uni-luebeck.de> wrote:

> Dear fieltrip users,
> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine with a
> 64-bit Matlab version and I am getting an error I don't know how to solve:
>
> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']);
> ??? SWITCH expression must be a scalar or string constant.
>
> Error in ==> read_4d_hdr at 60
>  switch format
>
> Error in ==> ft_read_header at 153
>    orig            = read_4d_hdr(datafile);
>
> If I try to read the same data on my Windows PC with 32-bit Matlab I have
> no problem reading the header file (but I can't even finish the
> preprocessing before it runs out of memory, therefore the switch to the
> Linux machine), so I'm pretty clueless here... Can any of you help me?
> Thanks,
> Nuria
>
>
>
> Nuria Doñamayor Alonso, MSc
> Universitätsklinikum Schleswig-Holstein
> Campus Lübeck
> Klinik für Neurologie
> Ratzeburger Allee 160
> 23538 Lübeck
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Y.Harpaz

a link to the BIU MEG lab:
http://faculty.biu.ac.il/~goldsa/index.html

*"Many were increasingly of the opinion that they'd all made a big mistake
in coming down from the trees in the first place. And some said that even
the trees had been a bad move, and that no one should ever have left the
oceans". Douglas Adams
*
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From nuria.donamayor at neuro.uni-luebeck.de  Fri May 13 14:34:36 2011
From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso)
Date: Fri, 13 May 2011 14:34:36 +0200
Subject: [FieldTrip] problem reading 4d header
In-Reply-To: <BANLkTikoifrBKypx74pbabzyiHWxfb33+w@mail.gmail.com>
References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>,
	<BANLkTikoifrBKypx74pbabzyiHWxfb33+w@mail.gmail.com>
Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>

Yes, it is exectly the same version. Better said, versions, because I tried both 20110413 and 20110512....

________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com]
Gesendet: Freitag, 13. Mai 2011 13:39
An: Email discussion list for the FieldTrip project
Betreff: Re: [FieldTrip] problem reading 4d header

Dear Nuria
Is it exactly the same fieldtrip version?
I hope someone will solve this.
as temporary work around you can read the header on windows and then move to linux

yuval

On 13 May 2011 11:42, Nuria Donamayor Alonso <nuria.donamayor at neuro.uni-luebeck.de<mailto:nuria.donamayor at neuro.uni-luebeck.de>> wrote:
Dear fieltrip users,
I am using fieldtrip to analyze my 4D/BTI data on a Linux machine with a 64-bit Matlab version and I am getting an error I don't know how to solve:

hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']);
??? SWITCH expression must be a scalar or string constant.

Error in ==> read_4d_hdr at 60
 switch format

Error in ==> ft_read_header at 153
   orig            = read_4d_hdr(datafile);

If I try to read the same data on my Windows PC with 32-bit Matlab I have no problem reading the header file (but I can't even finish the preprocessing before it runs out of memory, therefore the switch to the Linux machine), so I'm pretty clueless here... Can any of you help me?
Thanks,
Nuria



Nuria Doñamayor Alonso, MSc
Universitätsklinikum Schleswig-Holstein
Campus Lübeck
Klinik für Neurologie
Ratzeburger Allee 160
23538 Lübeck

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



--
Y.Harpaz

a link to the BIU MEG lab:
http://faculty.biu.ac.il/~goldsa/index.html<http://faculty.biu.ac.il/%7Egoldsa/index.html>

"Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams




From jan.schoffelen at donders.ru.nl  Fri May 13 16:43:41 2011
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Fri, 13 May 2011 16:43:41 +0200
Subject: [FieldTrip] problem reading 4d header
In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>
References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>,
	<BANLkTikoifrBKypx74pbabzyiHWxfb33+w@mail.gmail.com>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>
Message-ID: <C99C901A-901E-452F-91A5-954E76E27E2A@donders.ru.nl>

Hi Nuria,

Could you type dbstop if error on the command line, and evaluate what  
the variable 'format' is in your case?

Thanks,

Jan-Mathijs

On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote:

> Yes, it is exectly the same version. Better said, versions, because  
> I tried both 20110413 and 20110512....
>
> ________________________________________
> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- 
> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com 
> ]
> Gesendet: Freitag, 13. Mai 2011 13:39
> An: Email discussion list for the FieldTrip project
> Betreff: Re: [FieldTrip] problem reading 4d header
>
> Dear Nuria
> Is it exactly the same fieldtrip version?
> I hope someone will solve this.
> as temporary work around you can read the header on windows and then  
> move to linux
>
> yuval
>
> On 13 May 2011 11:42, Nuria Donamayor Alonso <nuria.donamayor at neuro.uni-luebeck.de 
> <mailto:nuria.donamayor at neuro.uni-luebeck.de>> wrote:
> Dear fieltrip users,
> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine  
> with a 64-bit Matlab version and I am getting an error I don't know  
> how to solve:
>
> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']);
> ??? SWITCH expression must be a scalar or string constant.
>
> Error in ==> read_4d_hdr at 60
> switch format
>
> Error in ==> ft_read_header at 153
>   orig            = read_4d_hdr(datafile);
>
> If I try to read the same data on my Windows PC with 32-bit Matlab I  
> have no problem reading the header file (but I can't even finish the  
> preprocessing before it runs out of memory, therefore the switch to  
> the Linux machine), so I'm pretty clueless here... Can any of you  
> help me?
> Thanks,
> Nuria
>
>
>
> Nuria Doñamayor Alonso, MSc
> Universitätsklinikum Schleswig-Holstein
> Campus Lübeck
> Klinik für Neurologie
> Ratzeburger Allee 160
> 23538 Lübeck
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Y.Harpaz
>
> a link to the BIU MEG lab:
> http://faculty.biu.ac.il/~goldsa/index.html<http://faculty.biu.ac.il/%7Egoldsa/index.html 
> >
>
> "Many were increasingly of the opinion that they'd all made a big  
> mistake in coming down from the trees in the first place. And some  
> said that even the trees had been a bad move, and that no one should  
> ever have left the oceans". Douglas Adams
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793




From anokhina at psychiatry.wustl.edu  Sat May 14 17:10:43 2011
From: anokhina at psychiatry.wustl.edu (Anokhin, Andrey)
Date: Sat, 14 May 2011 10:10:43 -0500
Subject: [FieldTrip] job announcement
Message-ID: <86712757862F3640B2F4BB5C14D8EDC4090EF4A245@wusmexmbx2.medpriv.wucon.wustl.edu>

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From l.frei at psy.gla.ac.uk  Sat May 14 22:37:45 2011
From: l.frei at psy.gla.ac.uk (Luisa Frei)
Date: Sat, 14 May 2011 21:37:45 +0100
Subject: [FieldTrip] stats on planar gradient topographies
Message-ID: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk>

Hi there,
I am trying to compute a simple cluster-based statistic in a between  
subjects design. I have followed the steps in the respective tutorial  
very closely.
This the code I used:

%%%%%%%%%%%%%%%%%%%%%%%%%%%
cfg = [];
cfg.method = 'montecarlo';
cfg.statistic = 'indepsamplesT';

cfg.correctm = 'cluster';
cfg.clusteralpha = 0.001;
cfg.clusterstatistic = 'maxsize';
cfg.minnbchan = 4;

cfg.tail = 0;
cfg.clustertail = 0;
cfg.alpha = 0.005;
cfg.numrandomization = 500;

design = [ones(1,13) ones(1,13)+1];

cfg.design = design;
cfg.ivar  = 1;

cfg.channel = {'MEG',sub(1).allbadchan{:}};
cfg.latency = [.15 .2];

[stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); %  
individuals kept
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

My problem is, that I'm not sure which time resolution to use. I  
would like to use a small resolution of 10 ms, but this leads to a  
fairly random pattern of significant sensors (see attached figure, on  
the right). Of course, the more time points I include, the less  
significant sensors are left over. However, another problem is, that  
the ones that are left (figure, left), are not related to big  
differences in the activation pattern at all. How is it possible that  
my significant sensors end up being so randomly distributed? Also,  
ft_timelockstatistics only comes up with one positive and one  
negative cluster., but the sign. sensors are not always connected.  
Could anyone give some helpful input here?

Thanks,
Luisa

Fyi: I have tried different thresholds and different numbers of  
neighbourhood channels, but there's not much of a change.
￼
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From julian.keil at gmail.com  Mon May 16 14:32:07 2011
From: julian.keil at gmail.com (Julian Keil)
Date: Mon, 16 May 2011 14:32:07 +0200
Subject: [FieldTrip] stats on planar gradient topographies
In-Reply-To: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk>
References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk>
Message-ID: <DDE1521C-448B-4F10-83BA-E53104178BC9@gmail.com>

Hi Luisa,

schnell from the top of my head: wie definierst du denn deine neighbors?
Ich seh nirgendwo ein Feld cfg.neighbors....
Ich muss das bei unserem 4D-System immer angeben....
Es könnte sein, dass du die Struktur, welche Kanäle neben welchen sind falsch definierst, so könntest du zu deinen "random" Clustern kommen.

Ich mache diese Neighbor-Struktur folgendermaßen:

cfg=[]; 
cfg.neighbourdist=0.1;
%cfg.grad=Comb_AV1_1{1}.grad;
cfg.layout='4D148.lay';
cfg.channel={'all'};
%cfg.grad.pnt=cfg.grad.pnt*100; 
dummy=neighbourselection(cfg);

Da bekomme ich auch immer einen Output, wie viele Channels so in der Umgebung sind (sollten in etwa 5 sein).

Hoffe das hilft dir weiter

Viele Grüße

Julian

Am 14.05.2011 um 22:37 schrieb Luisa Frei:

> Hi there,
> I am trying to compute a simple cluster-based statistic in a between subjects design. I have followed the steps in the respective tutorial very closely.
> This the code I used:
> 
> %%%%%%%%%%%%%%%%%%%%%%%%%%%
> cfg = [];
> cfg.method = 'montecarlo';       
> cfg.statistic = 'indepsamplesT'; 
>  
> cfg.correctm = 'cluster';
> cfg.clusteralpha = 0.001;         
> cfg.clusterstatistic = 'maxsize'; 
> cfg.minnbchan = 4;               
>  
> cfg.tail = 0;                    
> cfg.clustertail = 0;
> cfg.alpha = 0.005;               
> cfg.numrandomization = 500;      
>  
> design = [ones(1,13) ones(1,13)+1];
>  
> cfg.design = design;             
> cfg.ivar  = 1;                   
>  
> cfg.channel = {'MEG',sub(1).allbadchan{:}};
> cfg.latency = [.15 .2];
>  
> [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % individuals kept
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
> My problem is, that I'm not sure which time resolution to use. I would like to use a small resolution of 10 ms, but this leads to a fairly random pattern of significant sensors (see attached figure, on the right). Of course, the more time points I include, the less significant sensors are left over. However, another problem is, that the ones that are left (figure, left), are not related to big differences in the activation pattern at all. How is it possible that my significant sensors end up being so randomly distributed? Also, ft_timelockstatistics only comes up with one positive and one negative cluster., but the sign. sensors are not always connected. Could anyone give some helpful input here?
> 
> Thanks,
> Luisa
> 
> Fyi: I have tried different thresholds and different numbers of neighbourhood channels, but there's not much of a change.
> <Picture 2.png>
> _______________________________________________
> 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  Mon May 16 14:52:24 2011
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 16 May 2011 14:52:24 +0200
Subject: [FieldTrip] stats on planar gradient topographies
In-Reply-To: <DDE1521C-448B-4F10-83BA-E53104178BC9@gmail.com>
References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk>
	<DDE1521C-448B-4F10-83BA-E53104178BC9@gmail.com>
Message-ID: <4DD11E08.6050207@donders.ru.nl>

Hi all,

First of all, @julian: It would be nice if you wrote in English so that 
all people can understand what you are saying :)

Second, I would like to mention ft_neighbourplot, which is a relative 
new function and plots sensors and its' neighbours in 2D or 3D, 
depending on whether you got 2D or 3D coordinates. Using that function, 
you can verify whether your neighbourselection looks meaningful and 
makes sense.

Finally, we are currently working on changing/improving the 
neighbourselecion function. There will be different methods to choose 
from, and we (me) will create templates for the most common systems that 
can be used instead of relying on a particular mathematical selection 
method. We will announce this when it's done (probably soon).

Maybe Julian is right and Luisa's problem is due to a 'wrong' 
neighbourselection. Given that cfg.minnbhchan is set to 4, this might be 
likely, because not all of the found clusters consist of 4 or more 
channels. What system are you using?

Best,
Jörn


On 5/16/2011 2:32 PM, Julian Keil wrote:
> Hi Luisa,
>
> schnell from the top of my head: wie definierst du denn deine neighbors?
> Ich seh nirgendwo ein Feld cfg.neighbors....
> Ich muss das bei unserem 4D-System immer angeben....
> Es könnte sein, dass du die Struktur, welche Kanäle neben welchen sind 
> falsch definierst, so könntest du zu deinen "random" Clustern kommen.
>
> Ich mache diese Neighbor-Struktur folgendermaßen:
>
> cfg=[];
> cfg.neighbourdist=0.1;
> %cfg.grad=Comb_AV1_1{1}.grad;
> cfg.layout='4D148.lay';
> cfg.channel={'all'};
> %cfg.grad.pnt=cfg.grad.pnt*100;
> dummy=neighbourselection(cfg);
>
> Da bekomme ich auch immer einen Output, wie viele Channels so in der 
> Umgebung sind (sollten in etwa 5 sein).
>
> Hoffe das hilft dir weiter
>
> Viele Grüße
>
> Julian
>
> Am 14.05.2011 um 22:37 schrieb Luisa Frei:
>
>> Hi there,
>> I am trying to compute a simple cluster-based statistic in a between 
>> subjects design. I have followed the steps in the respective tutorial 
>> very closely.
>> This the code I used:
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%
>> cfg = [];
>> cfg.method = 'montecarlo';
>> cfg.statistic = 'indepsamplesT';
>>
>> cfg.correctm = 'cluster';
>> cfg.clusteralpha = 0.001;
>> cfg.clusterstatistic = 'maxsize';
>> cfg.minnbchan = 4;
>>
>> cfg.tail = 0;
>> cfg.clustertail = 0;
>> cfg.alpha = 0.005;
>> cfg.numrandomization = 500;
>>
>> design = [ones(1,13) ones(1,13)+1];
>>
>> cfg.design = design;
>> cfg.ivar  = 1;
>>
>> cfg.channel = {'MEG',sub(1).allbadchan{:}};
>> cfg.latency = [.15 .2];
>>
>> [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % 
>> individuals kept
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>
>> My problem is, that I'm not sure which time resolution to use. I 
>> would like to use a small resolution of 10 ms, but this leads to a 
>> fairly random pattern of significant sensors (see attached figure, on 
>> the right). Of course, the more time points I include, the less 
>> significant sensors are left over. However, another problem is, that 
>> the ones that are left (figure, left), are not related to big 
>> differences in the activation pattern at all. How is it possible that 
>> my significant sensors end up being so randomly distributed? Also, 
>> ft_timelockstatistics only comes up with one positive and one 
>> negative cluster., but the sign. sensors are not always connected. 
>> Could anyone give some helpful input here?
>>
>> Thanks,
>> Luisa
>>
>> Fyi: I have tried different thresholds and different numbers of 
>> neighbourhood channels, but there's not much of a change.
>> <Picture 2.png>_______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl <mailto: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

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
Kapitelweg 29
NL-6525 EN Nijmegen
The Netherlands

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From julian.keil at gmail.com  Mon May 16 14:58:35 2011
From: julian.keil at gmail.com (Julian Keil)
Date: Mon, 16 May 2011 14:58:35 +0200
Subject: [FieldTrip] stats on planar gradient topographies
In-Reply-To: <4DD11E08.6050207@donders.ru.nl>
References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk>
	<DDE1521C-448B-4F10-83BA-E53104178BC9@gmail.com>
	<4DD11E08.6050207@donders.ru.nl>
Message-ID: <D3815C73-F91F-4133-9CF3-BF995D4A5BC5@gmail.com>

Hi all,

sorry, I thought the answer would only go to Luisa. 

Apologies,
Julian

Am 16.05.2011 um 14:52 schrieb Jörn M. Horschig:

> Hi all,
> 
> First of all, @julian: It would be nice if you wrote in English so that all people can understand what you are saying :)
> 
> Second, I would like to mention ft_neighbourplot, which is a relative new function and plots sensors and its' neighbours in 2D or 3D, depending on whether you got 2D or 3D coordinates. Using that function, you can verify whether your neighbourselection looks meaningful and makes sense.
> 
> Finally, we are currently working on changing/improving the neighbourselecion function. There will be different methods to choose from, and we (me) will create templates for the most common systems that can be used instead of relying on a particular mathematical selection method. We will announce this when it's done (probably soon).
> 
> Maybe Julian is right and Luisa's problem is due to a 'wrong' neighbourselection. Given that cfg.minnbhchan is set to 4, this might be likely, because not all of the found clusters consist of 4 or more channels. What system are you using?
> 
> Best,
> Jörn
> 
> 
> On 5/16/2011 2:32 PM, Julian Keil wrote:
>> 
>> Hi Luisa,
>> 
>> schnell from the top of my head: wie definierst du denn deine neighbors?
>> Ich seh nirgendwo ein Feld cfg.neighbors....
>> Ich muss das bei unserem 4D-System immer angeben....
>> Es könnte sein, dass du die Struktur, welche Kanäle neben welchen sind falsch definierst, so könntest du zu deinen "random" Clustern kommen.
>> 
>> Ich mache diese Neighbor-Struktur folgendermaßen:
>> 
>> cfg=[]; 
>> cfg.neighbourdist=0.1;
>> %cfg.grad=Comb_AV1_1{1}.grad;
>> cfg.layout='4D148.lay';
>> cfg.channel={'all'};
>> %cfg.grad.pnt=cfg.grad.pnt*100; 
>> dummy=neighbourselection(cfg);
>> 
>> Da bekomme ich auch immer einen Output, wie viele Channels so in der Umgebung sind (sollten in etwa 5 sein).
>> 
>> Hoffe das hilft dir weiter
>> 
>> Viele Grüße
>> 
>> Julian
>> 
>> Am 14.05.2011 um 22:37 schrieb Luisa Frei:
>> 
>>> Hi there,
>>> I am trying to compute a simple cluster-based statistic in a between subjects design. I have followed the steps in the respective tutorial very closely.
>>> This the code I used:
>>> 
>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%
>>> cfg = [];
>>> cfg.method = 'montecarlo';       
>>> cfg.statistic = 'indepsamplesT'; 
>>>  
>>> cfg.correctm = 'cluster';
>>> cfg.clusteralpha = 0.001;         
>>> cfg.clusterstatistic = 'maxsize'; 
>>> cfg.minnbchan = 4;               
>>>  
>>> cfg.tail = 0;                    
>>> cfg.clustertail = 0;
>>> cfg.alpha = 0.005;               
>>> cfg.numrandomization = 500;      
>>>  
>>> design = [ones(1,13) ones(1,13)+1];
>>>  
>>> cfg.design = design;             
>>> cfg.ivar  = 1;                   
>>>  
>>> cfg.channel = {'MEG',sub(1).allbadchan{:}};
>>> cfg.latency = [.15 .2];
>>>  
>>> [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % individuals kept
>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>> 
>>> My problem is, that I'm not sure which time resolution to use. I would like to use a small resolution of 10 ms, but this leads to a fairly random pattern of significant sensors (see attached figure, on the right). Of course, the more time points I include, the less significant sensors are left over. However, another problem is, that the ones that are left (figure, left), are not related to big differences in                   the activation pattern at all. How is it possible that my significant sensors end up being so randomly distributed? Also, ft_timelockstatistics only comes up with one positive and one negative cluster., but the sign. sensors are not always connected. Could anyone give some helpful input here?
>>> 
>>> Thanks,
>>> Luisa
>>> 
>>> Fyi: I have tried different thresholds and different numbers of neighbourhood channels, but there's not much of a change.
>>> <Picture 2.png>_______________________________________________
>>> 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 
> 
> 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
> Kapitelweg 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 l.frei at psy.gla.ac.uk  Mon May 16 15:10:27 2011
From: l.frei at psy.gla.ac.uk (Luisa Frei)
Date: Mon, 16 May 2011 14:10:27 +0100
Subject: [FieldTrip] stats on planar gradient topographies
In-Reply-To: <D3815C73-F91F-4133-9CF3-BF995D4A5BC5@gmail.com>
References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk>
	<DDE1521C-448B-4F10-83BA-E53104178BC9@gmail.com>
	<4DD11E08.6050207@donders.ru.nl>
	<D3815C73-F91F-4133-9CF3-BF995D4A5BC5@gmail.com>
Message-ID: <95704E05-6DEC-4B66-A9EA-381B9C88CA12@psy.gla.ac.uk>

Thanks for all the answers, I'll try Julian's suggestion and let you  
know what happens.

Luisa

On 16 May 2011, at 13:58, Julian Keil wrote:

> Hi all,
>
> sorry, I thought the answer would only go to Luisa.
>
> Apologies,
> Julian
>
> Am 16.05.2011 um 14:52 schrieb Jörn M. Horschig:
>
>> Hi all,
>>
>> First of all, @julian: It would be nice if you wrote in English so  
>> that all people can understand what you are saying :)
>>
>> Second, I would like to mention ft_neighbourplot, which is a  
>> relative new function and plots sensors and its' neighbours in 2D  
>> or 3D, depending on whether you got 2D or 3D coordinates. Using  
>> that function, you can verify whether your neighbourselection  
>> looks meaningful and makes sense.
>>
>> Finally, we are currently working on changing/improving the  
>> neighbourselecion function. There will be different methods to  
>> choose from, and we (me) will create templates for the most common  
>> systems that can be used instead of relying on a particular  
>> mathematical selection method. We will announce this when it's  
>> done (probably soon).
>>
>> Maybe Julian is right and Luisa's problem is due to a 'wrong'  
>> neighbourselection. Given that cfg.minnbhchan is set to 4, this  
>> might be likely, because not all of the found clusters consist of  
>> 4 or more channels. What system are you using?
>>
>> Best,
>> Jörn
>>
>>
>> On 5/16/2011 2:32 PM, Julian Keil wrote:
>>>
>>> Hi Luisa,
>>>
>>> schnell from the top of my head: wie definierst du denn deine  
>>> neighbors?
>>> Ich seh nirgendwo ein Feld cfg.neighbors....
>>> Ich muss das bei unserem 4D-System immer angeben....
>>> Es könnte sein, dass du die Struktur, welche Kanäle neben welchen  
>>> sind falsch definierst, so könntest du zu deinen "random"  
>>> Clustern kommen.
>>>
>>> Ich mache diese Neighbor-Struktur folgendermaßen:
>>>
>>> cfg=[];
>>> cfg.neighbourdist=0.1;
>>> %cfg.grad=Comb_AV1_1{1}.grad;
>>> cfg.layout='4D148.lay';
>>> cfg.channel={'all'};
>>> %cfg.grad.pnt=cfg.grad.pnt*100;
>>> dummy=neighbourselection(cfg);
>>>
>>> Da bekomme ich auch immer einen Output, wie viele Channels so in  
>>> der Umgebung sind (sollten in etwa 5 sein).
>>>
>>> Hoffe das hilft dir weiter
>>>
>>> Viele Grüße
>>>
>>> Julian
>>>
>>> Am 14.05.2011 um 22:37 schrieb Luisa Frei:
>>>
>>>> Hi there,
>>>> I am trying to compute a simple cluster-based statistic in a  
>>>> between subjects design. I have followed the steps in the  
>>>> respective tutorial very closely.
>>>> This the code I used:
>>>>
>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>> cfg = [];
>>>> cfg.method = 'montecarlo';
>>>> cfg.statistic = 'indepsamplesT';
>>>>
>>>> cfg.correctm = 'cluster';
>>>> cfg.clusteralpha = 0.001;
>>>> cfg.clusterstatistic = 'maxsize';
>>>> cfg.minnbchan = 4;
>>>>
>>>> cfg.tail = 0;
>>>> cfg.clustertail = 0;
>>>> cfg.alpha = 0.005;
>>>> cfg.numrandomization = 500;
>>>>
>>>> design = [ones(1,13) ones(1,13)+1];
>>>>
>>>> cfg.design = design;
>>>> cfg.ivar  = 1;
>>>>
>>>> cfg.channel = {'MEG',sub(1).allbadchan{:}};
>>>> cfg.latency = [.15 .2];
>>>>
>>>> [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); %  
>>>> individuals kept
>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>>
>>>> My problem is, that I'm not sure which time resolution to use. I  
>>>> would like to use a small resolution of 10 ms, but this leads to  
>>>> a fairly random pattern of significant sensors (see attached  
>>>> figure, on the right). Of course, the more time points I  
>>>> include, the less significant sensors are left over. However,  
>>>> another problem is, that the ones that are left (figure, left),  
>>>> are not related to big differences in the activation pattern at  
>>>> all. How is it possible that my significant sensors end up being  
>>>> so randomly distributed? Also, ft_timelockstatistics only comes  
>>>> up with one positive and one negative cluster., but the sign.  
>>>> sensors are not always connected. Could anyone give some helpful  
>>>> input here?
>>>>
>>>> Thanks,
>>>> Luisa
>>>>
>>>> Fyi: I have tried different thresholds and different numbers of  
>>>> neighbourhood channels, but there's not much of a change.
>>>> <Picture 2.png>_______________________________________________
>>>> 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
>>
>> 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
>> Kapitelweg 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

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From d.lozanosoldevilla at fcdonders.ru.nl  Mon May 16 15:59:36 2011
From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego))
Date: Mon, 16 May 2011 15:59:36 +0200 (CEST)
Subject: [FieldTrip] ft_rejectvisual channel selection
Message-ID: <492082518.129940.1305554376843.JavaMail.root@sculptor.zimbra.ru.nl>

Dear Fieldtrippers,

I'm using ft_rejectvisual function to reject visually EOG artifacts of epoched trials. My problem consist that I'm not able to plot only the EOG channels even when I explicitly select them ignoring the 'MEG' channels (I get a plot with all channels MEG + EOG).

I directly used rejectvisual_channel (used in line 263 offt_rejectvisual) function selecting the EOG channels but I'm getting again all channels. Somebody could tell me what I'm doing wrong?

Thanks in advance,

Diego



PS: Code

%epoching
cfg = [];
cfg.dataset                     = [direc d(rr,1).name];
cfg.trialdef.eventtype          = 'frontpanel trigger';
cfg.trialdef.eventvalue         = 4;
cfg.trialdef.prestim            = 1; % in seconds
cfg.trialdef.poststim           = 4; % in seconds
cfg.trialdef.epochmoving        = 'inbackward';
cfg.trialdef.pivoteventvalue    = 2;% cue stimulus
cfg.trialdef.jumps              = 1;
cfg.trialfun                    = 'trialselec';

cfg = ft_definetrial(cfg);

cfg.channel                     = {'MEG' 'EEG057' 'EEG058'};
cfg.lpfilter                    = 'yes';
cfg.lpfreq                      = 250;
cfg.baselinewindow              = [-1 0];
cfg.keeptrials                  = 'yes';
cfg.demean                      = 'yes';
cfg.continuous                  = 'yes';

data    = ft_preprocessing(cfg);

%..............


%visual data rejection
cfg             = [];
cfg.channel     = {'EEG057' 'EEG058'};
cfg.method      = 'channel';
cfg.keepchannel = 'yes';
data_c          = ft_rejectvisual(cfg,data);



-- 
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Trigon, room 0.83
Kapittelweg 29
Radboud University Nijmegen
NL-6500 HB Nijmegen
The Netherlands
E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
Tel:      +31-(0)24-36-66274
Web:    http://www.neuosc.com/


From stan.vanpelt at fcdonders.ru.nl  Mon May 16 16:16:16 2011
From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt)
Date: Mon, 16 May 2011 16:16:16 +0200 (CEST)
Subject: [FieldTrip] ft_rejectvisual channel selection
In-Reply-To: <492082518.129940.1305554376843.JavaMail.root@sculptor.zimbra.ru.nl>
References: <492082518.129940.1305554376843.JavaMail.root@sculptor.zimbra.ru.nl>
Message-ID: <022901cc13d3$d13ec200$73bc4600$@vanpelt@fcdonders.ru.nl>

Hi Diego,

You could try using ft_databrowser instead of ft_rejectvisual (followed by
ft_rejectartifact), so:

cfg            = [];
cfg.continuous = 'no';
cfg.channel    = {'EEG057','EEG058'};
cfg            = ft_databrowser(cfg,data);

I think it should work like this.

Best,
Stan

-----Original Message-----
From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano Soldevilla,
D. (Diego)
Sent: Monday, May 16, 2011 4:00 PM
To: fieldtrip at donders.ru.nl
Subject: [FieldTrip] ft_rejectvisual channel selection

Dear Fieldtrippers,

I'm using ft_rejectvisual function to reject visually EOG artifacts of
epoched trials. My problem consist that I'm not able to plot only the EOG
channels even when I explicitly select them ignoring the 'MEG' channels (I
get a plot with all channels MEG + EOG).

I directly used rejectvisual_channel (used in line 263 offt_rejectvisual)
function selecting the EOG channels but I'm getting again all channels.
Somebody could tell me what I'm doing wrong?

Thanks in advance,

Diego



PS: Code

%epoching
cfg = [];
cfg.dataset                     = [direc d(rr,1).name];
cfg.trialdef.eventtype          = 'frontpanel trigger';
cfg.trialdef.eventvalue         = 4;
cfg.trialdef.prestim            = 1; % in seconds
cfg.trialdef.poststim           = 4; % in seconds
cfg.trialdef.epochmoving        = 'inbackward';
cfg.trialdef.pivoteventvalue    = 2;% cue stimulus
cfg.trialdef.jumps              = 1;
cfg.trialfun                    = 'trialselec';

cfg = ft_definetrial(cfg);

cfg.channel                     = {'MEG' 'EEG057' 'EEG058'};
cfg.lpfilter                    = 'yes';
cfg.lpfreq                      = 250;
cfg.baselinewindow              = [-1 0];
cfg.keeptrials                  = 'yes';
cfg.demean                      = 'yes';
cfg.continuous                  = 'yes';

data    = ft_preprocessing(cfg);

%..............


%visual data rejection
cfg             = [];
cfg.channel     = {'EEG057' 'EEG058'};
cfg.method      = 'channel';
cfg.keepchannel = 'yes';
data_c          = ft_rejectvisual(cfg,data);



-- 
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Trigon, room 0.83
Kapittelweg 29
Radboud University Nijmegen
NL-6500 HB Nijmegen
The Netherlands
E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
Tel:      +31-(0)24-36-66274
Web:    http://www.neuosc.com/
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From d.lozanosoldevilla at fcdonders.ru.nl  Mon May 16 16:24:38 2011
From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego))
Date: Mon, 16 May 2011 16:24:38 +0200 (CEST)
Subject: [FieldTrip] ft_rejectvisual channel selection
In-Reply-To: <022901cc13d3$d13ec200$73bc4600$@vanpelt@fcdonders.ru.nl>
Message-ID: <1082570781.130469.1305555878921.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Stan,

Thanks for your quickly answer. I get this error:

Warning: the data does not contain a trial definition, assuming that the trials are consecutive segments of a continuous recording
> In utilities/private/warning_once at 81
  In utilities/private/fixtrialdef at 52
  In ft_datatype_raw at 91
  In ft_checkdata at 161
  In ft_databrowser at 120
redrawing with viewmode butterfly
??? Improper index matrix reference.

Error in ==> ft_databrowser>redraw_cb at 910
  evtsample = [event(:).sample];

Error in ==> ft_databrowser at 419
redraw_cb(h);

I don't know why my data have no trial definition when I'm sure that is epoched... Any ideas?

Thanks in advance,

Diego



----- "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl> wrote:

> From: "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl>
> To: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
> Sent: Monday, 16 May, 2011 4:16:16 PM
> Subject: Re: [FieldTrip] ft_rejectvisual channel selection
>
> Hi Diego,
> 
> You could try using ft_databrowser instead of ft_rejectvisual
> (followed by
> ft_rejectartifact), so:
> 
> cfg            = [];
> cfg.continuous = 'no';
> cfg.channel    = {'EEG057','EEG058'};
> cfg            = ft_databrowser(cfg,data);
> 
> I think it should work like this.
> 
> Best,
> Stan
> 
> -----Original Message-----
> From: fieldtrip-bounces at donders.ru.nl
> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano
> Soldevilla,
> D. (Diego)
> Sent: Monday, May 16, 2011 4:00 PM
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] ft_rejectvisual channel selection
> 
> Dear Fieldtrippers,
> 
> I'm using ft_rejectvisual function to reject visually EOG artifacts
> of
> epoched trials. My problem consist that I'm not able to plot only the
> EOG
> channels even when I explicitly select them ignoring the 'MEG'
> channels (I
> get a plot with all channels MEG + EOG).
> 
> I directly used rejectvisual_channel (used in line 263
> offt_rejectvisual)
> function selecting the EOG channels but I'm getting again all
> channels.
> Somebody could tell me what I'm doing wrong?
> 
> Thanks in advance,
> 
> Diego
> 
> 
> 
> PS: Code
> 
> %epoching
> cfg = [];
> cfg.dataset                     = [direc d(rr,1).name];
> cfg.trialdef.eventtype          = 'frontpanel trigger';
> cfg.trialdef.eventvalue         = 4;
> cfg.trialdef.prestim            = 1; % in seconds
> cfg.trialdef.poststim           = 4; % in seconds
> cfg.trialdef.epochmoving        = 'inbackward';
> cfg.trialdef.pivoteventvalue    = 2;% cue stimulus
> cfg.trialdef.jumps              = 1;
> cfg.trialfun                    = 'trialselec';
> 
> cfg = ft_definetrial(cfg);
> 
> cfg.channel                     = {'MEG' 'EEG057' 'EEG058'};
> cfg.lpfilter                    = 'yes';
> cfg.lpfreq                      = 250;
> cfg.baselinewindow              = [-1 0];
> cfg.keeptrials                  = 'yes';
> cfg.demean                      = 'yes';
> cfg.continuous                  = 'yes';
> 
> data    = ft_preprocessing(cfg);
> 
> %..............
> 
> 
> %visual data rejection
> cfg             = [];
> cfg.channel     = {'EEG057' 'EEG058'};
> cfg.method      = 'channel';
> cfg.keepchannel = 'yes';
> data_c          = ft_rejectvisual(cfg,data);
> 
> 
> 
> -- 
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Trigon, room 0.83
> Kapittelweg 29
> Radboud University Nijmegen
> NL-6500 HB Nijmegen
> The Netherlands
> E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
> Tel:      +31-(0)24-36-66274
> Web:    http://www.neuosc.com/
> _______________________________________________
> 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

-- 
PhD Student
Donders Institute for Brain, Cognition and Behaviour 
Centre for Cognitive Neuroimaging
Trigon, room 0.83
Kapittelweg 29
Radboud University Nijmegen 
NL-6500 HB Nijmegen
The Netherlands
E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
Tel:      +31-(0)24-36-66274
Web:    http://www.neuosc.com/ 




From stan.vanpelt at fcdonders.ru.nl  Mon May 16 21:40:11 2011
From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt)
Date: Mon, 16 May 2011 21:40:11 +0200 (CEST)
Subject: [FieldTrip] ft_rejectvisual channel selection
In-Reply-To: <1082570781.130469.1305555878921.JavaMail.root@sculptor.zimbra.ru.nl>
References: <022901cc13d3$d13ec200$73bc4600$@vanpelt@fcdonders.ru.nl>
	<1082570781.130469.1305555878921.JavaMail.root@sculptor.zimbra.ru.nl>
Message-ID: <024701cc1401$122fb120$368f1360$@vanpelt@fcdonders.ru.nl>

Hi Diego,

Hm, sounds odd to me. Is your trial-definition output from ft_definetrial
correct? So a cfg.trl that is not empty?

Otherwise, you might try starting with an empty cfg again before calling
ft_preprocessing?

cfg=ft_definetrial(cfg);
trials=cfg.trl;

cfg=[];
cfg.trl=trials;
cfg.dataset                     = [direc d(rr,1).name];
cfg.channel                     = {'MEG' 'EEG057' 'EEG058'};
cfg.continuous                  = 'yes';
etc..
data                            = ft_preprocessing(cfg);

That should give you an output with a trial-structure, I'd say.

Best,
Stan

-----Original Message-----
From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano Soldevilla,
D. (Diego)
Sent: Monday, May 16, 2011 4:25 PM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] ft_rejectvisual channel selection

Hi Stan,

Thanks for your quickly answer. I get this error:

Warning: the data does not contain a trial definition, assuming that the
trials are consecutive segments of a continuous recording
> In utilities/private/warning_once at 81
  In utilities/private/fixtrialdef at 52
  In ft_datatype_raw at 91
  In ft_checkdata at 161
  In ft_databrowser at 120
redrawing with viewmode butterfly
??? Improper index matrix reference.

Error in ==> ft_databrowser>redraw_cb at 910
  evtsample = [event(:).sample];

Error in ==> ft_databrowser at 419
redraw_cb(h);

I don't know why my data have no trial definition when I'm sure that is
epoched... Any ideas?

Thanks in advance,

Diego



----- "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl> wrote:

> From: "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl>
> To: "Email discussion list for the FieldTrip project"
<fieldtrip at donders.ru.nl>
> Sent: Monday, 16 May, 2011 4:16:16 PM
> Subject: Re: [FieldTrip] ft_rejectvisual channel selection
>
> Hi Diego,
> 
> You could try using ft_databrowser instead of ft_rejectvisual
> (followed by
> ft_rejectartifact), so:
> 
> cfg            = [];
> cfg.continuous = 'no';
> cfg.channel    = {'EEG057','EEG058'};
> cfg            = ft_databrowser(cfg,data);
> 
> I think it should work like this.
> 
> Best,
> Stan
> 
> -----Original Message-----
> From: fieldtrip-bounces at donders.ru.nl
> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano
> Soldevilla,
> D. (Diego)
> Sent: Monday, May 16, 2011 4:00 PM
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] ft_rejectvisual channel selection
> 
> Dear Fieldtrippers,
> 
> I'm using ft_rejectvisual function to reject visually EOG artifacts
> of
> epoched trials. My problem consist that I'm not able to plot only the
> EOG
> channels even when I explicitly select them ignoring the 'MEG'
> channels (I
> get a plot with all channels MEG + EOG).
> 
> I directly used rejectvisual_channel (used in line 263
> offt_rejectvisual)
> function selecting the EOG channels but I'm getting again all
> channels.
> Somebody could tell me what I'm doing wrong?
> 
> Thanks in advance,
> 
> Diego
> 
> 
> 
> PS: Code
> 
> %epoching
> cfg = [];
> cfg.dataset                     = [direc d(rr,1).name];
> cfg.trialdef.eventtype          = 'frontpanel trigger';
> cfg.trialdef.eventvalue         = 4;
> cfg.trialdef.prestim            = 1; % in seconds
> cfg.trialdef.poststim           = 4; % in seconds
> cfg.trialdef.epochmoving        = 'inbackward';
> cfg.trialdef.pivoteventvalue    = 2;% cue stimulus
> cfg.trialdef.jumps              = 1;
> cfg.trialfun                    = 'trialselec';
> 
> cfg = ft_definetrial(cfg);
> 
> cfg.channel                     = {'MEG' 'EEG057' 'EEG058'};
> cfg.lpfilter                    = 'yes';
> cfg.lpfreq                      = 250;
> cfg.baselinewindow              = [-1 0];
> cfg.keeptrials                  = 'yes';
> cfg.demean                      = 'yes';
> cfg.continuous                  = 'yes';
> 
> data    = ft_preprocessing(cfg);
> 
> %..............
> 
> 
> %visual data rejection
> cfg             = [];
> cfg.channel     = {'EEG057' 'EEG058'};
> cfg.method      = 'channel';
> cfg.keepchannel = 'yes';
> data_c          = ft_rejectvisual(cfg,data);
> 
> 
> 
> -- 
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Trigon, room 0.83
> Kapittelweg 29
> Radboud University Nijmegen
> NL-6500 HB Nijmegen
> The Netherlands
> E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
> Tel:      +31-(0)24-36-66274
> Web:    http://www.neuosc.com/
> _______________________________________________
> 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

-- 
PhD Student
Donders Institute for Brain, Cognition and Behaviour 
Centre for Cognitive Neuroimaging
Trigon, room 0.83
Kapittelweg 29
Radboud University Nijmegen 
NL-6500 HB Nijmegen
The Netherlands
E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
Tel:      +31-(0)24-36-66274
Web:    http://www.neuosc.com/ 


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From d.lozanosoldevilla at fcdonders.ru.nl  Tue May 17 00:19:50 2011
From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego))
Date: Tue, 17 May 2011 00:19:50 +0200 (CEST)
Subject: [FieldTrip] ft_rejectvisual channel selection
In-Reply-To: <940868980.135061.1305583605111.JavaMail.root@sculptor.zimbra.ru.nl>
Message-ID: <729723926.135100.1305584390797.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Stan,

You're right. It seems that my problem lies in the lack of trl because I previously resample my data and this last function do not creates a new trl with the updated begin and end samples. If I create a new trl = round(data.cfg.previous.trl(:,1:3) * (1/data.cfg.origfs) *data.fsample);, I get the same error but not with the original data (without resampling). Then I'll use data without resampling to check my artifacts.

Thanks again,

Diego



----- "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl> wrote:

> From: "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl>
> To: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
> Sent: Monday, 16 May, 2011 9:40:11 PM
> Subject: Re: [FieldTrip] ft_rejectvisual channel selection
>
> Hi Diego,
> 
> Hm, sounds odd to me. Is your trial-definition output from
> ft_definetrial
> correct? So a cfg.trl that is not empty?
> 
> Otherwise, you might try starting with an empty cfg again before
> calling
> ft_preprocessing?
> 
> cfg=ft_definetrial(cfg);
> trials=cfg.trl;
> 
> cfg=[];
> cfg.trl=trials;
> cfg.dataset                     = [direc d(rr,1).name];
> cfg.channel                     = {'MEG' 'EEG057' 'EEG058'};
> cfg.continuous                  = 'yes';
> etc..
> data                            = ft_preprocessing(cfg);
> 
> That should give you an output with a trial-structure, I'd say.
> 
> Best,
> Stan
> 
> -----Original Message-----
> From: fieldtrip-bounces at donders.ru.nl
> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano
> Soldevilla,
> D. (Diego)
> Sent: Monday, May 16, 2011 4:25 PM
> To: Email discussion list for the FieldTrip project
> Subject: Re: [FieldTrip] ft_rejectvisual channel selection
> 
> Hi Stan,
> 
> Thanks for your quickly answer. I get this error:
> 
> Warning: the data does not contain a trial definition, assuming that
> the
> trials are consecutive segments of a continuous recording
> > In utilities/private/warning_once at 81
>   In utilities/private/fixtrialdef at 52
>   In ft_datatype_raw at 91
>   In ft_checkdata at 161
>   In ft_databrowser at 120
> redrawing with viewmode butterfly
> ??? Improper index matrix reference.
> 
> Error in ==> ft_databrowser>redraw_cb at 910
>   evtsample = [event(:).sample];
> 
> Error in ==> ft_databrowser at 419
> redraw_cb(h);
> 
> I don't know why my data have no trial definition when I'm sure that
> is
> epoched... Any ideas?
> 
> Thanks in advance,
> 
> Diego
> 
> 
> 
> ----- "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl> wrote:
> 
> > From: "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl>
> > To: "Email discussion list for the FieldTrip project"
> <fieldtrip at donders.ru.nl>
> > Sent: Monday, 16 May, 2011 4:16:16 PM
> > Subject: Re: [FieldTrip] ft_rejectvisual channel selection
> >
> > Hi Diego,
> > 
> > You could try using ft_databrowser instead of ft_rejectvisual
> > (followed by
> > ft_rejectartifact), so:
> > 
> > cfg            = [];
> > cfg.continuous = 'no';
> > cfg.channel    = {'EEG057','EEG058'};
> > cfg            = ft_databrowser(cfg,data);
> > 
> > I think it should work like this.
> > 
> > Best,
> > Stan
> > 
> > -----Original Message-----
> > From: fieldtrip-bounces at donders.ru.nl
> > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano
> > Soldevilla,
> > D. (Diego)
> > Sent: Monday, May 16, 2011 4:00 PM
> > To: fieldtrip at donders.ru.nl
> > Subject: [FieldTrip] ft_rejectvisual channel selection
> > 
> > Dear Fieldtrippers,
> > 
> > I'm using ft_rejectvisual function to reject visually EOG artifacts
> > of
> > epoched trials. My problem consist that I'm not able to plot only
> the
> > EOG
> > channels even when I explicitly select them ignoring the 'MEG'
> > channels (I
> > get a plot with all channels MEG + EOG).
> > 
> > I directly used rejectvisual_channel (used in line 263
> > offt_rejectvisual)
> > function selecting the EOG channels but I'm getting again all
> > channels.
> > Somebody could tell me what I'm doing wrong?
> > 
> > Thanks in advance,
> > 
> > Diego
> > 
> > 
> > 
> > PS: Code
> > 
> > %epoching
> > cfg = [];
> > cfg.dataset                     = [direc d(rr,1).name];
> > cfg.trialdef.eventtype          = 'frontpanel trigger';
> > cfg.trialdef.eventvalue         = 4;
> > cfg.trialdef.prestim            = 1; % in seconds
> > cfg.trialdef.poststim           = 4; % in seconds
> > cfg.trialdef.epochmoving        = 'inbackward';
> > cfg.trialdef.pivoteventvalue    = 2;% cue stimulus
> > cfg.trialdef.jumps              = 1;
> > cfg.trialfun                    = 'trialselec';
> > 
> > cfg = ft_definetrial(cfg);
> > 
> > cfg.channel                     = {'MEG' 'EEG057' 'EEG058'};
> > cfg.lpfilter                    = 'yes';
> > cfg.lpfreq                      = 250;
> > cfg.baselinewindow              = [-1 0];
> > cfg.keeptrials                  = 'yes';
> > cfg.demean                      = 'yes';
> > cfg.continuous                  = 'yes';
> > 
> > data    = ft_preprocessing(cfg);
> > 
> > %..............
> > 
> > 
> > %visual data rejection
> > cfg             = [];
> > cfg.channel     = {'EEG057' 'EEG058'};
> > cfg.method      = 'channel';
> > cfg.keepchannel = 'yes';
> > data_c          = ft_rejectvisual(cfg,data);
> > 
> > 
> > 
> > -- 
> > PhD Student
> > Donders Institute for Brain, Cognition and Behaviour
> > Centre for Cognitive Neuroimaging
> > Trigon, room 0.83
> > Kapittelweg 29
> > Radboud University Nijmegen
> > NL-6500 HB Nijmegen
> > The Netherlands
> > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
> > Tel:      +31-(0)24-36-66274
> > Web:    http://www.neuosc.com/
> > _______________________________________________
> > 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
> 
> -- 
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour 
> Centre for Cognitive Neuroimaging
> Trigon, room 0.83
> Kapittelweg 29
> Radboud University Nijmegen 
> NL-6500 HB Nijmegen
> The Netherlands
> E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
> Tel:      +31-(0)24-36-66274
> Web:    http://www.neuosc.com/ 
> 
> 
> _______________________________________________
> 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




From younes_zerouali at hotmail.com  Tue May 17 00:25:25 2011
From: younes_zerouali at hotmail.com (Younes Zerouali)
Date: Mon, 16 May 2011 18:25:25 -0400
Subject: [FieldTrip] Segment anatomy from MRI (spm8)
Message-ID: <snt144-w421EDF4E5F9E50BF217D0988D0@phx.gbl>


Hi all,

I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel).
My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before?

Best,


Younes


  		 	   		  
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From Gregor.Volberg at psychologie.uni-regensburg.de  Tue May 17 08:18:39 2011
From: Gregor.Volberg at psychologie.uni-regensburg.de (Gregor Volberg)
Date: Tue, 17 May 2011 08:18:39 +0200
Subject: [FieldTrip] Antw:  Segment anatomy from MRI (spm8)
In-Reply-To: <snt144-w421EDF4E5F9E50BF217D0988D0@phx.gbl>
References: <snt144-w421EDF4E5F9E50BF217D0988D0@phx.gbl>
Message-ID: <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de>


Hi Younes, 

this is actually not a problem with the function. The "ft_volumesegment" will only return segmentations of the anatomical mri with respect to three tissue types: grey matter, white matter, and csf. You can use gray and white matter segmentations to construct your brain compartement by typing e. g. "brain = (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order to get skull and skin compartements, you need your original mri.anatomy which holds the image intensity on a black-to-white scale. You can threshold the white values to segment the head from the background, and this is then your skin compartement (e. g., "skin = (mri.anatomy>300);" as shown in the tutorial). The skull compartement is the oversection of the skin compartement and the brain compartement after you blew up those compartements a bit, 
skin_a  = imerode(skin, s); 
brain_a = imdilate(brain, s); 
skull = (brain_a & skin_a); 
Especially the construction of the skin is a lot of work, as you need the wholes in the anatomical mri (eyes, ear, inhomogeneities) by hand. 

Best regards and good luck, 
Gregor 




-- 
Dr. rer. nat. Gregor Volberg <gregor.volberg at psychologie.uni-regensburg.de> ( mailto:gregor.volberg at psychologie.uni-regensburg.de )
University of Regensburg
Institute for Experimental Psychology
93040 Regensburg, Germany
Tel: +49 941 943 3862 
Fax: +49 941 943 3233
http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html


>>> Younes Zerouali <younes_zerouali at hotmail.com> 5/17/2011 12:25 AM >>>
Hi all,

I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel).
My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before?

Best,


Younes


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From jan.schoffelen at donders.ru.nl  Tue May 17 08:42:22 2011
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Tue, 17 May 2011 08:42:22 +0200
Subject: [FieldTrip] Antw:  Segment anatomy from MRI (spm8)
In-Reply-To: <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de>
References: <snt144-w421EDF4E5F9E50BF217D0988D0@phx.gbl>
	<4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de>
Message-ID: <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl>

Dear Gregor and Younes,

We recently added functionaity to ft_volumesegment to actually compute  
the brainmask or scalp surface. Gregor is right in that until a few  
weeks ago, ft_volumesegment only returned the probabilistic maps for  
the grey whit and csf compartments. Nowadays, given the appropriate  
cfg, it can do much more (see the documentation on the wiki for the  
cfg-settings). For this of course you need an up-to-date version of  
FieldTrip!

Best wishes,

Jan-Mathijs



On May 17, 2011, at 8:18 AM, Gregor Volberg wrote:

> Hi Younes,
>
> this is actually not a problem with the function. The  
> "ft_volumesegment" will only return segmentations of the anatomical  
> mri with respect to three tissue types: grey matter, white matter,  
> and csf. You can use gray and white matter segmentations to  
> construct your brain compartement by typing e. g. "brain =  
> (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order  
> to get skull and skin compartements, you need your original  
> mri.anatomy which holds the image intensity on a black-to-white  
> scale. You can threshold the white values to segment the head from  
> the background, and this is then your skin compartement (e. g.,  
> "skin = (mri.anatomy>300);" as shown in the tutorial). The skull  
> compartement is the oversection of the skin compartement and the  
> brain compartement after you blew up those compartements a bit,
> skin_a  = imerode(skin, s);
> brain_a = imdilate(brain, s);
> skull = (brain_a & skin_a);
> Especially the construction of the skin is a lot of work, as you  
> need the wholes in the anatomical mri (eyes, ear, inhomogeneities)  
> by hand.
>
> Best regards and good luck,
> Gregor
>
>
>
>
> -- 
> Dr. rer. nat. Gregor Volberg <gregor.volberg at psychologie.uni-regensburg.de 
> > ( mailto:gregor.volberg at psychologie.uni-regensburg.de )
> University of Regensburg
> Institute for Experimental Psychology
> 93040 Regensburg, Germany
> Tel: +49 941 943 3862
> Fax: +49 941 943 3233
> http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html
>
>
> >>> Younes Zerouali <younes_zerouali at hotmail.com> 5/17/2011 12:25 AM  
> >>>
> Hi all,
>
> I'm trying to segment head anatomical surfaces (scalp, skull) using  
> the mri scan from patient Colin27 (MNI, Montreal) following the  
> steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel 
> ).
> My problem is that the function "ft_volumesegment" doesn't return  
> all the variables that are mentionned in the tutorial. For example,  
> there is no field named "skull" or "scalp" in the argument returned  
> by this function. Anyone had this problem before?
>
> Best,
>
>
> Younes
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793

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From Gregor.Volberg at psychologie.uni-regensburg.de  Tue May 17 09:14:54 2011
From: Gregor.Volberg at psychologie.uni-regensburg.de (Gregor Volberg)
Date: Tue, 17 May 2011 09:14:54 +0200
Subject: [FieldTrip] Antw:  Segment anatomy from MRI (spm8)
In-Reply-To: <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl>
References: <snt144-w421EDF4E5F9E50BF217D0988D0@phx.gbl>
	<4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de>
	<8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl>
Message-ID: <4DD23C8E02000057000096DB@gwsmtp1.uni-regensburg.de>


Dear Jan-Matthijs, 

I wasn't aware of this! Thanks a lot dear fieldtrippers, this is surely a helpful addition to ft_volumesegment. 
Best regards, 
Gregor 



-- 
Dr. rer. nat. Gregor Volberg <gregor.volberg at psychologie.uni-regensburg.de> ( mailto:gregor.volberg at psychologie.uni-regensburg.de )
University of Regensburg
Institute for Experimental Psychology
93040 Regensburg, Germany
Tel: +49 941 943 3862 
Fax: +49 941 943 3233
http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html


>>> jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl> 5/17/2011 8:42 AM >>>
Dear Gregor and Younes, 



We recently added functionaity to ft_volumesegment to actually compute the brainmask or scalp surface. Gregor is right in that until a few weeks ago, ft_volumesegment only returned the probabilistic maps for the grey whit and csf compartments. Nowadays, given the appropriate cfg, it can do much more (see the documentation on the wiki for the cfg-settings). For this of course you need an up-to-date version of FieldTrip! 



Best wishes, 



Jan-Mathijs 







On May 17, 2011, at 8:18 AM, Gregor Volberg wrote: 





Hi Younes, 



this is actually not a problem with the function. The "ft_volumesegment" will only return segmentations of the anatomical mri with respect to three tissue types: grey matter, white matter, and csf. You can use gray and white matter segmentations to construct your brain compartement by typing e. g. "brain = (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order to get skull and skin compartements, you need your original mri.anatomy which holds the image intensity on a black-to-white scale. You can threshold the white values to segment the head from the background, and this is then your skin compartement (e. g., "skin = (mri.anatomy>300);" as shown in the tutorial). The skull compartement is the oversection of the skin compartement and the brain compartement after you blew up those compartements a bit, 

skin_a  = imerode(skin, s); 

brain_a = imdilate(brain, s); 

skull = (brain_a & skin_a); 

Especially the construction of the skin is a lot of work, as you need the wholes in the anatomical mri (eyes, ear, inhomogeneities) by hand. 



Best regards and good luck, 

Gregor 






-- 
Dr. rer. nat. Gregor Volberg <gregor.volberg at psychologie.uni-regensburg.de> ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) 
University of Regensburg 
Institute for Experimental Psychology 
93040 Regensburg, Germany 
Tel: +49 941 943 3862 
Fax: +49 941 943 3233 
http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html 


>>> Younes Zerouali <younes_zerouali at hotmail.com> 5/17/2011 12:25 AM >>>
Hi all,

I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel).
My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before?

Best,


Younes

 


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 
 



Dr. J.M. (Jan-Mathijs) Schoffelen  

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

J.Schoffelen at donders.ru.nl 

Telephone: 0031-24-3614793 


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From eelke.spaak at donders.ru.nl  Tue May 17 09:28:36 2011
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Tue, 17 May 2011 09:28:36 +0200
Subject: [FieldTrip] ft_rejectvisual channel selection
In-Reply-To: <729723926.135100.1305584390797.JavaMail.root@sculptor.zimbra.ru.nl>
References: <940868980.135061.1305583605111.JavaMail.root@sculptor.zimbra.ru.nl>
	<729723926.135100.1305584390797.JavaMail.root@sculptor.zimbra.ru.nl>
Message-ID: <BANLkTikOyOmc8y7Zvz1APRTgWT0QsW_=pQ@mail.gmail.com>

Hi Diego,

Indeed, it is probably a good idea to check for artifacts before
performing any resampling. The sample indices that are stored in trl
(or sampleinfo) matrices, should always correspond to sample indices
in the *original* dataset (on disk), and do not necessarily have any
direct relation to sample indices in the data you have in memory.
Therefore, if you resample the data, the samples in your data in
memory do not directly correspond to samples in the dataset on disk
anymore; so therefore trl or sampleinfo fields would not make sense,
and might even lead to inconsistencies. This is the reason that
ft_resampledata removes any such fields, if present, from your
(in-memory) dataset.

We are currently in the process of thinking hard about the trl and
sampleinfo matrices, and might revise how these are handled in the
future. In any case, it should become possible (already on our
todo-list) to use the artifact detection functions on in-data memory
without explicit sample indices.

But, for now, your solution is the quickest one :)

Best,
Eelke

2011/5/17 Lozano Soldevilla, D. (Diego) <d.lozanosoldevilla at fcdonders.ru.nl>:
> Hi Stan,
>
> You're right. It seems that my problem lies in the lack of trl because I previously resample my data and this last function do not creates a new trl with the updated begin and end samples. If I create a new trl = round(data.cfg.previous.trl(:,1:3) * (1/data.cfg.origfs) *data.fsample);, I get the same error but not with the original data (without resampling). Then I'll use data without resampling to check my artifacts.
>
> Thanks again,
>
> Diego
>
>
>
> ----- "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl> wrote:
>
>> From: "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl>
>> To: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
>> Sent: Monday, 16 May, 2011 9:40:11 PM
>> Subject: Re: [FieldTrip] ft_rejectvisual channel selection
>>
>> Hi Diego,
>>
>> Hm, sounds odd to me. Is your trial-definition output from
>> ft_definetrial
>> correct? So a cfg.trl that is not empty?
>>
>> Otherwise, you might try starting with an empty cfg again before
>> calling
>> ft_preprocessing?
>>
>> cfg=ft_definetrial(cfg);
>> trials=cfg.trl;
>>
>> cfg=[];
>> cfg.trl=trials;
>> cfg.dataset                     = [direc d(rr,1).name];
>> cfg.channel                     = {'MEG' 'EEG057' 'EEG058'};
>> cfg.continuous                  = 'yes';
>> etc..
>> data                            = ft_preprocessing(cfg);
>>
>> That should give you an output with a trial-structure, I'd say.
>>
>> Best,
>> Stan
>>
>> -----Original Message-----
>> From: fieldtrip-bounces at donders.ru.nl
>> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano
>> Soldevilla,
>> D. (Diego)
>> Sent: Monday, May 16, 2011 4:25 PM
>> To: Email discussion list for the FieldTrip project
>> Subject: Re: [FieldTrip] ft_rejectvisual channel selection
>>
>> Hi Stan,
>>
>> Thanks for your quickly answer. I get this error:
>>
>> Warning: the data does not contain a trial definition, assuming that
>> the
>> trials are consecutive segments of a continuous recording
>> > In utilities/private/warning_once at 81
>>   In utilities/private/fixtrialdef at 52
>>   In ft_datatype_raw at 91
>>   In ft_checkdata at 161
>>   In ft_databrowser at 120
>> redrawing with viewmode butterfly
>> ??? Improper index matrix reference.
>>
>> Error in ==> ft_databrowser>redraw_cb at 910
>>   evtsample = [event(:).sample];
>>
>> Error in ==> ft_databrowser at 419
>> redraw_cb(h);
>>
>> I don't know why my data have no trial definition when I'm sure that
>> is
>> epoched... Any ideas?
>>
>> Thanks in advance,
>>
>> Diego
>>
>>
>>
>> ----- "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl> wrote:
>>
>> > From: "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl>
>> > To: "Email discussion list for the FieldTrip project"
>> <fieldtrip at donders.ru.nl>
>> > Sent: Monday, 16 May, 2011 4:16:16 PM
>> > Subject: Re: [FieldTrip] ft_rejectvisual channel selection
>> >
>> > Hi Diego,
>> >
>> > You could try using ft_databrowser instead of ft_rejectvisual
>> > (followed by
>> > ft_rejectartifact), so:
>> >
>> > cfg            = [];
>> > cfg.continuous = 'no';
>> > cfg.channel    = {'EEG057','EEG058'};
>> > cfg            = ft_databrowser(cfg,data);
>> >
>> > I think it should work like this.
>> >
>> > Best,
>> > Stan
>> >
>> > -----Original Message-----
>> > From: fieldtrip-bounces at donders.ru.nl
>> > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano
>> > Soldevilla,
>> > D. (Diego)
>> > Sent: Monday, May 16, 2011 4:00 PM
>> > To: fieldtrip at donders.ru.nl
>> > Subject: [FieldTrip] ft_rejectvisual channel selection
>> >
>> > Dear Fieldtrippers,
>> >
>> > I'm using ft_rejectvisual function to reject visually EOG artifacts
>> > of
>> > epoched trials. My problem consist that I'm not able to plot only
>> the
>> > EOG
>> > channels even when I explicitly select them ignoring the 'MEG'
>> > channels (I
>> > get a plot with all channels MEG + EOG).
>> >
>> > I directly used rejectvisual_channel (used in line 263
>> > offt_rejectvisual)
>> > function selecting the EOG channels but I'm getting again all
>> > channels.
>> > Somebody could tell me what I'm doing wrong?
>> >
>> > Thanks in advance,
>> >
>> > Diego
>> >
>> >
>> >
>> > PS: Code
>> >
>> > %epoching
>> > cfg = [];
>> > cfg.dataset                     = [direc d(rr,1).name];
>> > cfg.trialdef.eventtype          = 'frontpanel trigger';
>> > cfg.trialdef.eventvalue         = 4;
>> > cfg.trialdef.prestim            = 1; % in seconds
>> > cfg.trialdef.poststim           = 4; % in seconds
>> > cfg.trialdef.epochmoving        = 'inbackward';
>> > cfg.trialdef.pivoteventvalue    = 2;% cue stimulus
>> > cfg.trialdef.jumps              = 1;
>> > cfg.trialfun                    = 'trialselec';
>> >
>> > cfg = ft_definetrial(cfg);
>> >
>> > cfg.channel                     = {'MEG' 'EEG057' 'EEG058'};
>> > cfg.lpfilter                    = 'yes';
>> > cfg.lpfreq                      = 250;
>> > cfg.baselinewindow              = [-1 0];
>> > cfg.keeptrials                  = 'yes';
>> > cfg.demean                      = 'yes';
>> > cfg.continuous                  = 'yes';
>> >
>> > data    = ft_preprocessing(cfg);
>> >
>> > %..............
>> >
>> >
>> > %visual data rejection
>> > cfg             = [];
>> > cfg.channel     = {'EEG057' 'EEG058'};
>> > cfg.method      = 'channel';
>> > cfg.keepchannel = 'yes';
>> > data_c          = ft_rejectvisual(cfg,data);
>> >
>> >
>> >
>> > --
>> > PhD Student
>> > Donders Institute for Brain, Cognition and Behaviour
>> > Centre for Cognitive Neuroimaging
>> > Trigon, room 0.83
>> > Kapittelweg 29
>> > Radboud University Nijmegen
>> > NL-6500 HB Nijmegen
>> > The Netherlands
>> > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
>> > Tel:      +31-(0)24-36-66274
>> > Web:    http://www.neuosc.com/
>> > _______________________________________________
>> > 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
>>
>> --
>> PhD Student
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Trigon, room 0.83
>> Kapittelweg 29
>> Radboud University Nijmegen
>> NL-6500 HB Nijmegen
>> The Netherlands
>> E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
>> Tel:      +31-(0)24-36-66274
>> Web:    http://www.neuosc.com/
>>
>>
>> _______________________________________________
>> 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
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



From d.lozanosoldevilla at fcdonders.ru.nl  Tue May 17 09:37:09 2011
From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego))
Date: Tue, 17 May 2011 09:37:09 +0200 (CEST)
Subject: [FieldTrip] ft_rejectvisual channel selection
In-Reply-To: <1942589717.137158.1305617671275.JavaMail.root@sculptor.zimbra.ru.nl>
Message-ID: <1909529539.137200.1305617829447.JavaMail.root@sculptor.zimbra.ru.nl>

Thanks for your explanation Eelke ;). Now all makes sense.

Diego




----- "Eelke Spaak" <eelke.spaak at donders.ru.nl> wrote:

> From: "Eelke Spaak" <eelke.spaak at donders.ru.nl>
> To: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
> Sent: Tuesday, 17 May, 2011 9:28:36 AM
> Subject: Re: [FieldTrip] ft_rejectvisual channel selection
>
> Hi Diego,
> 
> Indeed, it is probably a good idea to check for artifacts before
> performing any resampling. The sample indices that are stored in trl
> (or sampleinfo) matrices, should always correspond to sample indices
> in the *original* dataset (on disk), and do not necessarily have any
> direct relation to sample indices in the data you have in memory.
> Therefore, if you resample the data, the samples in your data in
> memory do not directly correspond to samples in the dataset on disk
> anymore; so therefore trl or sampleinfo fields would not make sense,
> and might even lead to inconsistencies. This is the reason that
> ft_resampledata removes any such fields, if present, from your
> (in-memory) dataset.
> 
> We are currently in the process of thinking hard about the trl and
> sampleinfo matrices, and might revise how these are handled in the
> future. In any case, it should become possible (already on our
> todo-list) to use the artifact detection functions on in-data memory
> without explicit sample indices.
> 
> But, for now, your solution is the quickest one :)
> 
> Best,
> Eelke
> 
> 2011/5/17 Lozano Soldevilla, D. (Diego)
> <d.lozanosoldevilla at fcdonders.ru.nl>:
> > Hi Stan,
> >
> > You're right. It seems that my problem lies in the lack of trl
> because I previously resample my data and this last function do not
> creates a new trl with the updated begin and end samples. If I create
> a new trl = round(data.cfg.previous.trl(:,1:3) * (1/data.cfg.origfs)
> *data.fsample);, I get the same error but not with the original data
> (without resampling). Then I'll use data without resampling to check
> my artifacts.
> >
> > Thanks again,
> >
> > Diego
> >
> >
> >
> > ----- "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl> wrote:
> >
> >> From: "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl>
> >> To: "Email discussion list for the FieldTrip project"
> <fieldtrip at donders.ru.nl>
> >> Sent: Monday, 16 May, 2011 9:40:11 PM
> >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection
> >>
> >> Hi Diego,
> >>
> >> Hm, sounds odd to me. Is your trial-definition output from
> >> ft_definetrial
> >> correct? So a cfg.trl that is not empty?
> >>
> >> Otherwise, you might try starting with an empty cfg again before
> >> calling
> >> ft_preprocessing?
> >>
> >> cfg=ft_definetrial(cfg);
> >> trials=cfg.trl;
> >>
> >> cfg=[];
> >> cfg.trl=trials;
> >> cfg.dataset                     = [direc d(rr,1).name];
> >> cfg.channel                     = {'MEG' 'EEG057' 'EEG058'};
> >> cfg.continuous                  = 'yes';
> >> etc..
> >> data                            = ft_preprocessing(cfg);
> >>
> >> That should give you an output with a trial-structure, I'd say.
> >>
> >> Best,
> >> Stan
> >>
> >> -----Original Message-----
> >> From: fieldtrip-bounces at donders.ru.nl
> >> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano
> >> Soldevilla,
> >> D. (Diego)
> >> Sent: Monday, May 16, 2011 4:25 PM
> >> To: Email discussion list for the FieldTrip project
> >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection
> >>
> >> Hi Stan,
> >>
> >> Thanks for your quickly answer. I get this error:
> >>
> >> Warning: the data does not contain a trial definition, assuming
> that
> >> the
> >> trials are consecutive segments of a continuous recording
> >> > In utilities/private/warning_once at 81
> >>   In utilities/private/fixtrialdef at 52
> >>   In ft_datatype_raw at 91
> >>   In ft_checkdata at 161
> >>   In ft_databrowser at 120
> >> redrawing with viewmode butterfly
> >> ??? Improper index matrix reference.
> >>
> >> Error in ==> ft_databrowser>redraw_cb at 910
> >>   evtsample = [event(:).sample];
> >>
> >> Error in ==> ft_databrowser at 419
> >> redraw_cb(h);
> >>
> >> I don't know why my data have no trial definition when I'm sure
> that
> >> is
> >> epoched... Any ideas?
> >>
> >> Thanks in advance,
> >>
> >> Diego
> >>
> >>
> >>
> >> ----- "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl> wrote:
> >>
> >> > From: "Stan van Pelt" <stan.vanpelt at fcdonders.ru.nl>
> >> > To: "Email discussion list for the FieldTrip project"
> >> <fieldtrip at donders.ru.nl>
> >> > Sent: Monday, 16 May, 2011 4:16:16 PM
> >> > Subject: Re: [FieldTrip] ft_rejectvisual channel selection
> >> >
> >> > Hi Diego,
> >> >
> >> > You could try using ft_databrowser instead of ft_rejectvisual
> >> > (followed by
> >> > ft_rejectartifact), so:
> >> >
> >> > cfg            = [];
> >> > cfg.continuous = 'no';
> >> > cfg.channel    = {'EEG057','EEG058'};
> >> > cfg            = ft_databrowser(cfg,data);
> >> >
> >> > I think it should work like this.
> >> >
> >> > Best,
> >> > Stan
> >> >
> >> > -----Original Message-----
> >> > From: fieldtrip-bounces at donders.ru.nl
> >> > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano
> >> > Soldevilla,
> >> > D. (Diego)
> >> > Sent: Monday, May 16, 2011 4:00 PM
> >> > To: fieldtrip at donders.ru.nl
> >> > Subject: [FieldTrip] ft_rejectvisual channel selection
> >> >
> >> > Dear Fieldtrippers,
> >> >
> >> > I'm using ft_rejectvisual function to reject visually EOG
> artifacts
> >> > of
> >> > epoched trials. My problem consist that I'm not able to plot
> only
> >> the
> >> > EOG
> >> > channels even when I explicitly select them ignoring the 'MEG'
> >> > channels (I
> >> > get a plot with all channels MEG + EOG).
> >> >
> >> > I directly used rejectvisual_channel (used in line 263
> >> > offt_rejectvisual)
> >> > function selecting the EOG channels but I'm getting again all
> >> > channels.
> >> > Somebody could tell me what I'm doing wrong?
> >> >
> >> > Thanks in advance,
> >> >
> >> > Diego
> >> >
> >> >
> >> >
> >> > PS: Code
> >> >
> >> > %epoching
> >> > cfg = [];
> >> > cfg.dataset                     = [direc d(rr,1).name];
> >> > cfg.trialdef.eventtype          = 'frontpanel trigger';
> >> > cfg.trialdef.eventvalue         = 4;
> >> > cfg.trialdef.prestim            = 1; % in seconds
> >> > cfg.trialdef.poststim           = 4; % in seconds
> >> > cfg.trialdef.epochmoving        = 'inbackward';
> >> > cfg.trialdef.pivoteventvalue    = 2;% cue stimulus
> >> > cfg.trialdef.jumps              = 1;
> >> > cfg.trialfun                    = 'trialselec';
> >> >
> >> > cfg = ft_definetrial(cfg);
> >> >
> >> > cfg.channel                     = {'MEG' 'EEG057' 'EEG058'};
> >> > cfg.lpfilter                    = 'yes';
> >> > cfg.lpfreq                      = 250;
> >> > cfg.baselinewindow              = [-1 0];
> >> > cfg.keeptrials                  = 'yes';
> >> > cfg.demean                      = 'yes';
> >> > cfg.continuous                  = 'yes';
> >> >
> >> > data    = ft_preprocessing(cfg);
> >> >
> >> > %..............
> >> >
> >> >
> >> > %visual data rejection
> >> > cfg             = [];
> >> > cfg.channel     = {'EEG057' 'EEG058'};
> >> > cfg.method      = 'channel';
> >> > cfg.keepchannel = 'yes';
> >> > data_c          = ft_rejectvisual(cfg,data);
> >> >
> >> >
> >> >
> >> > --
> >> > PhD Student
> >> > Donders Institute for Brain, Cognition and Behaviour
> >> > Centre for Cognitive Neuroimaging
> >> > Trigon, room 0.83
> >> > Kapittelweg 29
> >> > Radboud University Nijmegen
> >> > NL-6500 HB Nijmegen
> >> > The Netherlands
> >> > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
> >> > Tel:      +31-(0)24-36-66274
> >> > Web:    http://www.neuosc.com/
> >> > _______________________________________________
> >> > 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
> >>
> >> --
> >> PhD Student
> >> Donders Institute for Brain, Cognition and Behaviour
> >> Centre for Cognitive Neuroimaging
> >> Trigon, room 0.83
> >> Kapittelweg 29
> >> Radboud University Nijmegen
> >> NL-6500 HB Nijmegen
> >> The Netherlands
> >> E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
> >> Tel:      +31-(0)24-36-66274
> >> Web:    http://www.neuosc.com/
> >>
> >>
> >> _______________________________________________
> >> 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
> >
> >
> > _______________________________________________
> > 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

-- 
PhD Student
Donders Institute for Brain, Cognition and Behaviour 
Centre for Cognitive Neuroimaging
Trigon, room 0.83
Kapittelweg 29
Radboud University Nijmegen 
NL-6500 HB Nijmegen
The Netherlands
E-Mail: d.lozanosoldevilla at fcdonders.ru.nl
Tel:      +31-(0)24-36-66274
Web:    http://www.neuosc.com/ 





From nuria.donamayor at neuro.uni-luebeck.de  Tue May 17 10:03:50 2011
From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso)
Date: Tue, 17 May 2011 10:03:50 +0200
Subject: [FieldTrip] problem reading 4d header
In-Reply-To: <C99C901A-901E-452F-91A5-954E76E27E2A@donders.ru.nl>
References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>,
	<BANLkTikoifrBKypx74pbabzyiHWxfb33+w@mail.gmail.com>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>,
	<C99C901A-901E-452F-91A5-954E76E27E2A@donders.ru.nl>
Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>

Hi Jan-Mathijs,
sorry it took me this long to answer. The variable format seems to be empty....
Nuria
________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl]
Gesendet: Freitag, 13. Mai 2011 16:43
An: Email discussion list for the FieldTrip project
Betreff: Re: [FieldTrip] problem reading 4d header

Hi Nuria,

Could you type dbstop if error on the command line, and evaluate what
the variable 'format' is in your case?

Thanks,

Jan-Mathijs

On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote:

> Yes, it is exectly the same version. Better said, versions, because
> I tried both 20110413 and 20110512....
>
> ________________________________________
> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-
> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com
> ]
> Gesendet: Freitag, 13. Mai 2011 13:39
> An: Email discussion list for the FieldTrip project
> Betreff: Re: [FieldTrip] problem reading 4d header
>
> Dear Nuria
> Is it exactly the same fieldtrip version?
> I hope someone will solve this.
> as temporary work around you can read the header on windows and then
> move to linux
>
> yuval
>
> On 13 May 2011 11:42, Nuria Donamayor Alonso <nuria.donamayor at neuro.uni-luebeck.de
> <mailto:nuria.donamayor at neuro.uni-luebeck.de>> wrote:
> Dear fieltrip users,
> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine
> with a 64-bit Matlab version and I am getting an error I don't know
> how to solve:
>
> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']);
> ??? SWITCH expression must be a scalar or string constant.
>
> Error in ==> read_4d_hdr at 60
> switch format
>
> Error in ==> ft_read_header at 153
>   orig            = read_4d_hdr(datafile);
>
> If I try to read the same data on my Windows PC with 32-bit Matlab I
> have no problem reading the header file (but I can't even finish the
> preprocessing before it runs out of memory, therefore the switch to
> the Linux machine), so I'm pretty clueless here... Can any of you
> help me?
> Thanks,
> Nuria
>
>
>
> Nuria Doñamayor Alonso, MSc
> Universitätsklinikum Schleswig-Holstein
> Campus Lübeck
> Klinik für Neurologie
> Ratzeburger Allee 160
> 23538 Lübeck
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Y.Harpaz
>
> a link to the BIU MEG lab:
> http://faculty.biu.ac.il/~goldsa/index.html<http://faculty.biu.ac.il/%7Egoldsa/index.html
> >
>
> "Many were increasingly of the opinion that they'd all made a big
> mistake in coming down from the trees in the first place. And some
> said that even the trees had been a bad move, and that no one should
> ever have left the oceans". Douglas Adams
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From amelie.serpollet at cea.fr  Tue May 17 15:58:49 2011
From: amelie.serpollet at cea.fr (=?iso-8859-1?Q?SERPOLLET_Am=E9lie_228173?=)
Date: Tue, 17 May 2011 15:58:49 +0200
Subject: [FieldTrip] questions about realtime buffer
Message-ID: <D0FE4A0F7910F4499DBC0FB25772F464920371@TAIPEI.intra.cea.fr>

Dear Fieldtrip users,

 

I'm implementing a realtime buffer in C++ pretty much like in "demo_combined" : my application creates a buffer server and an acquisition client.

I encountered a first problem when trying to close the buffer server cleanly, but with some small changes in tcpsocket.c and tcpserver.c, I think I solved the problem.

If these modifications can be useful for other users and do not create other problems, I will share them.

 

I encounter now a new problem : what if there are several acquisition clients ? 

I tried to create several couples "buffer-server + acquisition client" in different threads in my application, but it does not work at all, because of global variables (I suppose).

It seems that one buffer server can not manage several acquisition clients, but I'm not sure of this point.

Did anyone encounter this problem (or solve it) ?

Or do anyone have an idea ? 

 

Best regards,

Amelie Serpollet

 

 

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From younes_zerouali at hotmail.com  Tue May 17 16:11:36 2011
From: younes_zerouali at hotmail.com (Younes Zerouali)
Date: Tue, 17 May 2011 10:11:36 -0400
Subject: [FieldTrip] Antw:  Segment anatomy from MRI (spm8)
In-Reply-To: <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl>
References: <snt144-w421EDF4E5F9E50BF217D0988D0@phx.gbl>,
	<4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de>,
	<8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl>
Message-ID: <SNT144-w3400D3A6FA22FD692AB02D988C0@phx.gbl>


Dear Gregor and Jan-Mathijs,

Thank you both for prompt answers, I'll get to work and try that!

Best,

Younes


From: jan.schoffelen at donders.ru.nl
To: fieldtrip at donders.ru.nl
Date: Tue, 17 May 2011 08:42:22 +0200
Subject: Re: [FieldTrip] Antw:  Segment anatomy from MRI (spm8)

Dear Gregor and Younes,
We recently added functionaity to ft_volumesegment to actually compute the brainmask or scalp surface. Gregor is right in that until a few weeks ago, ft_volumesegment only returned the probabilistic maps for the grey whit and csf compartments. Nowadays, given the appropriate cfg, it can do much more (see the documentation on the wiki for the cfg-settings). For this of course you need an up-to-date version of FieldTrip!
Best wishes,
Jan-Mathijs


On May 17, 2011, at 8:18 AM, Gregor Volberg wrote:Hi Younes,
this is actually not a problem with the function. The "ft_volumesegment" will only return segmentations of the anatomical mri with respect to three tissue types: grey matter, white matter, and csf. You can use gray and white matter segmentations to construct your brain compartement by typing e. g. "brain = (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order to get skull and skin compartements, you need your original mri.anatomy which holds the image intensity on a black-to-white scale. You can threshold the white values to segment the head from the background, and this is then your skin compartement (e. g., "skin = (mri.anatomy>300);" as shown in the tutorial). The skull compartement is the oversection of the skin compartement and the brain compartement after you blew up those compartements a bit,skin_a  = imerode(skin, s);brain_a = imdilate(brain, s);skull = (brain_a & skin_a);Especially the construction of the skin is a lot of work, as you need the wholes in the anatomical mri (eyes, ear, inhomogeneities) by hand.
Best regards and good luck,Gregor



-- 
Dr. rer. nat. Gregor Volberg <gregor.volberg at psychologie.uni-regensburg.de> ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) 
University of Regensburg 
Institute for Experimental Psychology 
93040 Regensburg, Germany 
Tel: +49 941 943 3862 
Fax: +49 941 943 3233 
http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html 


>>> Younes Zerouali <younes_zerouali at hotmail.com> 5/17/2011 12:25 AM >>>
Hi all,

I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel).
My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before?

Best,


Younes




_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
 Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The NetherlandsJ.Schoffelen at donders.ru.nlTelephone: 0031-24-3614793 

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 		 	   		  
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From jan.schoffelen at donders.ru.nl  Tue May 17 16:24:21 2011
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Tue, 17 May 2011 16:24:21 +0200
Subject: [FieldTrip] problem reading 4d header
In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>
References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>,
	<BANLkTikoifrBKypx74pbabzyiHWxfb33+w@mail.gmail.com>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>,
	<C99C901A-901E-452F-91A5-954E76E27E2A@donders.ru.nl>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>
Message-ID: <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl>

Hi Nuria,

Strange. Format should contain a number. What matlab version are you  
running on the Linux machine?

Best,

Jan-Mathijs


On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote:

> Hi Jan-Mathijs,
> sorry it took me this long to answer. The variable format seems to  
> be empty....
> Nuria
> ________________________________________
> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- 
> bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl 
> ]
> Gesendet: Freitag, 13. Mai 2011 16:43
> An: Email discussion list for the FieldTrip project
> Betreff: Re: [FieldTrip] problem reading 4d header
>
> Hi Nuria,
>
> Could you type dbstop if error on the command line, and evaluate what
> the variable 'format' is in your case?
>
> Thanks,
>
> Jan-Mathijs
>
> On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote:
>
>> Yes, it is exectly the same version. Better said, versions, because
>> I tried both 20110413 and 20110512....
>>
>> ________________________________________
>> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-
>> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com
>> ]
>> Gesendet: Freitag, 13. Mai 2011 13:39
>> An: Email discussion list for the FieldTrip project
>> Betreff: Re: [FieldTrip] problem reading 4d header
>>
>> Dear Nuria
>> Is it exactly the same fieldtrip version?
>> I hope someone will solve this.
>> as temporary work around you can read the header on windows and then
>> move to linux
>>
>> yuval
>>
>> On 13 May 2011 11:42, Nuria Donamayor Alonso <nuria.donamayor at neuro.uni-luebeck.de
>> <mailto:nuria.donamayor at neuro.uni-luebeck.de>> wrote:
>> Dear fieltrip users,
>> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine
>> with a 64-bit Matlab version and I am getting an error I don't know
>> how to solve:
>>
>> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']);
>> ??? SWITCH expression must be a scalar or string constant.
>>
>> Error in ==> read_4d_hdr at 60
>> switch format
>>
>> Error in ==> ft_read_header at 153
>>  orig            = read_4d_hdr(datafile);
>>
>> If I try to read the same data on my Windows PC with 32-bit Matlab I
>> have no problem reading the header file (but I can't even finish the
>> preprocessing before it runs out of memory, therefore the switch to
>> the Linux machine), so I'm pretty clueless here... Can any of you
>> help me?
>> Thanks,
>> Nuria
>>
>>
>>
>> Nuria Doñamayor Alonso, MSc
>> Universitätsklinikum Schleswig-Holstein
>> Campus Lübeck
>> Klinik für Neurologie
>> Ratzeburger Allee 160
>> 23538 Lübeck
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> --
>> Y.Harpaz
>>
>> a link to the BIU MEG lab:
>> http://faculty.biu.ac.il/~goldsa/index.html<http://faculty.biu.ac.il/%7Egoldsa/index.html
>>>
>>
>> "Many were increasingly of the opinion that they'd all made a big
>> mistake in coming down from the trees in the first place. And some
>> said that even the trees had been a bad move, and that no one should
>> ever have left the oceans". Douglas Adams
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> Dr. J.M. (Jan-Mathijs) Schoffelen
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: 0031-24-3614793
>
>
> _______________________________________________
> 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

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793




From nuria.donamayor at neuro.uni-luebeck.de  Tue May 17 16:49:17 2011
From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso)
Date: Tue, 17 May 2011 16:49:17 +0200
Subject: [FieldTrip] problem reading 4d header
In-Reply-To: <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl>
References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>,
	<BANLkTikoifrBKypx74pbabzyiHWxfb33+w@mail.gmail.com>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>,
	<C99C901A-901E-452F-91A5-954E76E27E2A@donders.ru.nl>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>,
	<5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl>
Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de>

Hi Jan-Mathijs,
I'm using Matlab 7.11.0 (R2010b).
Best,
Nuria


________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl]
Gesendet: Dienstag, 17. Mai 2011 16:24
An: Email discussion list for the FieldTrip project
Betreff: Re: [FieldTrip] problem reading 4d header

Hi Nuria,

Strange. Format should contain a number. What matlab version are you
running on the Linux machine?

Best,

Jan-Mathijs


On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote:

> Hi Jan-Mathijs,
> sorry it took me this long to answer. The variable format seems to
> be empty....
> Nuria
> ________________________________________
> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-
> bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl
> ]
> Gesendet: Freitag, 13. Mai 2011 16:43
> An: Email discussion list for the FieldTrip project
> Betreff: Re: [FieldTrip] problem reading 4d header
>
> Hi Nuria,
>
> Could you type dbstop if error on the command line, and evaluate what
> the variable 'format' is in your case?
>
> Thanks,
>
> Jan-Mathijs
>
> On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote:
>
>> Yes, it is exectly the same version. Better said, versions, because
>> I tried both 20110413 and 20110512....
>>
>> ________________________________________
>> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-
>> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com
>> ]
>> Gesendet: Freitag, 13. Mai 2011 13:39
>> An: Email discussion list for the FieldTrip project
>> Betreff: Re: [FieldTrip] problem reading 4d header
>>
>> Dear Nuria
>> Is it exactly the same fieldtrip version?
>> I hope someone will solve this.
>> as temporary work around you can read the header on windows and then
>> move to linux
>>
>> yuval
>>
>> On 13 May 2011 11:42, Nuria Donamayor Alonso <nuria.donamayor at neuro.uni-luebeck.de
>> <mailto:nuria.donamayor at neuro.uni-luebeck.de>> wrote:
>> Dear fieltrip users,
>> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine
>> with a 64-bit Matlab version and I am getting an error I don't know
>> how to solve:
>>
>> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']);
>> ??? SWITCH expression must be a scalar or string constant.
>>
>> Error in ==> read_4d_hdr at 60
>> switch format
>>
>> Error in ==> ft_read_header at 153
>>  orig            = read_4d_hdr(datafile);
>>
>> If I try to read the same data on my Windows PC with 32-bit Matlab I
>> have no problem reading the header file (but I can't even finish the
>> preprocessing before it runs out of memory, therefore the switch to
>> the Linux machine), so I'm pretty clueless here... Can any of you
>> help me?
>> Thanks,
>> Nuria
>>
>>
>>
>> Nuria Doñamayor Alonso, MSc
>> Universitätsklinikum Schleswig-Holstein
>> Campus Lübeck
>> Klinik für Neurologie
>> Ratzeburger Allee 160
>> 23538 Lübeck
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> --
>> Y.Harpaz
>>
>> a link to the BIU MEG lab:
>> http://faculty.biu.ac.il/~goldsa/index.html<http://faculty.biu.ac.il/%7Egoldsa/index.html
>>>
>>
>> "Many were increasingly of the opinion that they'd all made a big
>> mistake in coming down from the trees in the first place. And some
>> said that even the trees had been a bad move, and that no one should
>> ever have left the oceans". Douglas Adams
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> Dr. J.M. (Jan-Mathijs) Schoffelen
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: 0031-24-3614793
>
>
> _______________________________________________
> 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

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From batrod at gmail.com  Tue May 17 20:50:43 2011
From: batrod at gmail.com (Rodolphe Nenert)
Date: Tue, 17 May 2011 13:50:43 -0500
Subject: [FieldTrip] Problem with recent version of eeglab2fieldtrip
Message-ID: <BANLkTim92M67SZK5u29OH30LCPfFgY4+dQ@mail.gmail.com>

Dear Fieldtrip users,

Recently i experienced problems doing sone Time-freq analysis and i realized
it's coming from the eeglab2fieldtrip function and more precisely one line
that has been changed, apparently without being reported on the eeglab
revision history and neither in fieldtrip revision history (but i may be
wrong with this last one, i checked very quickly on google code)

The problem occurs at the Line 47:

data.label = { EEG.chanlocs(1:EEG.nbchan).labels }; % Eeglab version 9.0.2.3

data.label = { EEG.chanlocs(EEG.icachansind).labels }; % Eeglab verion
9.0.4.4

The old version works, whereas the new version will cause problem if you
dont perform an ICA with eeglab, prior to the conversion.

Hope this helps,

Rodolphe.
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From arno at cerco.ups-tlse.fr  Wed May 18 00:08:36 2011
From: arno at cerco.ups-tlse.fr (Arnaud Delorme)
Date: Tue, 17 May 2011 15:08:36 -0700
Subject: [FieldTrip] Problem with recent version of eeglab2fieldtrip
In-Reply-To: <BANLkTim92M67SZK5u29OH30LCPfFgY4+dQ@mail.gmail.com>
References: <BANLkTim92M67SZK5u29OH30LCPfFgY4+dQ@mail.gmail.com>
Message-ID: <07D46921-50BF-4C27-AA81-E4E96FD49698@cerco.ups-tlse.fr>

Dear Rodolphe,

I had changed that line because I could not fit dipoles for some ICA components (which is the main reason this function was originally designed for).
The attached function should work for both components and channel data.
Let me know if it does not.

Best,

Arno

ps: the change was actually documented on the web (http://sccn.ucsd.edu/wiki/EEGLAB_revision_history_version_9) as "eeglab2fieldtrip.m, fix performing dipole fitting on subset of channels (SVN 9092 - Arno)"



On May 17, 2011, at 11:50 AM, Rodolphe Nenert wrote:

> Dear Fieldtrip users, 
> 
> Recently i experienced problems doing sone Time-freq analysis and i realized it's coming from the eeglab2fieldtrip function and more precisely one line that has been changed, apparently without being reported on the eeglab revision history and neither in fieldtrip revision history (but i may be wrong with this last one, i checked very quickly on google code)
> 
> The problem occurs at the Line 47:
> 
> data.label = { EEG.chanlocs(1:EEG.nbchan).labels }; % Eeglab version 9.0.2.3
> 
> data.label = { EEG.chanlocs(EEG.icachansind).labels }; % Eeglab verion 9.0.4.4
> 
> The old version works, whereas the new version will cause problem if you dont perform an ICA with eeglab, prior to the conversion.
> 
> Hope this helps, 
> 
> Rodolphe.
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


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From drivolta81 at gmail.com  Wed May 18 10:51:14 2011
From: drivolta81 at gmail.com (Davide Rivolta)
Date: Wed, 18 May 2011 10:51:14 +0200
Subject: [FieldTrip] Tutorial error
Message-ID: <BANLkTikZVo3+Up=MgtjVD=5hLsWmrpKndA@mail.gmail.com>

Dear all,

I am a very beginner with fieldtrip.

I have tried to run the tutorial a couple of weeks ago, and it worked
smoothly.

Yesterday I have tried again, but surprisngly I got anerror message, as soon
as I started the tutorial (the first step entitled: "reading and processing
the interesting trials"):


cfg                                = [];
cfg.dataset                    = 'Subject01.ds';
cfg.trialdef.eventtype      = 'backpanel trigger';
cfg.trialdef.eventvalue     = 3; % the value of the stimulus trigger for
fully incongruent (FIC).
cfg.trialdef.prestim         = 1; % in seconds
cfg.trialdef.poststim       = 2; % in seconds

cfg = ft_definetrial(cfg);


??? Attempt to reference field of non-structure array

Error in ==> trialfun_general at 117
for i=find(strcmp(cfg.trialdef.eventtype, {event.type}))




This sounds really weird since it worked 2 weeks ago on the same machine and
with the same version of Fieldtrip.

Any advice would be very appreciated.

Best wishes,

Davide
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From jan.schoffelen at donders.ru.nl  Wed May 18 11:02:29 2011
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Wed, 18 May 2011 11:02:29 +0200
Subject: [FieldTrip] Tutorial error
In-Reply-To: <BANLkTikZVo3+Up=MgtjVD=5hLsWmrpKndA@mail.gmail.com>
References: <BANLkTikZVo3+Up=MgtjVD=5hLsWmrpKndA@mail.gmail.com>
Message-ID: <746130EC-C81A-4276-8C83-ADB61811B2A3@donders.ru.nl>

Dear Davide,

I am not sure whether you are using the same fieldtrip version. There  
has been a glitch recently with the trialfun_general, but this should  
be fixed by now. Could you update to a superrecent version of  
fieldtrip and try again?

Thanks,

Jan-Mathijs

PS: I cannot reproduce your error so I expect it to go away if you  
update.

On May 18, 2011, at 10:51 AM, Davide Rivolta wrote:

> Dear all,
>
> I am a very beginner with fieldtrip.
>
> I have tried to run the tutorial a couple of weeks ago, and it  
> worked smoothly.
>
> Yesterday I have tried again, but surprisngly I got anerror message,  
> as soon as I started the tutorial (the first step entitled: "reading  
> and processing the interesting trials"):
>
>
> cfg                                = [];
> cfg.dataset                    = 'Subject01.ds';
> cfg.trialdef.eventtype      = 'backpanel trigger';
> cfg.trialdef.eventvalue     = 3; % the value of the stimulus trigger  
> for fully incongruent (FIC).
> cfg.trialdef.prestim         = 1; % in seconds
> cfg.trialdef.poststim       = 2; % in seconds
>
> cfg = ft_definetrial(cfg);
>
>
> ??? Attempt to reference field of non-structure array
>
> Error in ==> trialfun_general at 117
> for i=find(strcmp(cfg.trialdef.eventtype, {event.type}))
>
>
>
>
> This sounds really weird since it worked 2 weeks ago on the same  
> machine and with the same version of Fieldtrip.
>
> Any advice would be very appreciated.
>
> Best wishes,
>
> Davide
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793



From jan.schoffelen at donders.ru.nl  Wed May 18 12:13:27 2011
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Wed, 18 May 2011 12:13:27 +0200
Subject: [FieldTrip] problem reading 4d header
In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de>
References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>,
	<BANLkTikoifrBKypx74pbabzyiHWxfb33+w@mail.gmail.com>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>,
	<C99C901A-901E-452F-91A5-954E76E27E2A@donders.ru.nl>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>,
	<5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de>
Message-ID: <0CBFB37A-FE20-436C-A5DA-FB7901EA2E80@donders.ru.nl>

Hi Nuria,

I cannot reproduce your problem on a linux machine we have here,  
running matlab 2010b (64-bit).
Either there is something wrong with your dataset (does it happen as  
well for another dataset?), or there is something different with  
respect to the configuration of your Linux machine.

Best,

Jan-Mathijs

On May 17, 2011, at 4:49 PM, Nuria Donamayor Alonso wrote:

> Hi Jan-Mathijs,
> I'm using Matlab 7.11.0 (R2010b).
> Best,
> Nuria
>
>
> ________________________________________
> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- 
> bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl 
> ]
> Gesendet: Dienstag, 17. Mai 2011 16:24
> An: Email discussion list for the FieldTrip project
> Betreff: Re: [FieldTrip] problem reading 4d header
>
> Hi Nuria,
>
> Strange. Format should contain a number. What matlab version are you
> running on the Linux machine?
>
> Best,
>
> Jan-Mathijs
>
>
> On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote:
>
>> Hi Jan-Mathijs,
>> sorry it took me this long to answer. The variable format seems to
>> be empty....
>> Nuria
>> ________________________________________
>> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-
>> bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl
>> ]
>> Gesendet: Freitag, 13. Mai 2011 16:43
>> An: Email discussion list for the FieldTrip project
>> Betreff: Re: [FieldTrip] problem reading 4d header
>>
>> Hi Nuria,
>>
>> Could you type dbstop if error on the command line, and evaluate what
>> the variable 'format' is in your case?
>>
>> Thanks,
>>
>> Jan-Mathijs
>>
>> On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote:
>>
>>> Yes, it is exectly the same version. Better said, versions, because
>>> I tried both 20110413 and 20110512....
>>>
>>> ________________________________________
>>> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-
>>> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com
>>> ]
>>> Gesendet: Freitag, 13. Mai 2011 13:39
>>> An: Email discussion list for the FieldTrip project
>>> Betreff: Re: [FieldTrip] problem reading 4d header
>>>
>>> Dear Nuria
>>> Is it exactly the same fieldtrip version?
>>> I hope someone will solve this.
>>> as temporary work around you can read the header on windows and then
>>> move to linux
>>>
>>> yuval
>>>
>>> On 13 May 2011 11:42, Nuria Donamayor Alonso <nuria.donamayor at neuro.uni-luebeck.de
>>> <mailto:nuria.donamayor at neuro.uni-luebeck.de>> wrote:
>>> Dear fieltrip users,
>>> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine
>>> with a 64-bit Matlab version and I am getting an error I don't know
>>> how to solve:
>>>
>>> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']);
>>> ??? SWITCH expression must be a scalar or string constant.
>>>
>>> Error in ==> read_4d_hdr at 60
>>> switch format
>>>
>>> Error in ==> ft_read_header at 153
>>> orig            = read_4d_hdr(datafile);
>>>
>>> If I try to read the same data on my Windows PC with 32-bit Matlab I
>>> have no problem reading the header file (but I can't even finish the
>>> preprocessing before it runs out of memory, therefore the switch to
>>> the Linux machine), so I'm pretty clueless here... Can any of you
>>> help me?
>>> Thanks,
>>> Nuria
>>>
>>>
>>>
>>> Nuria Doñamayor Alonso, MSc
>>> Universitätsklinikum Schleswig-Holstein
>>> Campus Lübeck
>>> Klinik für Neurologie
>>> Ratzeburger Allee 160
>>> 23538 Lübeck
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>>
>>> --
>>> Y.Harpaz
>>>
>>> a link to the BIU MEG lab:
>>> http://faculty.biu.ac.il/~goldsa/index.html<http://faculty.biu.ac.il/%7Egoldsa/index.html
>>>>
>>>
>>> "Many were increasingly of the opinion that they'd all made a big
>>> mistake in coming down from the trees in the first place. And some
>>> said that even the trees had been a bad move, and that no one should
>>> ever have left the oceans". Douglas Adams
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> Dr. J.M. (Jan-Mathijs) Schoffelen
>> Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>> J.Schoffelen at donders.ru.nl
>> Telephone: 0031-24-3614793
>>
>>
>> _______________________________________________
>> 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
>
> Dr. J.M. (Jan-Mathijs) Schoffelen
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: 0031-24-3614793
>
>
> _______________________________________________
> 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

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793




From drivolta81 at gmail.com  Wed May 18 13:40:11 2011
From: drivolta81 at gmail.com (Davide Rivolta)
Date: Wed, 18 May 2011 13:40:11 +0200
Subject: [FieldTrip] Tutorial error
In-Reply-To: <746130EC-C81A-4276-8C83-ADB61811B2A3@donders.ru.nl>
References: <BANLkTikZVo3+Up=MgtjVD=5hLsWmrpKndA@mail.gmail.com>
	<746130EC-C81A-4276-8C83-ADB61811B2A3@donders.ru.nl>
Message-ID: <BANLkTimKZ=n0BXDkMStuDFgi6FJd1kuXyA@mail.gmail.com>

Dear Jan-Mathijs

This is the funny part. I run it (and worked) on the 201105053 version two
weeks ago. Yesterday it did not work on the same version. So, I have
downloaded the most recent version 20110516, but it is still not working.

I do not really know what to do with it.

Thanks for your kind help,

Davide



On Wed, May 18, 2011 at 11:02 AM, jan-mathijs schoffelen <
jan.schoffelen at donders.ru.nl> wrote:

> Dear Davide,
>
> I am not sure whether you are using the same fieldtrip version. There has
> been a glitch recently with the trialfun_general, but this should be fixed
> by now. Could you update to a superrecent version of fieldtrip and try
> again?
>
> Thanks,
>
> Jan-Mathijs
>
> PS: I cannot reproduce your error so I expect it to go away if you update.
>
>
> On May 18, 2011, at 10:51 AM, Davide Rivolta wrote:
>
>   Dear all,
>>
>> I am a very beginner with fieldtrip.
>>
>> I have tried to run the tutorial a couple of weeks ago, and it worked
>> smoothly.
>>
>> Yesterday I have tried again, but surprisngly I got anerror message, as
>> soon as I started the tutorial (the first step entitled: "reading and
>> processing the interesting trials"):
>>
>>
>> cfg                                = [];
>> cfg.dataset                    = 'Subject01.ds';
>> cfg.trialdef.eventtype      = 'backpanel trigger';
>> cfg.trialdef.eventvalue     = 3; % the value of the stimulus trigger for
>> fully incongruent (FIC).
>> cfg.trialdef.prestim         = 1; % in seconds
>> cfg.trialdef.poststim       = 2; % in seconds
>>
>> cfg = ft_definetrial(cfg);
>>
>>
>> ??? Attempt to reference field of non-structure array
>>
>> Error in ==> trialfun_general at 117
>> for i=find(strcmp(cfg.trialdef.eventtype, {event.type}))
>>
>>
>>
>>
>> This sounds really weird since it worked 2 weeks ago on the same machine
>> and with the same version of Fieldtrip.
>>
>> Any advice would be very appreciated.
>>
>> Best wishes,
>>
>> Davide
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
> Dr. J.M. (Jan-Mathijs) Schoffelen
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: 0031-24-3614793
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Davide Rivolta, PhD
-------------- next part --------------
An HTML attachment was scrubbed...
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From nuria.donamayor at neuro.uni-luebeck.de  Wed May 18 15:00:33 2011
From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso)
Date: Wed, 18 May 2011 15:00:33 +0200
Subject: [FieldTrip] problem reading 4d header
In-Reply-To: <0CBFB37A-FE20-436C-A5DA-FB7901EA2E80@donders.ru.nl>
References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>,
	<BANLkTikoifrBKypx74pbabzyiHWxfb33+w@mail.gmail.com>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>,
	<C99C901A-901E-452F-91A5-954E76E27E2A@donders.ru.nl>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>,
	<5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl>
	<810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de>,
	<0CBFB37A-FE20-436C-A5DA-FB7901EA2E80@donders.ru.nl>
Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F903D@solaris.neuro.uni-luebeck.de>

Hi Jan-Mathijs,
I get the same error message with all my datasets. Maybe it does have to do with my Linux machine... Any idea what I should look for to fix it?
Thanks,
Nuria


________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl]
Gesendet: Mittwoch, 18. Mai 2011 12:13
An: Email discussion list for the FieldTrip project
Betreff: Re: [FieldTrip] problem reading 4d header

Hi Nuria,

I cannot reproduce your problem on a linux machine we have here,
running matlab 2010b (64-bit).
Either there is something wrong with your dataset (does it happen as
well for another dataset?), or there is something different with
respect to the configuration of your Linux machine.

Best,

Jan-Mathijs

On May 17, 2011, at 4:49 PM, Nuria Donamayor Alonso wrote:

> Hi Jan-Mathijs,
> I'm using Matlab 7.11.0 (R2010b).
> Best,
> Nuria
>
>
> ________________________________________
> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-
> bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl
> ]
> Gesendet: Dienstag, 17. Mai 2011 16:24
> An: Email discussion list for the FieldTrip project
> Betreff: Re: [FieldTrip] problem reading 4d header
>
> Hi Nuria,
>
> Strange. Format should contain a number. What matlab version are you
> running on the Linux machine?
>
> Best,
>
> Jan-Mathijs
>
>
> On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote:
>
>> Hi Jan-Mathijs,
>> sorry it took me this long to answer. The variable format seems to
>> be empty....
>> Nuria
>> ________________________________________
>> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-
>> bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl
>> ]
>> Gesendet: Freitag, 13. Mai 2011 16:43
>> An: Email discussion list for the FieldTrip project
>> Betreff: Re: [FieldTrip] problem reading 4d header
>>
>> Hi Nuria,
>>
>> Could you type dbstop if error on the command line, and evaluate what
>> the variable 'format' is in your case?
>>
>> Thanks,
>>
>> Jan-Mathijs
>>
>> On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote:
>>
>>> Yes, it is exectly the same version. Better said, versions, because
>>> I tried both 20110413 and 20110512....
>>>
>>> ________________________________________
>>> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-
>>> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com
>>> ]
>>> Gesendet: Freitag, 13. Mai 2011 13:39
>>> An: Email discussion list for the FieldTrip project
>>> Betreff: Re: [FieldTrip] problem reading 4d header
>>>
>>> Dear Nuria
>>> Is it exactly the same fieldtrip version?
>>> I hope someone will solve this.
>>> as temporary work around you can read the header on windows and then
>>> move to linux
>>>
>>> yuval
>>>
>>> On 13 May 2011 11:42, Nuria Donamayor Alonso <nuria.donamayor at neuro.uni-luebeck.de
>>> <mailto:nuria.donamayor at neuro.uni-luebeck.de>> wrote:
>>> Dear fieltrip users,
>>> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine
>>> with a 64-bit Matlab version and I am getting an error I don't know
>>> how to solve:
>>>
>>> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']);
>>> ??? SWITCH expression must be a scalar or string constant.
>>>
>>> Error in ==> read_4d_hdr at 60
>>> switch format
>>>
>>> Error in ==> ft_read_header at 153
>>> orig            = read_4d_hdr(datafile);
>>>
>>> If I try to read the same data on my Windows PC with 32-bit Matlab I
>>> have no problem reading the header file (but I can't even finish the
>>> preprocessing before it runs out of memory, therefore the switch to
>>> the Linux machine), so I'm pretty clueless here... Can any of you
>>> help me?
>>> Thanks,
>>> Nuria
>>>
>>>
>>>
>>> Nuria Doñamayor Alonso, MSc
>>> Universitätsklinikum Schleswig-Holstein
>>> Campus Lübeck
>>> Klinik für Neurologie
>>> Ratzeburger Allee 160
>>> 23538 Lübeck
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>>
>>> --
>>> Y.Harpaz
>>>
>>> a link to the BIU MEG lab:
>>> http://faculty.biu.ac.il/~goldsa/index.html<http://faculty.biu.ac.il/%7Egoldsa/index.html
>>>>
>>>
>>> "Many were increasingly of the opinion that they'd all made a big
>>> mistake in coming down from the trees in the first place. And some
>>> said that even the trees had been a bad move, and that no one should
>>> ever have left the oceans". Douglas Adams
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> Dr. J.M. (Jan-Mathijs) Schoffelen
>> Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>> J.Schoffelen at donders.ru.nl
>> Telephone: 0031-24-3614793
>>
>>
>> _______________________________________________
>> 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
>
> Dr. J.M. (Jan-Mathijs) Schoffelen
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: 0031-24-3614793
>
>
> _______________________________________________
> 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

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From michael.hanke at gmail.com  Wed May 18 15:10:26 2011
From: michael.hanke at gmail.com (Michael Hanke)
Date: Wed, 18 May 2011 09:10:26 -0400
Subject: [FieldTrip] Neuroscience software survey: What is popular,
 what has problems? Immediate results
Message-ID: <20110518131026.GD19084@meiner>

[Apologies for cross-posting]

Dear neuroscience researchers and their IT staff

We invite you to participate in a survey on software usage and computing
environments in neuroscience research. It will take no more than five
minutes to fill it out. Immediately after sending your answers you will
get to see a summary of how other participants have responded before.
This data will eventually be made available to software vendors and
distributors to determine advantages and issue of popular computing
environments in neuroscience research.

Learn about what fellow neuroscientists are doing to address their computing
demands -- take the survey!

    http://goo.gl/euIMc

Thanks,
-- 
PyMVPA/NeuroDebian Team:   Yaroslav O. Halchenko   &    Michael Hanke
Postdoctoral Fellows,  Department of Psychological and Brain Sciences
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755


From jdien07 at mac.com  Fri May 20 04:30:59 2011
From: jdien07 at mac.com (Joseph Dien)
Date: Thu, 19 May 2011 22:30:59 -0400
Subject: [FieldTrip] problems using ft_freqanalysis
Message-ID: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>

Hi,
  I'm just starting to get up to speed on spectral analysis (I'm an ERPer).  
I'm using the following set-up:

I tried the following (for one second long trials with an Fs of 250Hz and interest in frequencies below 30Hz):

cfg.method='mtmwelch';
cfg.output='pow';
[freq] = ft_freqanalysis(cfg, data);

I got the error message:

-------------------------
the input is raw data with 128 channels and 160 trials
'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used
taking every sample as time of interest
the input is raw data with 128 channels and 160 trials
??? Error using ==> ft_freqanalysis at 216
you must specify a smoothing parameter with taper = dpss

Error in ==> ft_freqanalysis_mtmwelch at 107
freq = ft_freqanalysis(cfgconvol, data);

Error in ==> ft_freqanalysis at 271
[freq] =
feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg,
data);

-----------------------
Two things:

1) What would be an appropriate smoothing parameter?

2) Is this a bug?  It defaulted to dpss as specified by the documentation but it didn't provide a default smoothing parameter so the default still resulted in a crash.

Anyway, given the advice in the tutlrial to use a hanning window rather than a multi-taper like dpss for frequencies below 30, I tried the following:

cfg.foi=[1:1:30];
cfg.taper='hanning';

which resulted in:

--------------------------
>> [freq] = ft_freqanalysis(cfg, data);
the input is raw data with 128 channels and 160 trials
'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used
taking every sample as time of interest
the input is raw data with 128 channels and 160 trials
processing trials
??? Reference to non-existent field 't_ftimwin'.

Error in ==> ft_freqanalysis at 454
      [spectrum_mtmconvol,ntaper,foi,toi] =
      ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi,
      'timwin', cfg.t_ftimwin, 'taper', ...

Error in ==> ft_freqanalysis_mtmwelch at 107
freq = ft_freqanalysis(cfgconvol, data);

Error in ==> ft_freqanalysis at 271
[freq] =
feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg,
data);


--------------------
What am I doing wrong?  I looked through the code but couldn't figure out what the problem was.  I am very confused...

fieldtrip-20110519
MATLAB Version 7.11.0.584 (R2010b)
Operating System: Mac OS X  Version: 10.6.7 Build: 10J869 


>> cfg

cfg = 

    dataset: 'SLI_3011m_40m_POA.egis'
     method: 'mtmwelch'
     output: 'pow'
      taper: 'hanning'
  tapsmofrq: 4
        foi: [1x30 double]

>> data

data = 

         hdr: [1x1 struct]
       label: {128x1 cell}
        time: {1x160 cell}
       trial: {1x160 cell}
     fsample: 250
  sampleinfo: [160x2 double]
         cfg: [1x1 struct]


Thanks for any help you can give!

Joe


From jan.schoffelen at donders.ru.nl  Fri May 20 07:36:03 2011
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Fri, 20 May 2011 07:36:03 +0200
Subject: [FieldTrip] problems using ft_freqanalysis
In-Reply-To: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>
References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>
Message-ID: <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>

Dear Joe,

To begin with, since you are still 'tabula rasa' in the field of  
frequency analysis, I'd like you to forget about the 'mtmwelch'  
method ;o). I believe that at some point this method was implemented  
to 'just have it in the package'. As far as I am aware, it is hardly  
ever used and not actively maintained.
Essentially, Welch's method cuts the data into overlapping segments,  
computes a power spectrum, and averages across the segments again. The  
way it is implemented in Fieldtrip, is that one needs to specify the  
length of the timewindow in which to cut the data. This is the  
cfg.t_ftimwin. (as a side note: for the underlying computations  
fieldtrip relies on the method 'mtmconvol', which allows for a  
frequency specific segment length, which in this context does not  
really make sense, but is handy to emulate a wavelet analysis).
In your case however, I would advice to use cfg.method = 'mtmfft',  
because at this stage you are not interested in the temporal dimension  
of your spectrum. This method requires a slightly different cfg (in  
terms of fields and their content) with respect to mtmwelch/mtmconvol,  
but I hope that you can find your way around in the documentation to  
get it up and running. As to the 'tapsmofrq' in this case, if you have  
sufficiently long trials, you can still use some smoothing for the  
estimation of the low frequencies. The advice to use hanning for the  
lower frequencies specifically pertains to time-frequency estimation.

Cheers,

Jan-Mathijs



On May 20, 2011, at 4:30 AM, Joseph Dien wrote:

> Hi,
>  I'm just starting to get up to speed on spectral analysis (I'm an  
> ERPer).
> I'm using the following set-up:
>
> I tried the following (for one second long trials with an Fs of  
> 250Hz and interest in frequencies below 30Hz):
>
> cfg.method='mtmwelch';
> cfg.output='pow';
> [freq] = ft_freqanalysis(cfg, data);
>
> I got the error message:
>
> -------------------------
> the input is raw data with 128 channels and 160 trials
> 'mtmwelch' has not been implemented yet in the specest toolbox, the  
> old implementation is being used
> taking every sample as time of interest
> the input is raw data with 128 channels and 160 trials
> ??? Error using ==> ft_freqanalysis at 216
> you must specify a smoothing parameter with taper = dpss
>
> Error in ==> ft_freqanalysis_mtmwelch at 107
> freq = ft_freqanalysis(cfgconvol, data);
>
> Error in ==> ft_freqanalysis at 271
> [freq] =
> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg,
> data);
>
> -----------------------
> Two things:
>
> 1) What would be an appropriate smoothing parameter?
>
> 2) Is this a bug?  It defaulted to dpss as specified by the  
> documentation but it didn't provide a default smoothing parameter so  
> the default still resulted in a crash.
>
> Anyway, given the advice in the tutlrial to use a hanning window  
> rather than a multi-taper like dpss for frequencies below 30, I  
> tried the following:
>
> cfg.foi=[1:1:30];
> cfg.taper='hanning';
>
> which resulted in:
>
> --------------------------
>>> [freq] = ft_freqanalysis(cfg, data);
> the input is raw data with 128 channels and 160 trials
> 'mtmwelch' has not been implemented yet in the specest toolbox, the  
> old implementation is being used
> taking every sample as time of interest
> the input is raw data with 128 channels and 160 trials
> processing trials
> ??? Reference to non-existent field 't_ftimwin'.
>
> Error in ==> ft_freqanalysis at 454
>      [spectrum_mtmconvol,ntaper,foi,toi] =
>      ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi,
>      'timwin', cfg.t_ftimwin, 'taper', ...
>
> Error in ==> ft_freqanalysis_mtmwelch at 107
> freq = ft_freqanalysis(cfgconvol, data);
>
> Error in ==> ft_freqanalysis at 271
> [freq] =
> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg,
> data);
>
>
> --------------------
> What am I doing wrong?  I looked through the code but couldn't  
> figure out what the problem was.  I am very confused...
>
> fieldtrip-20110519
> MATLAB Version 7.11.0.584 (R2010b)
> Operating System: Mac OS X  Version: 10.6.7 Build: 10J869
>
>
>>> cfg
>
> cfg =
>
>    dataset: 'SLI_3011m_40m_POA.egis'
>     method: 'mtmwelch'
>     output: 'pow'
>      taper: 'hanning'
>  tapsmofrq: 4
>        foi: [1x30 double]
>
>>> data
>
> data =
>
>         hdr: [1x1 struct]
>       label: {128x1 cell}
>        time: {1x160 cell}
>       trial: {1x160 cell}
>     fsample: 250
>  sampleinfo: [160x2 double]
>         cfg: [1x1 struct]
>
>
> Thanks for any help you can give!
>
> Joe
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793



From Elena.Orekhova at neuro.gu.se  Fri May 20 14:00:40 2011
From: Elena.Orekhova at neuro.gu.se (Elena Orekhova)
Date: Fri, 20 May 2011 12:00:40 +0000
Subject: [FieldTrip] ft_read_vol with Neuromag
Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EBDF0C@exchccr1.neuro.gu.se>

Hi,
I try to read volume from the Neuromag .fif file using

vol = ft_read_vol(NEUROMAG_FIF_FILE_NAME, 'fileformat', 'neuromag_fif')

I get the error:
***********************
??? Undefined variable "cfg" or class "cfg.gradfile".

Error in ==> ft_read_vol at 77
    fprintf('using Neuromag gradiometer definition from %s\n', cfg.gradfile);

Any advice?

Elena

________________________________
Elena V Orekhova, Ph.D.
Inst. Neuroscience and Physiology
University of Gothenburg
S-413 45 Gothenburg, Sweden
phone: +46 31 342 48 02
elena at neuro.gu.se
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From jdien07 at mac.com  Fri May 20 16:54:16 2011
From: jdien07 at mac.com (Joseph Dien)
Date: Fri, 20 May 2011 10:54:16 -0400
Subject: [FieldTrip] problems using ft_freqanalysis
In-Reply-To: <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>
References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>
	<543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>
Message-ID: <08A9B8BE-658D-4503-94D3-74D2CB0692DF@mac.com>

Thanks for this helpful explanation!  Can you provide me with guidance on what is involved in deciding the setting for the spectral smoothing parameter 'tapsmofrq' for dpss?  Or where to look for information on this issue?

Thanks again!

Joe


On May 20, 2011, at 1:36 AM, jan-mathijs schoffelen wrote:

> Dear Joe,
> 
> To begin with, since you are still 'tabula rasa' in the field of frequency analysis, I'd like you to forget about the 'mtmwelch' method ;o). I believe that at some point this method was implemented to 'just have it in the package'. As far as I am aware, it is hardly ever used and not actively maintained.
> Essentially, Welch's method cuts the data into overlapping segments, computes a power spectrum, and averages across the segments again. The way it is implemented in Fieldtrip, is that one needs to specify the length of the timewindow in which to cut the data. This is the cfg.t_ftimwin. (as a side note: for the underlying computations fieldtrip relies on the method 'mtmconvol', which allows for a frequency specific segment length, which in this context does not really make sense, but is handy to emulate a wavelet analysis).
> In your case however, I would advice to use cfg.method = 'mtmfft', because at this stage you are not interested in the temporal dimension of your spectrum. This method requires a slightly different cfg (in terms of fields and their content) with respect to mtmwelch/mtmconvol, but I hope that you can find your way around in the documentation to get it up and running. As to the 'tapsmofrq' in this case, if you have sufficiently long trials, you can still use some smoothing for the estimation of the low frequencies. The advice to use hanning for the lower frequencies specifically pertains to time-frequency estimation.
> 
> Cheers,
> 
> Jan-Mathijs
> 
> 
> 
> On May 20, 2011, at 4:30 AM, Joseph Dien wrote:
> 
>> Hi,
>> I'm just starting to get up to speed on spectral analysis (I'm an ERPer).
>> I'm using the following set-up:
>> 
>> I tried the following (for one second long trials with an Fs of 250Hz and interest in frequencies below 30Hz):
>> 
>> cfg.method='mtmwelch';
>> cfg.output='pow';
>> [freq] = ft_freqanalysis(cfg, data);
>> 
>> I got the error message:
>> 
>> -------------------------
>> the input is raw data with 128 channels and 160 trials
>> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used
>> taking every sample as time of interest
>> the input is raw data with 128 channels and 160 trials
>> ??? Error using ==> ft_freqanalysis at 216
>> you must specify a smoothing parameter with taper = dpss
>> 
>> Error in ==> ft_freqanalysis_mtmwelch at 107
>> freq = ft_freqanalysis(cfgconvol, data);
>> 
>> Error in ==> ft_freqanalysis at 271
>> [freq] =
>> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg,
>> data);
>> 
>> -----------------------
>> Two things:
>> 
>> 1) What would be an appropriate smoothing parameter?
>> 
>> 2) Is this a bug?  It defaulted to dpss as specified by the documentation but it didn't provide a default smoothing parameter so the default still resulted in a crash.
>> 
>> Anyway, given the advice in the tutlrial to use a hanning window rather than a multi-taper like dpss for frequencies below 30, I tried the following:
>> 
>> cfg.foi=[1:1:30];
>> cfg.taper='hanning';
>> 
>> which resulted in:
>> 
>> --------------------------
>>>> [freq] = ft_freqanalysis(cfg, data);
>> the input is raw data with 128 channels and 160 trials
>> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used
>> taking every sample as time of interest
>> the input is raw data with 128 channels and 160 trials
>> processing trials
>> ??? Reference to non-existent field 't_ftimwin'.
>> 
>> Error in ==> ft_freqanalysis at 454
>>     [spectrum_mtmconvol,ntaper,foi,toi] =
>>     ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi,
>>     'timwin', cfg.t_ftimwin, 'taper', ...
>> 
>> Error in ==> ft_freqanalysis_mtmwelch at 107
>> freq = ft_freqanalysis(cfgconvol, data);
>> 
>> Error in ==> ft_freqanalysis at 271
>> [freq] =
>> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg,
>> data);
>> 
>> 
>> --------------------
>> What am I doing wrong?  I looked through the code but couldn't figure out what the problem was.  I am very confused...
>> 
>> fieldtrip-20110519
>> MATLAB Version 7.11.0.584 (R2010b)
>> Operating System: Mac OS X  Version: 10.6.7 Build: 10J869
>> 
>> 
>>>> cfg
>> 
>> cfg =
>> 
>>   dataset: 'SLI_3011m_40m_POA.egis'
>>    method: 'mtmwelch'
>>    output: 'pow'
>>     taper: 'hanning'
>> tapsmofrq: 4
>>       foi: [1x30 double]
>> 
>>>> data
>> 
>> data =
>> 
>>        hdr: [1x1 struct]
>>      label: {128x1 cell}
>>       time: {1x160 cell}
>>      trial: {1x160 cell}
>>    fsample: 250
>> sampleinfo: [160x2 double]
>>        cfg: [1x1 struct]
>> 
>> 
>> Thanks for any help you can give!
>> 
>> Joe
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> Dr. J.M. (Jan-Mathijs) Schoffelen
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: 0031-24-3614793
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip













From dgroppe at cogsci.ucsd.edu  Fri May 20 17:38:50 2011
From: dgroppe at cogsci.ucsd.edu (David Groppe)
Date: Fri, 20 May 2011 08:38:50 -0700
Subject: [FieldTrip] problems using ft_freqanalysis
In-Reply-To: <08A9B8BE-658D-4503-94D3-74D2CB0692DF@mac.com>
References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>
	<543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>
	<08A9B8BE-658D-4503-94D3-74D2CB0692DF@mac.com>
Message-ID: <BANLkTin=ay4JG6NRSy7e4TdhaV2EM7vRgQ@mail.gmail.com>

Hi Joe,
   David Kleinfeld and Partha Mitra have an excellent tutorial on
multitaper spectral analysis that should help:
http://www-physics.ucsd.edu/neurophysics/publications/CSHL_2009_SPECTRA_4.pdf

 -D


On Fri, May 20, 2011 at 7:54 AM, Joseph Dien <jdien07 at mac.com> wrote:
> Thanks for this helpful explanation!  Can you provide me with guidance on what is involved in deciding the setting for the spectral smoothing parameter 'tapsmofrq' for dpss?  Or where to look for information on this issue?
>
> Thanks again!
>
> Joe
>
>
> On May 20, 2011, at 1:36 AM, jan-mathijs schoffelen wrote:
>
>> Dear Joe,
>>
>> To begin with, since you are still 'tabula rasa' in the field of frequency analysis, I'd like you to forget about the 'mtmwelch' method ;o). I believe that at some point this method was implemented to 'just have it in the package'. As far as I am aware, it is hardly ever used and not actively maintained.
>> Essentially, Welch's method cuts the data into overlapping segments, computes a power spectrum, and averages across the segments again. The way it is implemented in Fieldtrip, is that one needs to specify the length of the timewindow in which to cut the data. This is the cfg.t_ftimwin. (as a side note: for the underlying computations fieldtrip relies on the method 'mtmconvol', which allows for a frequency specific segment length, which in this context does not really make sense, but is handy to emulate a wavelet analysis).
>> In your case however, I would advice to use cfg.method = 'mtmfft', because at this stage you are not interested in the temporal dimension of your spectrum. This method requires a slightly different cfg (in terms of fields and their content) with respect to mtmwelch/mtmconvol, but I hope that you can find your way around in the documentation to get it up and running. As to the 'tapsmofrq' in this case, if you have sufficiently long trials, you can still use some smoothing for the estimation of the low frequencies. The advice to use hanning for the lower frequencies specifically pertains to time-frequency estimation.
>>
>> Cheers,
>>
>> Jan-Mathijs
>>
>>
>>
>> On May 20, 2011, at 4:30 AM, Joseph Dien wrote:
>>
>>> Hi,
>>> I'm just starting to get up to speed on spectral analysis (I'm an ERPer).
>>> I'm using the following set-up:
>>>
>>> I tried the following (for one second long trials with an Fs of 250Hz and interest in frequencies below 30Hz):
>>>
>>> cfg.method='mtmwelch';
>>> cfg.output='pow';
>>> [freq] = ft_freqanalysis(cfg, data);
>>>
>>> I got the error message:
>>>
>>> -------------------------
>>> the input is raw data with 128 channels and 160 trials
>>> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used
>>> taking every sample as time of interest
>>> the input is raw data with 128 channels and 160 trials
>>> ??? Error using ==> ft_freqanalysis at 216
>>> you must specify a smoothing parameter with taper = dpss
>>>
>>> Error in ==> ft_freqanalysis_mtmwelch at 107
>>> freq = ft_freqanalysis(cfgconvol, data);
>>>
>>> Error in ==> ft_freqanalysis at 271
>>> [freq] =
>>> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg,
>>> data);
>>>
>>> -----------------------
>>> Two things:
>>>
>>> 1) What would be an appropriate smoothing parameter?
>>>
>>> 2) Is this a bug?  It defaulted to dpss as specified by the documentation but it didn't provide a default smoothing parameter so the default still resulted in a crash.
>>>
>>> Anyway, given the advice in the tutlrial to use a hanning window rather than a multi-taper like dpss for frequencies below 30, I tried the following:
>>>
>>> cfg.foi=[1:1:30];
>>> cfg.taper='hanning';
>>>
>>> which resulted in:
>>>
>>> --------------------------
>>>>> [freq] = ft_freqanalysis(cfg, data);
>>> the input is raw data with 128 channels and 160 trials
>>> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used
>>> taking every sample as time of interest
>>> the input is raw data with 128 channels and 160 trials
>>> processing trials
>>> ??? Reference to non-existent field 't_ftimwin'.
>>>
>>> Error in ==> ft_freqanalysis at 454
>>>     [spectrum_mtmconvol,ntaper,foi,toi] =
>>>     ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi,
>>>     'timwin', cfg.t_ftimwin, 'taper', ...
>>>
>>> Error in ==> ft_freqanalysis_mtmwelch at 107
>>> freq = ft_freqanalysis(cfgconvol, data);
>>>
>>> Error in ==> ft_freqanalysis at 271
>>> [freq] =
>>> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg,
>>> data);
>>>
>>>
>>> --------------------
>>> What am I doing wrong?  I looked through the code but couldn't figure out what the problem was.  I am very confused...
>>>
>>> fieldtrip-20110519
>>> MATLAB Version 7.11.0.584 (R2010b)
>>> Operating System: Mac OS X  Version: 10.6.7 Build: 10J869
>>>
>>>
>>>>> cfg
>>>
>>> cfg =
>>>
>>>   dataset: 'SLI_3011m_40m_POA.egis'
>>>    method: 'mtmwelch'
>>>    output: 'pow'
>>>     taper: 'hanning'
>>> tapsmofrq: 4
>>>       foi: [1x30 double]
>>>
>>>>> data
>>>
>>> data =
>>>
>>>        hdr: [1x1 struct]
>>>      label: {128x1 cell}
>>>       time: {1x160 cell}
>>>      trial: {1x160 cell}
>>>    fsample: 250
>>> sampleinfo: [160x2 double]
>>>        cfg: [1x1 struct]
>>>
>>>
>>> Thanks for any help you can give!
>>>
>>> Joe
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> Dr. J.M. (Jan-Mathijs) Schoffelen
>> Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>> J.Schoffelen at donders.ru.nl
>> Telephone: 0031-24-3614793
>>
>> _______________________________________________
>> 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
>



-- 
David Groppe, Ph.D.
Postdoctoral Researcher
Kutaslab
Dept. of Cognitive Science
University of California, San Diego
http://www.cogsci.ucsd.edu/~dgroppe/



From Elena.Orekhova at neuro.gu.se  Sat May 21 14:11:41 2011
From: Elena.Orekhova at neuro.gu.se (Elena Orekhova)
Date: Sat, 21 May 2011 12:11:41 +0000
Subject: [FieldTrip] rpa/nas/lpa coordinates
Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se>

Hi
I Just started to use Fieldtrip with my Neuromag MEG data and try to follow  the example script
‘read_neuromag_mri_and_create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space’


The instruction suggests to take voxel coordinates of fiduscials from the Neuromag
GUI for MRI-MEG Integration. I have already performed this step and saved the
transformed mri in the /sets/XXX.fif file.

Should I write any  rpa/nas/lpa coordinates in this case?

cfg.fiducial.rpa  = [y x z];

cfg.fiducial.nas  = [y x z];

cfg.fiducial.lpa  = [y x z];

I have 2 4X4 transformations in the .fif file, not sure what they mean.

mri.hdr.trans.trans

0.9913    0.1210    0.0518   -0.0032
   -0.0948    0.9291   -0.3574    0.0254
   -0.0914    0.3494    0.9325   -0.0519
         0         0         0    1.0000
mri.hdr.voxel_trans.trans

   -0.0000   -0.0000   -0.0010    0.1058
   -0.0005    0.0000    0.0000    0.1597
         0   -0.0005    0.0001    0.1058
         0         0         0    1.0000

I'll be most grateful for the help!
Regards,
Elena






________________________________
Elena V Orekhova, Ph.D.
Inst. Neuroscience and Physiology
University of Gothenburg
S-413 45 Gothenburg, Sweden
phone: +46 31 342 48 02
elena at neuro.gu.se
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From r.oostenveld at donders.ru.nl  Mon May 23 09:33:34 2011
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Mon, 23 May 2011 09:33:34 +0200
Subject: [FieldTrip] rpa/nas/lpa coordinates
In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se>
References: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se>
Message-ID: <D38FF82C-3B03-4305-9692-2ECB0B0ECDAF@donders.ru.nl>

Dear Elena

> On 21 May 2011, at 14:11, Elena Orekhova wrote:
>
>> Hi
>> I Just started to use Fieldtrip with my Neuromag MEG data and try  
>> to follow  the example script
>> ‘read_neuromag_mri_and_create_single- 
>> subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space 
>> ’

I don't know all details of the Neuromag system, but recently we did  
add the http://fieldtrip.fcdonders.nl/getting_started/yokogawa  
documentation that explains reasonably general how coordinate system  
coregistration works. We also added a new function (FT_SENSORREALIGN)  
to ease the coregistration and we are working towards a more  
consistent representation of the corodinate systems in the relevant  
fieldtrip data structures.

Although the details for your system are different (see http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined) 
, you might get a better overview of the steps that are involved by  
reading the yokogawa getting started.

> The instruction suggests to take voxel coordinates of fiduscials  
> from the Neuromag
> GUI for MRI-MEG Integration. I have already performed this step and  
> saved the
> transformed mri in the /sets/XXX.fif file.

I suggest you use the FT_DETERMINE_COORDSYS to perform a visual  
inspection of the coordinate systems of your anatomical MRI and of  
your sensor positions (data.grad, or you can use FT_READ_SENS to read  
them directly from the MEG fif file). Note that you have to use the  
function twice (on the mri and on the grad) and compare the figures  
yourself.


>  Should I write any  rpa/nas/lpa coordinates in this case?
> cfg.fiducial.rpa  = [y x z];
> cfg.fiducial.nas  = [y x z];
> cfg.fiducial.lpa  = [y x z];

if you need them (see above), then these should be [x y z] and not [y  
x z].

>
> I have 2 4X4 transformations in the .fif file, not sure what they  
> mean.

Please read this page, which is a general introduction.

>
> mri.hdr.trans.trans
>
> 0.9913    0.1210    0.0518   -0.0032
>    -0.0948    0.9291   -0.3574    0.0254
>    -0.0914    0.3494    0.9325   -0.0519
>          0         0         0    1.0000
> mri.hdr.voxel_trans.trans
>
>    -0.0000   -0.0000   -0.0010    0.1058
>    -0.0005    0.0000    0.0000    0.1597
>          0   -0.0005    0.0001    0.1058
>          0         0         0    1.0000

the mri header is system specific, so I am not sure. But I guess that  
the first is the homogenous transformation matrix in head coordinates  
(linked to the fiducials) and the second is the homogenous  
transformation matrix in MRI coordinates. The first one appears to be  
in mm, the second one in meter.

Please try

mri.transform = mri.hdr.voxel_trans.trans;
figure
ft_determine_coordsys(mri)  % press ctrl-c

mri.transform = mri.hdr.trans.trans;
figure
ft_determine_coordsys(mri)  % press ctrl-c

The two figures will show you the origin, the direction of axes of the  
coordinate system and the scale.

best regards,
Robert







From r.oostenveld at donders.ru.nl  Mon May 23 09:41:17 2011
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Mon, 23 May 2011 09:41:17 +0200
Subject: [FieldTrip] ft_read_vol with Neuromag
In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03EBDF0C@exchccr1.neuro.gu.se>
References: <32CC77C0C8A7AD4B9410934642608E1F03EBDF0C@exchccr1.neuro.gu.se>
Message-ID: <4BFE3CE0-268F-4ACC-8863-5017DC5957AF@donders.ru.nl>

Hi Elena

Although some years ago FieldTrip was supporting volume conduction  
models from Neuromag using the meg-pd and the (closed source) meg-calc  
toolboxes from the company itself, I suspect that nobody has been  
using them the last few years. The mex files in meg-pd and meg-calc  
were often problematic to work with due to platform and library  
issues. The single-shell volume conduction model that is avaialble in  
Fieldtrip is currently the preferred volume model.

Looking at the code, there is indeed a bug since cfg.gradfile is not  
defined. If you want to continue along the path of meg-pd and meg- 
calc, you could hardcode the filename and see how far you get. But I'd  
suspect that you don't have the required (commercial) mex files from  
meg-calc anyway.

best regards
Robert




On 20 May 2011, at 14:00, Elena Orekhova wrote:

> Hi,
> I try to read volume from the Neuromag .fif file using
>
> vol = ft_read_vol(NEUROMAG_FIF_FILE_NAME, 'fileformat',  
> 'neuromag_fif')
>
> I get the error:
> ***********************
> ??? Undefined variable "cfg" or class "cfg.gradfile".
>
> Error in ==> ft_read_vol at 77
>     fprintf('using Neuromag gradiometer definition from %s\n',  
> cfg.gradfile);
>
> Any advice?
>
> Elena
>
> Elena V Orekhova, Ph.D.
> Inst. Neuroscience and Physiology
> University of Gothenburg
> S-413 45 Gothenburg, Sweden
> phone: +46 31 342 48 02
> elena at neuro.gu.se
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From Elena.Orekhova at neuro.gu.se  Mon May 23 10:00:15 2011
From: Elena.Orekhova at neuro.gu.se (Elena Orekhova)
Date: Mon, 23 May 2011 08:00:15 +0000
Subject: [FieldTrip] segmentation problem with Neuromag
Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EC7CC3@exchccr1.neuro.gu.se>

Dear Fieldtrip users and developers,

I would like to start using Fieldtrip for the source analysis of the MEG data, but
I  have some problem with mri segmentation using  Neuromag-306 .fif MRI file.

I do:
1) import .fif, (Coordinate alignment was already done in Neuromag).
mriname = 'NEUROMAGxxx.fif'
[mri] = ft_read_mri(mriname)
cfg  = [];
ft_sourceplot(cfg,mri);

***** attachment: mri.jpg ******

2) do segmentation
cfg                = [];
cfg.template       = 'T1.nii'; %spm8
cfg.coordsys       = 'neuromag';
cfg.write          = 'no';
cfg.name           = 'temp';
cfg.interactive    = 'yes';
[segmentedmri]     = ft_volumesegment(cfg, mri)

3) plot the original and segmented mri
cfg                = [];
test.dim = [512  512 180];
test               = segmentedmri;
test.avg.pow       = test.gray+test.white;
test.anatomy       = mri.anatomy;
cfg.funparameter   = 'avg.pow';
cfg.interactive    = 'yes';
ft_sourceplot(cfg,test);

***** attachment : mri_segmented.jpg ******


Apparently, there is a displacement of the segmented mri image. It seems also that the  segmented mri  is bigger then the original mri.
The similar (although not the same) picture is observed when I do coordinate alignment in the MNE and use the /sets/CORxxx.fif saved from the MNE sohtware.
I have seen some discussions on this topic, but I have not found the solution.

Should I   swap x and y coordinates? How can I do it?

I would be most grateful for help!

Elena

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From odidodi at hotmail.com  Mon May 23 10:44:31 2011
From: odidodi at hotmail.com (odelia nakar)
Date: Mon, 23 May 2011 08:44:31 +0000
Subject: [FieldTrip] ICA+frqanalysis questions
In-Reply-To: <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>
References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>,
	<543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>
Message-ID: <BAY162-w15103E26B01D0271AD3F6EAB720@phx.gbl>


Hi all,

I'm troubled by the fact that when I use ICA for 
blinks\eyes movements removal, I remove the relevant components also 
from trials that do not contain blinks\eyes movements. In order to avoid
 this bias we thought to combine the data before ICA ("data" structure) 
with the data after ICA ("dataica" structure), only in specific trials, 
as follows:

datall=dataica;
datall.trial=data.trial;
datall.time=data.time;
blinks=[2 4 5 8 bla bla 156];
for ind=1:length(blinks)
     datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)};
end

To my first question: I just wanted to check that there is no problem with that, or any reason not to use it.

Another
 issue- I use motor learning task, and I'm trying to understand what 
happens through the process, in terms of power-frequency changes through
 the process. How would you recommend that I'd use the ft_freqanalysis 
function? What method to use (or what do I need to consider when 
choosing the method field)? 


Thanks a lot,
Odelia.
 		 	   		  
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From Elena.Orekhova at neuro.gu.se  Mon May 23 12:03:11 2011
From: Elena.Orekhova at neuro.gu.se (Elena Orekhova)
Date: Mon, 23 May 2011 10:03:11 +0000
Subject: [FieldTrip] rpa/nas/lpa coordinates
In-Reply-To: <D38FF82C-3B03-4305-9692-2ECB0B0ECDAF@donders.ru.nl>
References: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se>,
	<D38FF82C-3B03-4305-9692-2ECB0B0ECDAF@donders.ru.nl>
Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EC8D07@exchccr1.neuro.gu.se>

Dear Robert, 
As you advised, I tried to use 'ft_determine_coordsys' to look at my non-segmented MRI, but got the error (see below).
What can be the reason?

/Elena


>> 
>> mri

mri = 

          dim: [512 512 180]
      anatomy: [512x512x180 int16]
          hdr: [1x1 struct]
    transform: [4x4 double]
         unit: 'm'

>> [dataout] = ft_determine_coordsys(mri)
??? Error using ==> surface
Z must be a matrix, not a scalar or vector

Error in ==> ft_plot_slice at 184
h      = surface(Xh, Yh, Zh, V);

Error in ==> ft_plot_ortho at 94
  hx = ft_plot_slice(dat, varargin{:});

Error in ==> ft_determine_coordsys at 192
  ft_plot_ortho(data.(funparam), 'transform', data.transform, 'resolution', 1,
  'style', 'intersect');
 
>> 

________________________________________
From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Robert Oostenveld [r.oostenveld at donders.ru.nl]
Sent: Monday, May 23, 2011 9:33 AM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] rpa/nas/lpa coordinates

Dear Elena

> On 21 May 2011, at 14:11, Elena Orekhova wrote:
>
>> Hi
>> I Just started to use Fieldtrip with my Neuromag MEG data and try
>> to follow  the example script
>> ‘read_neuromag_mri_and_create_single-
>> subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space
>> ’

I don't know all details of the Neuromag system, but recently we did
add the http://fieldtrip.fcdonders.nl/getting_started/yokogawa
documentation that explains reasonably general how coordinate system
coregistration works. We also added a new function (FT_SENSORREALIGN)
to ease the coregistration and we are working towards a more
consistent representation of the corodinate systems in the relevant
fieldtrip data structures.

Although the details for your system are different (see http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined)
, you might get a better overview of the steps that are involved by
reading the yokogawa getting started.

> The instruction suggests to take voxel coordinates of fiduscials
> from the Neuromag
> GUI for MRI-MEG Integration. I have already performed this step and
> saved the
> transformed mri in the /sets/XXX.fif file.

I suggest you use the FT_DETERMINE_COORDSYS to perform a visual
inspection of the coordinate systems of your anatomical MRI and of
your sensor positions (data.grad, or you can use FT_READ_SENS to read
them directly from the MEG fif file). Note that you have to use the
function twice (on the mri and on the grad) and compare the figures
yourself.


>  Should I write any  rpa/nas/lpa coordinates in this case?
> cfg.fiducial.rpa  = [y x z];
> cfg.fiducial.nas  = [y x z];
> cfg.fiducial.lpa  = [y x z];

if you need them (see above), then these should be [x y z] and not [y
x z].

>
> I have 2 4X4 transformations in the .fif file, not sure what they
> mean.

Please read this page, which is a general introduction.

>
> mri.hdr.trans.trans
>
> 0.9913    0.1210    0.0518   -0.0032
>    -0.0948    0.9291   -0.3574    0.0254
>    -0.0914    0.3494    0.9325   -0.0519
>          0         0         0    1.0000
> mri.hdr.voxel_trans.trans
>
>    -0.0000   -0.0000   -0.0010    0.1058
>    -0.0005    0.0000    0.0000    0.1597
>          0   -0.0005    0.0001    0.1058
>          0         0         0    1.0000

the mri header is system specific, so I am not sure. But I guess that
the first is the homogenous transformation matrix in head coordinates
(linked to the fiducials) and the second is the homogenous
transformation matrix in MRI coordinates. The first one appears to be
in mm, the second one in meter.

Please try

mri.transform = mri.hdr.voxel_trans.trans;
figure
ft_determine_coordsys(mri)  % press ctrl-c

mri.transform = mri.hdr.trans.trans;
figure
ft_determine_coordsys(mri)  % press ctrl-c

The two figures will show you the origin, the direction of axes of the
coordinate system and the scale.

best regards,
Robert





_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From jinyinz at ece.cmu.edu  Mon May 23 15:46:20 2011
From: jinyinz at ece.cmu.edu (jinyinz at ece.cmu.edu)
Date: Mon, 23 May 2011 09:46:20 -0400 (EDT)
Subject: [FieldTrip] the source space for MEG/EEG source localization
Message-ID: <4412.128.2.133.95.1306158380.squirrel@webmail.ece.cmu.edu>

Dear Fieldtrippers,

I have a question about the source space selection for MEG/EEG source
localization.

Some source localization algorithms restrict the reconstruction to sources
located on cortical surface. To implement such kind of algorithm, I used
mne_setup_source_space to create a source space on cortical surface. By
default mne_setup_source_space creates a decimated dipole grid on the
white matter surface. Although this setting is widely used, some papers
create a source space on the gray matter surface instead. Are there any
specific reasons for selecting any of the two options?

Thanks,
Jinyin



From dgroppe at cogsci.ucsd.edu  Mon May 23 17:57:25 2011
From: dgroppe at cogsci.ucsd.edu (David Groppe)
Date: Mon, 23 May 2011 08:57:25 -0700
Subject: [FieldTrip] ICA+frqanalysis questions
In-Reply-To: <BAY162-w15103E26B01D0271AD3F6EAB720@phx.gbl>
References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>
	<543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>
	<BAY162-w15103E26B01D0271AD3F6EAB720@phx.gbl>
Message-ID: <BANLkTi=YxtpPqFfvORYKmO-23o8zp-Tc3w@mail.gmail.com>

Hi Odelia,
   When you use ICA (or any other spatial filter) to correct for EEG
artifacts, you're going to distort your data some by removing true EEG
activity in addition to the artifact (for an explanation, see:
http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf).
 So to minimize distortion, it would be better not to apply ICA
artifact correction to artifact-free data.  However, if the frequency
of the artifact differs across experimental conditions, it could
confound your analysis.  For example, I suspect people blink more
often to targets in an oddball experiment than standards.  Thus if you
apply ICA only to blinky trials, you could find a difference between
the EEG response to standards and targets that simply reflects the
fact ICA removed more EEG activity in the target trials (i.e., it
wouldn't reflect a true difference in neural processing).
      hope this helps,
         -David

On Mon, May 23, 2011 at 1:44 AM, odelia nakar <odidodi at hotmail.com> wrote:
> Hi all,
>
> I'm troubled by the fact that when I use ICA for blinks\eyes movements
> removal, I remove the relevant components also from trials that do not
> contain blinks\eyes movements. In order to avoid this bias we thought to
> combine the data before ICA ("data" structure) with the data after ICA
> ("dataica" structure), only in specific trials, as follows:
>
> datall=dataica;
> datall.trial=data.trial;
> datall.time=data.time;
> blinks=[2 4 5 8 bla bla 156];
> for ind=1:length(blinks)
>      datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)};
> end
>
> To my first question: I just wanted to check that there is no problem with
> that, or any reason not to use it.
>
> Another issue- I use motor learning task, and I'm trying to understand what
> happens through the process, in terms of power-frequency changes through the
> process. How would you recommend that I'd use the ft_freqanalysis function?
> What method to use (or what do I need to consider when choosing the method
> field)?
>
>
> Thanks a lot,
> Odelia.
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
David Groppe, Ph.D.
Postdoctoral Researcher
Kutaslab
Dept. of Cognitive Science
University of California, San Diego
http://www.cogsci.ucsd.edu/~dgroppe/



From jdien07 at mac.com  Tue May 24 03:07:57 2011
From: jdien07 at mac.com (Joseph Dien)
Date: Mon, 23 May 2011 21:07:57 -0400
Subject: [FieldTrip] ICA+frqanalysis questions
In-Reply-To: <BANLkTi=YxtpPqFfvORYKmO-23o8zp-Tc3w@mail.gmail.com>
References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>
	<543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>
	<BAY162-w15103E26B01D0271AD3F6EAB720@phx.gbl>
	<BANLkTi=YxtpPqFfvORYKmO-23o8zp-Tc3w@mail.gmail.com>
Message-ID: <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com>

I agree with David's reasoning.  You may find the following article to be of help as well in understanding the issues involved:

Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763.

Cheers!

Joe

On May 23, 2011, at 11:57 AM, David Groppe wrote:

> Hi Odelia,
>   When you use ICA (or any other spatial filter) to correct for EEG
> artifacts, you're going to distort your data some by removing true EEG
> activity in addition to the artifact (for an explanation, see:
> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf).
> So to minimize distortion, it would be better not to apply ICA
> artifact correction to artifact-free data.  However, if the frequency
> of the artifact differs across experimental conditions, it could
> confound your analysis.  For example, I suspect people blink more
> often to targets in an oddball experiment than standards.  Thus if you
> apply ICA only to blinky trials, you could find a difference between
> the EEG response to standards and targets that simply reflects the
> fact ICA removed more EEG activity in the target trials (i.e., it
> wouldn't reflect a true difference in neural processing).
>      hope this helps,
>         -David
> 
> On Mon, May 23, 2011 at 1:44 AM, odelia nakar <odidodi at hotmail.com> wrote:
>> Hi all,
>> 
>> I'm troubled by the fact that when I use ICA for blinks\eyes movements
>> removal, I remove the relevant components also from trials that do not
>> contain blinks\eyes movements. In order to avoid this bias we thought to
>> combine the data before ICA ("data" structure) with the data after ICA
>> ("dataica" structure), only in specific trials, as follows:
>> 
>> datall=dataica;
>> datall.trial=data.trial;
>> datall.time=data.time;
>> blinks=[2 4 5 8 bla bla 156];
>> for ind=1:length(blinks)
>>      datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)};
>> end
>> 
>> To my first question: I just wanted to check that there is no problem with
>> that, or any reason not to use it.
>> 
>> Another issue- I use motor learning task, and I'm trying to understand what
>> happens through the process, in terms of power-frequency changes through the
>> process. How would you recommend that I'd use the ft_freqanalysis function?
>> What method to use (or what do I need to consider when choosing the method
>> field)?
>> 
>> 
>> Thanks a lot,
>> Odelia.
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> 
> 
> 
> 
> -- 
> David Groppe, Ph.D.
> Postdoctoral Researcher
> Kutaslab
> Dept. of Cognitive Science
> University of California, San Diego
> http://www.cogsci.ucsd.edu/~dgroppe/
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


--------------------------------------------------------------------------------

Joseph Dien
E-mail: jdien07 at mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://homepage.mac.com/jdien07/








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From shackman at wisc.edu  Tue May 24 04:00:34 2011
From: shackman at wisc.edu (Alexander J. Shackman)
Date: Mon, 23 May 2011 21:00:34 -0500
Subject: [FieldTrip] ICA+frqanalysis questions
In-Reply-To: <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com>
References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>
	<543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>
	<BAY162-w15103E26B01D0271AD3F6EAB720@phx.gbl>
	<BANLkTi=YxtpPqFfvORYKmO-23o8zp-Tc3w@mail.gmail.com>
	<09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com>
Message-ID: <BANLkTikHLHhjes_pF_5wdrF6QjNna3T_Mg@mail.gmail.com>

And for a related perspective, see

McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. J.
(2011). Electromyogenic artifacts and electroencephalographic inferences
revisited, *Neuroimage**, 54*, 4-9.

http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf


On Mon, May 23, 2011 at 8:07 PM, Joseph Dien <jdien07 at mac.com> wrote:

> I agree with David's reasoning.  You may find the following article to be
> of help as well in understanding the issues involved:
>
> Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of
> simulated ERPs: Promax versus Infomax rotations. *Human Brain Mapping*, 28
> (8), 742-763.
>
> Cheers!
>
> Joe
>
> On May 23, 2011, at 11:57 AM, David Groppe wrote:
>
> Hi Odelia,
>   When you use ICA (or any other spatial filter) to correct for EEG
> artifacts, you're going to distort your data some by removing true EEG
> activity in addition to the artifact (for an explanation, see:
> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf).
> So to minimize distortion, it would be better not to apply ICA
> artifact correction to artifact-free data.  However, if the frequency
> of the artifact differs across experimental conditions, it could
> confound your analysis.  For example, I suspect people blink more
> often to targets in an oddball experiment than standards.  Thus if you
> apply ICA only to blinky trials, you could find a difference between
> the EEG response to standards and targets that simply reflects the
> fact ICA removed more EEG activity in the target trials (i.e., it
> wouldn't reflect a true difference in neural processing).
>      hope this helps,
>         -David
>
> On Mon, May 23, 2011 at 1:44 AM, odelia nakar <odidodi at hotmail.com> wrote:
>
> Hi all,
>
>
> I'm troubled by the fact that when I use ICA for blinks\eyes movements
>
> removal, I remove the relevant components also from trials that do not
>
> contain blinks\eyes movements. In order to avoid this bias we thought to
>
> combine the data before ICA ("data" structure) with the data after ICA
>
> ("dataica" structure), only in specific trials, as follows:
>
>
> datall=dataica;
>
> datall.trial=data.trial;
>
> datall.time=data.time;
>
> blinks=[2 4 5 8 bla bla 156];
>
> for ind=1:length(blinks)
>
>      datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)};
>
> end
>
>
> To my first question: I just wanted to check that there is no problem with
>
> that, or any reason not to use it.
>
>
> Another issue- I use motor learning task, and I'm trying to understand what
>
> happens through the process, in terms of power-frequency changes through
> the
>
> process. How would you recommend that I'd use the ft_freqanalysis function?
>
> What method to use (or what do I need to consider when choosing the method
>
> field)?
>
>
>
> Thanks a lot,
>
> Odelia.
>
>
> _______________________________________________
>
> fieldtrip mailing list
>
> fieldtrip at donders.ru.nl
>
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
>
> --
> David Groppe, Ph.D.
> Postdoctoral Researcher
> Kutaslab
> Dept. of Cognitive Science
> University of California, San Diego
> http://www.cogsci.ucsd.edu/~dgroppe/
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> --------------------------------------------------------------------------------
>
> Joseph Dien
> E-mail: jdien07 at mac.com
> Phone: 301-226-8848
> Fax: 301-226-8811
> http://homepage.mac.com/jdien07/
>
>
>
>
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>


-- 
Alexander J. Shackman, Ph.D.
Wisconsin Psychiatric Institute & Clinics and
Department of Psychology
University of Wisconsin-Madison
1202 West Johnson Street
Madison, Wisconsin 53706

Telephone: +1 (608) 358-5025
Fax: +1 (608) 265-2875
Email: shackman at wisc.edu
http://psyphz.psych.wisc.edu/~shackman
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From odidodi at hotmail.com  Tue May 24 08:46:55 2011
From: odidodi at hotmail.com (odelia nakar)
Date: Tue, 24 May 2011 06:46:55 +0000
Subject: [FieldTrip] ICA+frqanalysis questions
In-Reply-To: <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com>
References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>,
	<543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>,
	<BAY162-w15103E26B01D0271AD3F6EAB720@phx.gbl>,
	<BANLkTi=YxtpPqFfvORYKmO-23o8zp-Tc3w@mail.gmail.com>,
	<09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com>
Message-ID: <BAY162-w18FC64413E752E490C316FAB750@phx.gbl>



Thank you all- Joe, Alexander and David, it is indeed very helpful and enlightening. 
I actually don't have any stimulus, but I wasn't aware of the hidden EMG. 
Have a good day (or night :))!
Odelia.
From: jdien07 at mac.com
Date: Mon, 23 May 2011 21:07:57 -0400
To: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] ICA+frqanalysis questions



I agree with David's reasoning.  You may find the following article to be of help as well in understanding the issues involved:
Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763.
Cheers!
Joe
On May 23, 2011, at 11:57 AM, David Groppe wrote:Hi Odelia,
   When you use ICA (or any other spatial filter) to correct for EEG
artifacts, you're going to distort your data some by removing true EEG
activity in addition to the artifact (for an explanation, see:
http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf).
 So to minimize distortion, it would be better not to apply ICA
artifact correction to artifact-free data.  However, if the frequency
of the artifact differs across experimental conditions, it could
confound your analysis.  For example, I suspect people blink more
often to targets in an oddball experiment than standards.  Thus if you
apply ICA only to blinky trials, you could find a difference between
the EEG response to standards and targets that simply reflects the
fact ICA removed more EEG activity in the target trials (i.e., it
wouldn't reflect a true difference in neural processing).
      hope this helps,
         -David

On Mon, May 23, 2011 at 1:44 AM, odelia nakar <odidodi at hotmail.com> wrote:
Hi all,

I'm troubled by the fact that when I use ICA for blinks\eyes movements
removal, I remove the relevant components also from trials that do not
contain blinks\eyes movements. In order to avoid this bias we thought to
combine the data before ICA ("data" structure) with the data after ICA
("dataica" structure), only in specific trials, as follows:

datall=dataica;
datall.trial=data.trial;
datall.time=data.time;
blinks=[2 4 5 8 bla bla 156];
for ind=1:length(blinks)
     datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)};
end

To my first question: I just wanted to check that there is no problem with
that, or any reason not to use it.

Another issue- I use motor learning task, and I'm trying to understand what
happens through the process, in terms of power-frequency changes through the
process. How would you recommend that I'd use the ft_freqanalysis function?
What method to use (or what do I need to consider when choosing the method
field)?


Thanks a lot,
Odelia.

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip




-- 
David Groppe, Ph.D.
Postdoctoral Researcher
Kutaslab
Dept. of Cognitive Science
University of California, San Diego
http://www.cogsci.ucsd.edu/~dgroppe/

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



--------------------------------------------------------------------------------
Joseph DienE-mail: jdien07 at mac.comPhone: 301-226-8848Fax: 301-226-8811http://homepage.mac.com/jdien07/







_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip 		 	   		  
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From stefan.debener at uni-oldenburg.de  Tue May 24 09:11:16 2011
From: stefan.debener at uni-oldenburg.de (Stefan Debener)
Date: Tue, 24 May 2011 09:11:16 +0200
Subject: [FieldTrip] ICA+frqanalysis questions
In-Reply-To: <BANLkTikHLHhjes_pF_5wdrF6QjNna3T_Mg@mail.gmail.com>
References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>	<543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>	<BAY162-w15103E26B01D0271AD3F6EAB720@phx.gbl>	<BANLkTi=YxtpPqFfvORYKmO-23o8zp-Tc3w@mail.gmail.com>	<09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com>
	<BANLkTikHLHhjes_pF_5wdrF6QjNna3T_Mg@mail.gmail.com>
Message-ID: <4DDB5A14.3090102@uni-oldenburg.de>

Hi Odelia,

I have a slightly different opinion here. It is certainly true that any 
filter has the tendency to distort data (with distortion I mean that 
data consists of a mixture of some wanted, true signal and some unwanted 
signal, and that the removal of the unwanted part of the signal is 
neither complete nor specific). In our lab we regularly use ICA for 
artefact removal (and more), and the benefit/gain is clearly are much 
larger than the distortion. In fact there are a number of examples out 
showing that currently only ICA (or related tools) can recover the study 
of (a substantial fraction of the wanted) EEG signal (but again, it is 
NOT a perfect tool at all), in particular in cases where other means of 
SNR enhancement don't work well (averaging, spectral analysis). I am 
happy to provide references if you are interested...

For the evaluation of outcome it would be reasonable to not evaluate the 
ERP alone, as this could be misleading. Better evaluate the sensitivity 
and specificity of an eye blink attentuation approach on the single 
trial (and single subject) level, this will give you good insight. And 
it is worth keeping in mind that the preprocessing of the data (among 
other issues, like the quality of the recording and so on) largely 
determines the quality of the output (for some introduction you may look 
up chapter 3.1 in Ullsperger & Debener, 2010, Simultaneous EEG and FMRI, 
Oxford University Press). Just by a different preprocessing ICA output 
could vary between crap and excellent unmixing. Thus a poor ICA eye 
blink attenuation would make me a bit suspicious...

Best,
Stefan


Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman:
> And for a related perspective, see
>
> McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. 
> J. (2011). Electromyogenic artifacts and electroencephalographic 
> inferences revisited, */Neuroimage/*/, 54/, 4-9.
>
> http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf 
> <http://psyphz.psych.wisc.edu/%7Eshackman/mcmenamin_shackman_ni2011.pdf>
>
>
> On Mon, May 23, 2011 at 8:07 PM, Joseph Dien <jdien07 at mac.com 
> <mailto:jdien07 at mac.com>> wrote:
>
>     I agree with David's reasoning.  You may find the following
>     article to be of help as well in understanding the issues involved:
>
>     Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and
>     ICA of simulated ERPs: Promax versus Infomax rotations. /Human
>     Brain Mapping/, 28(8), 742-763.
>
>     Cheers!
>
>     Joe
>
>     On May 23, 2011, at 11:57 AM, David Groppe wrote:
>
>>     Hi Odelia,
>>       When you use ICA (or any other spatial filter) to correct for EEG
>>     artifacts, you're going to distort your data some by removing
>>     true EEG
>>     activity in addition to the artifact (for an explanation, see:
>>     http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf).
>>     So to minimize distortion, it would be better not to apply ICA
>>     artifact correction to artifact-free data.  However, if the frequency
>>     of the artifact differs across experimental conditions, it could
>>     confound your analysis.  For example, I suspect people blink more
>>     often to targets in an oddball experiment than standards.  Thus
>>     if you
>>     apply ICA only to blinky trials, you could find a difference between
>>     the EEG response to standards and targets that simply reflects the
>>     fact ICA removed more EEG activity in the target trials (i.e., it
>>     wouldn't reflect a true difference in neural processing).
>>          hope this helps,
>>             -David
>>
>>     On Mon, May 23, 2011 at 1:44 AM, odelia nakar
>>     <odidodi at hotmail.com <mailto:odidodi at hotmail.com>> wrote:
>>>     Hi all,
>>>
>>>     I'm troubled by the fact that when I use ICA for blinks\eyes
>>>     movements
>>>     removal, I remove the relevant components also from trials that
>>>     do not
>>>     contain blinks\eyes movements. In order to avoid this bias we
>>>     thought to
>>>     combine the data before ICA ("data" structure) with the data
>>>     after ICA
>>>     ("dataica" structure), only in specific trials, as follows:
>>>
>>>     datall=dataica;
>>>     datall.trial=data.trial;
>>>     datall.time=data.time;
>>>     blinks=[2 4 5 8 bla bla 156];
>>>     for ind=1:length(blinks)
>>>          datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)};
>>>     end
>>>
>>>     To my first question: I just wanted to check that there is no
>>>     problem with
>>>     that, or any reason not to use it.
>>>
>>>     Another issue- I use motor learning task, and I'm trying to
>>>     understand what
>>>     happens through the process, in terms of power-frequency changes
>>>     through the
>>>     process. How would you recommend that I'd use the
>>>     ft_freqanalysis function?
>>>     What method to use (or what do I need to consider when choosing
>>>     the method
>>>     field)?
>>>
>>>
>>>     Thanks a lot,
>>>     Odelia.
>>>
>>>     _______________________________________________
>>>     fieldtrip mailing list
>>>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>>
>>     -- 
>>     David Groppe, Ph.D.
>>     Postdoctoral Researcher
>>     Kutaslab
>>     Dept. of Cognitive Science
>>     University of California, San Diego
>>     http://www.cogsci.ucsd.edu/~dgroppe/
>>     <http://www.cogsci.ucsd.edu/%7Edgroppe/>
>>
>>     _______________________________________________
>>     fieldtrip mailing list
>>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>     --------------------------------------------------------------------------------
>
>     Joseph Dien
>     E-mail: jdien07 at mac.com <mailto:jdien07 at mac.com>
>     Phone: 301-226-8848 <tel:301-226-8848>
>     Fax: 301-226-8811 <tel:301-226-8811>
>     http://homepage.mac.com/jdien07/
>
>
>
>
>
>
>
>
>
>     _______________________________________________
>     fieldtrip mailing list
>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> -- 
> Alexander J. Shackman, Ph.D.
> Wisconsin Psychiatric Institute & Clinics and
> Department of Psychology
> University of Wisconsin-Madison
> 1202 West Johnson Street
> Madison, Wisconsin 53706
>
> Telephone: +1 (608) 358-5025
> Fax: +1 (608) 265-2875
> Email: shackman at wisc.edu <mailto:shackman at wisc.edu>
> http://psyphz.psych.wisc.edu/~shackman 
> <http://psyphz.psych.wisc.edu/%7Eshackman>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Prof. Dr. Stefan Debener
Neuropsychology	Lab
Department of Psychology
University of Oldenburg
D-26111 Oldenburg
Germany

Office: A7 0-038
Phone: +49-441-798-4271
Fax:   +49-441-798-5522
Email: stefan.debener at uni-oldenburg.de

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From dgroppe at cogsci.ucsd.edu  Tue May 24 23:47:39 2011
From: dgroppe at cogsci.ucsd.edu (David Groppe)
Date: Tue, 24 May 2011 14:47:39 -0700
Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine
Message-ID: <BANLkTi=h++PEHmok8UaVPadGj_Jmf0fs=w@mail.gmail.com>

Hi there,
   My lab is running MATLAB 7.8 on a Linux network and when we plot
spectrograms using ft_multiplotTFR.m the computer we're using will
often reboot.  It appears to happen most often (if not exclusively),
when we close the figure window produced by ft_multiplotTFR.m.  The
problem happens even if we create non-interactive figures (i.e., we
set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e.,
Java disabled).  Has anyone else had this problem?   Does anyone have
an idea as to what a solution might be?  Puzzlingly, we don't have
this problem when running MATLAB on a Mac.
          much appreciated,
                -David

-- 
David Groppe, Ph.D.
Postdoctoral Researcher
Kutaslab
Dept. of Cognitive Science
University of California, San Diego
http://www.cogsci.ucsd.edu/~dgroppe/


From r.vandermeij at donders.ru.nl  Wed May 25 00:23:58 2011
From: r.vandermeij at donders.ru.nl (Roemer van der Meij)
Date: Tue, 24 May 2011 15:23:58 -0700
Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine
In-Reply-To: <BANLkTi=h++PEHmok8UaVPadGj_Jmf0fs=w@mail.gmail.com>
References: <BANLkTi=h++PEHmok8UaVPadGj_Jmf0fs=w@mail.gmail.com>
Message-ID: <4DDC2FFE.9000600@donders.ru.nl>

Hi David,

Depending on what you mean by crashing, it could be the opengl drivers. 
I've experienced similar issues with complex plotting functions. Try 
creating the figure-window (note, not the plot) using the zbuffer to 
circumvent it by figure('renderer','zbuffer')

Hope it helps,
Roemer



On 24-May-11 14:47, David Groppe wrote:
> Hi there,
>     My lab is running MATLAB 7.8 on a Linux network and when we plot
> spectrograms using ft_multiplotTFR.m the computer we're using will
> often reboot.  It appears to happen most often (if not exclusively),
> when we close the figure window produced by ft_multiplotTFR.m.  The
> problem happens even if we create non-interactive figures (i.e., we
> set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e.,
> Java disabled).  Has anyone else had this problem?   Does anyone have
> an idea as to what a solution might be?  Puzzlingly, we don't have
> this problem when running MATLAB on a Mac.
>            much appreciated,
>                  -David
>

-- 
Roemer van der Meij M.Sc.
PhD student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognition
Radboud University Nijmegen
P.O. Box 9104
6500 HE Nijmegen
The Netherlands
Tel: +31(0)24 3655932
E-mail: r.vandermeij at donders.ru.nl
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From dgroppe at cogsci.ucsd.edu  Wed May 25 02:10:02 2011
From: dgroppe at cogsci.ucsd.edu (David Groppe)
Date: Tue, 24 May 2011 17:10:02 -0700
Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine
In-Reply-To: <4DDC2FFE.9000600@donders.ru.nl>
References: <BANLkTi=h++PEHmok8UaVPadGj_Jmf0fs=w@mail.gmail.com>
	<4DDC2FFE.9000600@donders.ru.nl>
Message-ID: <BANLkTi=CP_4T9vEKM-vTvVpHQ7bFt-M2Lg@mail.gmail.com>

Thanks very much for the response Roemer.  By "crashing," I mean the
screen suddenly goes blank and the machine reverts to the login
screen.  I've tried your suggestion and so far it looks like it's
working!  I'll let you know if the problem returns.
     greatly appreciated,
          -David

On Tue, May 24, 2011 at 3:23 PM, Roemer van der Meij
<r.vandermeij at donders.ru.nl> wrote:
> Hi David,
>
> Depending on what you mean by crashing, it could be the opengl drivers. I've
> experienced similar issues with complex plotting functions. Try creating the
> figure-window (note, not the plot) using the zbuffer to circumvent it by
> figure('renderer','zbuffer')
>
> Hope it helps,
> Roemer
>
>
>
> On 24-May-11 14:47, David Groppe wrote:
>
> Hi there,
>    My lab is running MATLAB 7.8 on a Linux network and when we plot
> spectrograms using ft_multiplotTFR.m the computer we're using will
> often reboot.  It appears to happen most often (if not exclusively),
> when we close the figure window produced by ft_multiplotTFR.m.  The
> problem happens even if we create non-interactive figures (i.e., we
> set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e.,
> Java disabled).  Has anyone else had this problem?   Does anyone have
> an idea as to what a solution might be?  Puzzlingly, we don't have
> this problem when running MATLAB on a Mac.
>           much appreciated,
>                 -David
>
>
> --
> Roemer van der Meij M.Sc.
> PhD student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognition
> Radboud University Nijmegen
> P.O. Box 9104
> 6500 HE Nijmegen
> The Netherlands
> Tel: +31(0)24 3655932
> E-mail: r.vandermeij at donders.ru.nl
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
David Groppe, Ph.D.
Postdoctoral Researcher
Kutaslab
Dept. of Cognitive Science
University of California, San Diego
http://www.cogsci.ucsd.edu/~dgroppe/


From g.piantoni at nin.knaw.nl  Wed May 25 08:59:20 2011
From: g.piantoni at nin.knaw.nl (Gio Piantoni)
Date: Wed, 25 May 2011 08:59:20 +0200
Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine
In-Reply-To: <BANLkTi=CP_4T9vEKM-vTvVpHQ7bFt-M2Lg@mail.gmail.com>
References: <BANLkTi=h++PEHmok8UaVPadGj_Jmf0fs=w@mail.gmail.com>
	<4DDC2FFE.9000600@donders.ru.nl>
	<BANLkTi=CP_4T9vEKM-vTvVpHQ7bFt-M2Lg@mail.gmail.com>
Message-ID: <BANLkTike=FBZ0XGU+U4c=tAVEHzvtLTcCw@mail.gmail.com>

Hi David,

I also had similar problems, such as crashing of the VNC window on a
remote server.
I agree with Roemer that it's probably due to buggy opengl drivers.
More information at:
http://www.mathworks.com/support/tech-notes/1200/1201.html#Section_4

Briefly, you can run as first command:
>> opengl software

to force matlab to use the (less buggy) software implementation of opengl.

Then the trick "figure('renderer','zbuffer')" should not be necessary.
Hope this helps.

Gio

-- 
Giovanni Piantoni, Ph.D. student
Dept. Sleep & Cognition
Netherlands Institute for Neuroscience
Meibergdreef 47
1105 BA Amsterdam (NL)

+31 (0)20 5665492
g.piantoni at nin.knaw.nl
www.giovannipiantoni.com

On Wed, May 25, 2011 at 02:10, David Groppe <dgroppe at cogsci.ucsd.edu> wrote:
> Thanks very much for the response Roemer.  By "crashing," I mean the
> screen suddenly goes blank and the machine reverts to the login
> screen.  I've tried your suggestion and so far it looks like it's
> working!  I'll let you know if the problem returns.
>     greatly appreciated,
>          -David
>
> On Tue, May 24, 2011 at 3:23 PM, Roemer van der Meij
> <r.vandermeij at donders.ru.nl> wrote:
>> Hi David,
>>
>> Depending on what you mean by crashing, it could be the opengl drivers. I've
>> experienced similar issues with complex plotting functions. Try creating the
>> figure-window (note, not the plot) using the zbuffer to circumvent it by
>> figure('renderer','zbuffer')
>>
>> Hope it helps,
>> Roemer
>>
>>
>>
>> On 24-May-11 14:47, David Groppe wrote:
>>
>> Hi there,
>>    My lab is running MATLAB 7.8 on a Linux network and when we plot
>> spectrograms using ft_multiplotTFR.m the computer we're using will
>> often reboot.  It appears to happen most often (if not exclusively),
>> when we close the figure window produced by ft_multiplotTFR.m.  The
>> problem happens even if we create non-interactive figures (i.e., we
>> set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e.,
>> Java disabled).  Has anyone else had this problem?   Does anyone have
>> an idea as to what a solution might be?  Puzzlingly, we don't have
>> this problem when running MATLAB on a Mac.
>>           much appreciated,
>>                 -David
>>
>>
>> --
>> Roemer van der Meij M.Sc.
>> PhD student
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognition
>> Radboud University Nijmegen
>> P.O. Box 9104
>> 6500 HE Nijmegen
>> The Netherlands
>> Tel: +31(0)24 3655932
>> E-mail: r.vandermeij at donders.ru.nl
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> David Groppe, Ph.D.
> Postdoctoral Researcher
> Kutaslab
> Dept. of Cognitive Science
> University of California, San Diego
> http://www.cogsci.ucsd.edu/~dgroppe/
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



From g.dimitriadis at donders.ru.nl  Wed May 25 09:48:49 2011
From: g.dimitriadis at donders.ru.nl (George Dimitriadis)
Date: Wed, 25 May 2011 09:48:49 +0200
Subject: [FieldTrip] (no subject)
Message-ID: <039701cc1ab0$32773060$97659120$@dimitriadis@donders.ru.nl>

Hello guys,

 

I just run an ft_freqanalysis using cfg.taper='dssp'. By mistake I took the
cfg. tapsmofrq to be too small resulting in a single taper. This was fine,
but when I run freqanalysis I got an error saying that the warning_once
(ft_specest_mtmfft at 89) was not found. Apparently it was there to warn me
about using only 1 tapper for smoothing with 'dssp'. I am just letting you
know that for some reason the warning_once(char) function couldn't be found.

 

Thanks

 

George

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From jan.schoffelen at donders.ru.nl  Wed May 25 10:10:02 2011
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Wed, 25 May 2011 10:10:02 +0200
Subject: [FieldTrip] (no subject)
In-Reply-To: <039701cc1ab0$32773060$97659120$@dimitriadis@donders.ru.nl>
References: <039701cc1ab0$32773060$97659120$@dimitriadis@donders.ru.nl>
Message-ID: <6F47EF43-DE4D-4031-8BCC-F5C9D9AA13D3@donders.ru.nl>

Hi George,

Sorry about this. If you are running a local copy of fieldtrip, you  
can copy warning_once.m from fieldtrip/private into fieldtrip/specest/ 
private. It should work then. I'll fix it in the release version asap.

Cheers,

JM

On May 25, 2011, at 9:48 AM, George Dimitriadis wrote:

> Hello guys,
>
> I just run an ft_freqanalysis using cfg.taper=’dssp’. By mistake I  
> took the cfg. tapsmofrq to be too small resulting in a single taper.  
> This was fine, but when I run freqanalysis I got an error saying  
> that the warning_once (ft_specest_mtmfft at 89) was not found.  
> Apparently it was there to warn me about using only 1 tapper for  
> smoothing with ‘dssp’. I am just letting you know that for some  
> reason the warning_once(char) function couldn’t be found.
>
> Thanks
>
> George
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793

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From S.N.Maijers at student.ru.nl  Wed May 25 11:50:16 2011
From: S.N.Maijers at student.ru.nl (Sander Maijers)
Date: Wed, 25 May 2011 11:50:16 +0200
Subject: [FieldTrip] [multivariate] MEX compiling for 32-bit MATLAB under
 64-bit Linux: who helps?
Message-ID: <20110525115016.0fc02ea6@thuisrekenaar>

Dear readers,

I am running MATLAB R2011a 32-bit under Ubuntu Linux 10.10 64-bit (Linux thuisrekenaar 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 x86_64 GNU/Linux).

When I call "ft_timelockstatistics()" with "cfg.mva ={ft_mv_standardizer() ft_mv_svm()};"

It fails:

"selected 60 channels
selected 351 time bins
selected 1 frequency bins
using "statistics_crossvalidate" for the statistical testing
initializing random number generator with seed 1
validating 1 dataset(s)
input 1 consists of 439 examples and 21060 features
output 1 consists of 439 examples and 1 features
validating using 5-fold cross-validation
using 5 folds for 1 datasets
dataset 1: validating fold 1 of 5 using 351 training samples and 88 test samples Compiling tprod for first use
/usr/bin/ld: skipping
incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when searching for -lstdc++ /usr/bin/ld: skipping
incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching for -lstdc++ /usr/bin/ld: skipping
incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when searching for -lstdc++ /usr/bin/ld: skipping
incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching for -lstdc++ /usr/bin/ld:
	cannot find -lstdc++ collect2: ld returned 1 exit status

mex: link of ' "tprod.mexglx"' failed.

??? Error using ==> tprod at 132 unable to compile MEX version of '/mnt/data1/0/9/data/software/UNIX/scientific/FieldTrip/bin/fieldtrip-read-only/multivariate/external/farquhar/tprod/tprod', please make sure your MEX compiler is set up correctly (try 'mex -setup')."


I have followed the instructions on
https://help.ubuntu.com/community/MATLAB#MEX functions to enable MEX compiling but it was not successful.

-> Before I singlehandedly bring my operating system configuration into disarray, I would like to learn from you the following. Do you know of ways to use a gcc to compile code written for a 32-bit architecture ona 64-bit machine? Or if necessary another compiler that works under Linux?
-> If such a thing is certainly impossible, are there ways to avoid MEX compiling? Or could someone provide precompiled MEX files that would suit my configuration?

[*] I have installed the Ubuntu package "ia32-libs" (version 20090808ubuntu9.1)
[*] It seems that the only thing I need is 32-bit binaries for libstdc++. Perhaps I can introduce these in some creative way, but I would like to check with you all first.

I hope you are willing to help me. As a novice to FieldTrip and even MATLAB, I have encountered many obstacles but I am determined to surmount them.

Kind regards,
Sander Maijers (BA Linguistics student)


From S.N.Maijers at student.ru.nl  Wed May 25 12:13:01 2011
From: S.N.Maijers at student.ru.nl (Sander Maijers)
Date: Wed, 25 May 2011 12:13:01 +0200
Subject: [FieldTrip] [multivariate] "multivariate" subdirectory not included
 upon "addpath" of FieldTrip root directory
Message-ID: <20110525121301.2f896b3e@thuisrekenaar>

Dear readers,

While all other functional subdirectories do get included after an
"addpath" of the FieldTrip root directory, the "multivariate"
subdirectories does not get included.

It assume this is because of automatical detection that requirements of
the FieldTrip multivariate module were not met.

Yet while some parts of the multivariate module seem to rely on
features exclusive to MATLAB 64-bit editions, others (like the ridge
regression functionality) do not.

>From my (tentative) investigation it appears that there is no standard
way to add a path recursively from a startup.m file, even though that
can be done with the graphical interface of MATLAB. 

What are your thoughts about this? 

Can anyone offer a method to automatically add FieldTrip including the
multivariate module to the path upon startup of MATLAB that works in
my situation?

Kind regards,
Sander Maijers

P.S.:
In case it would be relevant: I use MATLAB R2011a 32-bit under 64-bit
Linux.



From ekanal at cmu.edu  Wed May 25 14:53:53 2011
From: ekanal at cmu.edu (Kanal Eliezer)
Date: Wed, 25 May 2011 08:53:53 -0400
Subject: [FieldTrip] [multivariate] "multivariate" subdirectory not
	included upon "addpath" of FieldTrip root directory
In-Reply-To: <20110525121301.2f896b3e@thuisrekenaar>
References: <20110525121301.2f896b3e@thuisrekenaar>
Message-ID: <31810FB1-D384-4B77-8BCA-E2369C8A4F4C@cmu.edu>

Hello Sander -

Just so you know, there is a way to recursively add folders to a path, using the `genpath` command:

addpath(genpath(path/to/folder))

However, as you said, it's probably just a better idea to add it to the `ft_defaults` file so it's added automatically, as you suggested.

Elli


On May 25, 2011, at 6:13 AM, Sander Maijers wrote:

> Dear readers,
> 
> While all other functional subdirectories do get included after an
> "addpath" of the FieldTrip root directory, the "multivariate"
> subdirectories does not get included.
> 
> It assume this is because of automatical detection that requirements of
> the FieldTrip multivariate module were not met.
> 
> Yet while some parts of the multivariate module seem to rely on
> features exclusive to MATLAB 64-bit editions, others (like the ridge
> regression functionality) do not.
> 
>> From my (tentative) investigation it appears that there is no standard
> way to add a path recursively from a startup.m file, even though that
> can be done with the graphical interface of MATLAB. 
> 
> What are your thoughts about this? 
> 
> Can anyone offer a method to automatically add FieldTrip including the
> multivariate module to the path upon startup of MATLAB that works in
> my situation?
> 
> Kind regards,
> Sander Maijers
> 
> P.S.:
> In case it would be relevant: I use MATLAB R2011a 32-bit under 64-bit
> Linux.
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip




From batrod at gmail.com  Wed May 25 17:39:02 2011
From: batrod at gmail.com (Rodolphe Nenert)
Date: Wed, 25 May 2011 10:39:02 -0500
Subject: [FieldTrip] [multivariate] "multivariate" subdirectory not
 included upon "addpath" of FieldTrip root directory
In-Reply-To: <31810FB1-D384-4B77-8BCA-E2369C8A4F4C@cmu.edu>
References: <20110525121301.2f896b3e@thuisrekenaar>
	<31810FB1-D384-4B77-8BCA-E2369C8A4F4C@cmu.edu>
Message-ID: <BANLkTin__HFAwXs8DXjhsEFmKT4BQvFY+w@mail.gmail.com>

Hello Sander,

Elli's suggestion is right. As you apparently want to do that on matlab
startup and using Linux, you can add a matlab shortcut  on your panel with
the following instructions : matlab -r "yourinstructions"
"yourinstructions" can be an addpath or wathever you want.
I often use this initialization to avoid default path conflicts between spm,
fieldtrip, eeglab, etc...

Hope this helps,

Rodolphe

On Wed, May 25, 2011 at 7:53 AM, Kanal Eliezer <ekanal at cmu.edu> wrote:

> Hello Sander -
>
> Just so you know, there is a way to recursively add folders to a path,
> using the `genpath` command:
>
> addpath(genpath(path/to/folder))
>
> However, as you said, it's probably just a better idea to add it to the
> `ft_defaults` file so it's added automatically, as you suggested.
>
> Elli
>
>
> On May 25, 2011, at 6:13 AM, Sander Maijers wrote:
>
> > Dear readers,
> >
> > While all other functional subdirectories do get included after an
> > "addpath" of the FieldTrip root directory, the "multivariate"
> > subdirectories does not get included.
> >
> > It assume this is because of automatical detection that requirements of
> > the FieldTrip multivariate module were not met.
> >
> > Yet while some parts of the multivariate module seem to rely on
> > features exclusive to MATLAB 64-bit editions, others (like the ridge
> > regression functionality) do not.
> >
> >> From my (tentative) investigation it appears that there is no standard
> > way to add a path recursively from a startup.m file, even though that
> > can be done with the graphical interface of MATLAB.
> >
> > What are your thoughts about this?
> >
> > Can anyone offer a method to automatically add FieldTrip including the
> > multivariate module to the path upon startup of MATLAB that works in
> > my situation?
> >
> > Kind regards,
> > Sander Maijers
> >
> > P.S.:
> > In case it would be relevant: I use MATLAB R2011a 32-bit under 64-bit
> > Linux.
> >
> > _______________________________________________
> > 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
>
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From batrod at gmail.com  Wed May 25 18:32:19 2011
From: batrod at gmail.com (Rodolphe Nenert)
Date: Wed, 25 May 2011 11:32:19 -0500
Subject: [FieldTrip] Filtering and oscillations
Message-ID: <BANLkTi=LjrwntXDioaTA_gA-b+WHv_yWEw@mail.gmail.com>

Dear Fieldtrippers,

i have a theoretical question.
Im interested into phase-lock analysis between sensors in alpha
oscillations.
Prior to do so, my data were bandpassed between 2 and 30 Hz. However, i
heard that such a low-pass filter can alter informations usefull to
phase-lock analysis.

Any suggestions on that?
Best regards,

Rodolphe.
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From jenwhitman at gmail.com  Wed May 25 19:53:28 2011
From: jenwhitman at gmail.com (Jen Whitman)
Date: Wed, 25 May 2011 10:53:28 -0700
Subject: [FieldTrip] [multivariate] MEX compiling for 32-bit MATLAB
 under 64-bit Linux: who helps?
In-Reply-To: <20110525115016.0fc02ea6@thuisrekenaar>
References: <20110525115016.0fc02ea6@thuisrekenaar>
Message-ID: <BANLkTikVHYNcSdxOc=zYM+=-gAYdvTSX_Q@mail.gmail.com>

As another ubuntu 64-bit user, I'd say your problem is with your matlab
install rather than with fieldtrip. You may have inadvertently specified
32-bit instead of 64-bit when you installed matlab. If you type "computer"
at the matlab prompt, it should say "GLNXA64". If not, I recommend redoing
the matlab installation and making sure you specify your OS as 64-bit. If
you still get error message about libstdc++.so, you may need to install that
library using the 'synaptic package manger' (in your system menu under
administration). A good resource for help if you have further difficulty may
be linuxquestions.org.

Best of luck!

On Wed, May 25, 2011 at 2:50 AM, Sander Maijers
<S.N.Maijers at student.ru.nl>wrote:

> Dear readers,
>
> I am running MATLAB R2011a 32-bit under Ubuntu Linux 10.10 64-bit (Linux
> thuisrekenaar 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011
> x86_64 GNU/Linux).
>
> When I call "ft_timelockstatistics()" with "cfg.mva ={ft_mv_standardizer()
> ft_mv_svm()};"
>
> It fails:
>
> "selected 60 channels
> selected 351 time bins
> selected 1 frequency bins
> using "statistics_crossvalidate" for the statistical testing
> initializing random number generator with seed 1
> validating 1 dataset(s)
> input 1 consists of 439 examples and 21060 features
> output 1 consists of 439 examples and 1 features
> validating using 5-fold cross-validation
> using 5 folds for 1 datasets
> dataset 1: validating fold 1 of 5 using 351 training samples and 88 test
> samples Compiling tprod for first use
> /usr/bin/ld: skipping
> incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when
> searching for -lstdc++ /usr/bin/ld: skipping
> incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching
> for -lstdc++ /usr/bin/ld: skipping
> incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when
> searching for -lstdc++ /usr/bin/ld: skipping
> incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching
> for -lstdc++ /usr/bin/ld:
>        cannot find -lstdc++ collect2: ld returned 1 exit status
>
> mex: link of ' "tprod.mexglx"' failed.
>
> ??? Error using ==> tprod at 132 unable to compile MEX version of
> '/mnt/data1/0/9/data/software/UNIX/scientific/FieldTrip/bin/fieldtrip-read-only/multivariate/external/farquhar/tprod/tprod',
> please make sure your MEX compiler is set up correctly (try 'mex -setup')."
>
>
> I have followed the instructions on
> https://help.ubuntu.com/community/MATLAB#MEX functions to enable MEX
> compiling but it was not successful.
>
> -> Before I singlehandedly bring my operating system configuration into
> disarray, I would like to learn from you the following. Do you know of ways
> to use a gcc to compile code written for a 32-bit architecture ona 64-bit
> machine? Or if necessary another compiler that works under Linux?
> -> If such a thing is certainly impossible, are there ways to avoid MEX
> compiling? Or could someone provide precompiled MEX files that would suit my
> configuration?
>
> [*] I have installed the Ubuntu package "ia32-libs" (version
> 20090808ubuntu9.1)
> [*] It seems that the only thing I need is 32-bit binaries for libstdc++.
> Perhaps I can introduce these in some creative way, but I would like to
> check with you all first.
>
> I hope you are willing to help me. As a novice to FieldTrip and even
> MATLAB, I have encountered many obstacles but I am determined to surmount
> them.
>
> Kind regards,
> Sander Maijers (BA Linguistics student)
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From S.N.Maijers at student.ru.nl  Thu May 26 16:23:39 2011
From: S.N.Maijers at student.ru.nl (Sander Maijers)
Date: Thu, 26 May 2011 16:23:39 +0200
Subject: [FieldTrip] [multivariate] MEX compiling for 32-bit MATLAB
 under 64-bit Linux: who helps?
In-Reply-To: <BANLkTikVHYNcSdxOc=zYM+=-gAYdvTSX_Q@mail.gmail.com>
References: <20110525115016.0fc02ea6@thuisrekenaar>
	<BANLkTikVHYNcSdxOc=zYM+=-gAYdvTSX_Q@mail.gmail.com>
Message-ID: <20110526162339.65dd030c@thuisrekenaar>

Jen, thanks for your suggestion. That problem I had fixed before. I am
among those who could not even get a 64-bit install if they wished so,
because the Student edition of MATLAB is still 32-bit-only.

This problem will occur later on, in case some MEX-compilation needs to
be done, in my case with the multivariate module!

I have succeeded in fixing the problem however. Those who are
confronted with it as well, can read:
http://fieldtrip.fcdonders.nl/faq/compile?&#fixing_mex-compilation_with_32-bit_variants_of_matlab_running_under_64-bit_linux .


On Wed, 25 May 2011 10:53:28 -0700
Jen Whitman <jenwhitman at gmail.com> wrote:

> As another ubuntu 64-bit user, I'd say your problem is with your
> matlab install rather than with fieldtrip. You may have inadvertently
> specified 32-bit instead of 64-bit when you installed matlab. If you
> type "computer" at the matlab prompt, it should say "GLNXA64". If
> not, I recommend redoing the matlab installation and making sure you
> specify your OS as 64-bit. If you still get error message about
> libstdc++.so, you may need to install that library using the
> 'synaptic package manger' (in your system menu under administration).
> A good resource for help if you have further difficulty may be
> linuxquestions.org.
> 
> Best of luck!
> 
> On Wed, May 25, 2011 at 2:50 AM, Sander Maijers
> <S.N.Maijers at student.ru.nl>wrote:
> 
> > Dear readers,
> >
> > I am running MATLAB R2011a 32-bit under Ubuntu Linux 10.10 64-bit
> > (Linux thuisrekenaar 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18
> > 18:42:20 UTC 2011 x86_64 GNU/Linux).
> >
> > When I call "ft_timelockstatistics()" with "cfg.mva
> > ={ft_mv_standardizer() ft_mv_svm()};"
> >
> > It fails:
> >
> > "selected 60 channels
> > selected 351 time bins
> > selected 1 frequency bins
> > using "statistics_crossvalidate" for the statistical testing
> > initializing random number generator with seed 1
> > validating 1 dataset(s)
> > input 1 consists of 439 examples and 21060 features
> > output 1 consists of 439 examples and 1 features
> > validating using 5-fold cross-validation
> > using 5 folds for 1 datasets
> > dataset 1: validating fold 1 of 5 using 351 training samples and 88
> > test samples Compiling tprod for first use
> > /usr/bin/ld: skipping
> > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when
> > searching for -lstdc++ /usr/bin/ld: skipping
> > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when
> > searching for -lstdc++ /usr/bin/ld: skipping
> > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when
> > searching for -lstdc++ /usr/bin/ld: skipping
> > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when
> > searching for -lstdc++ /usr/bin/ld:
> >        cannot find -lstdc++ collect2: ld returned 1 exit status
> >
> > mex: link of ' "tprod.mexglx"' failed.
> >
> > ??? Error using ==> tprod at 132 unable to compile MEX version of
> > '/mnt/data1/0/9/data/software/UNIX/scientific/FieldTrip/bin/fieldtrip-read-only/multivariate/external/farquhar/tprod/tprod',
> > please make sure your MEX compiler is set up correctly (try 'mex
> > -setup')."
> >
> >
> > I have followed the instructions on
> > https://help.ubuntu.com/community/MATLAB#MEX functions to enable MEX
> > compiling but it was not successful.
> >
> > -> Before I singlehandedly bring my operating system configuration
> > into disarray, I would like to learn from you the following. Do you
> > know of ways to use a gcc to compile code written for a 32-bit
> > architecture ona 64-bit machine? Or if necessary another compiler
> > that works under Linux? -> If such a thing is certainly impossible,
> > are there ways to avoid MEX compiling? Or could someone provide
> > precompiled MEX files that would suit my configuration?
> >
> > [*] I have installed the Ubuntu package "ia32-libs" (version
> > 20090808ubuntu9.1)
> > [*] It seems that the only thing I need is 32-bit binaries for
> > libstdc++. Perhaps I can introduce these in some creative way, but
> > I would like to check with you all first.
> >
> > I hope you are willing to help me. As a novice to FieldTrip and even
> > MATLAB, I have encountered many obstacles but I am determined to
> > surmount them.
> >
> > Kind regards,
> > Sander Maijers (BA Linguistics student)
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >


From dgroppe at cogsci.ucsd.edu  Fri May 27 03:54:35 2011
From: dgroppe at cogsci.ucsd.edu (David Groppe)
Date: Thu, 26 May 2011 18:54:35 -0700
Subject: [FieldTrip] duplicate spm directories
Message-ID: <BANLkTinHBVGCGpvRDpAMusbhQF+nLvFY3Q@mail.gmail.com>

Hi again,
   I'm running the March 28th version of Fieldtrip and am getting the
following warning:

Warning: multiple versions of SPM on your path will confuse FieldTrip
> In fieldtrip-20110328/private/warning_once at 75
  In ft_defaults at 45
  In ft_preprocessing at 179
Warning: one version of SPM is found here:
/Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm2/spm.m
> In ft_defaults at 48
  In ft_preprocessing at 179
Warning: one version of SPM is found here:
/Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm8/spm.m


Can I simply remove the spm2 directory?
      thanks in advance,
            -D

-- 
David Groppe, Ph.D.
Postdoctoral Researcher
Kutaslab
Dept. of Cognitive Science
University of California, San Diego
http://www.cogsci.ucsd.edu/~dgroppe/


From jdien07 at mac.com  Fri May 27 05:16:03 2011
From: jdien07 at mac.com (Joseph Dien)
Date: Thu, 26 May 2011 23:16:03 -0400
Subject: [FieldTrip] ICA+frqanalysis questions
In-Reply-To: <4DDB5A14.3090102@uni-oldenburg.de>
References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>
	<543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>
	<BAY162-w15103E26B01D0271AD3F6EAB720@phx.gbl>
	<BANLkTi=YxtpPqFfvORYKmO-23o8zp-Tc3w@mail.gmail.com>
	<09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com>
	<BANLkTikHLHhjes_pF_5wdrF6QjNna3T_Mg@mail.gmail.com>
	<4DDB5A14.3090102@uni-oldenburg.de>
Message-ID: <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com>

Stefan, just to be clear, I don't think any of us were saying not to use ICA to correct blinks.  David was just saying that there are potential concerns when one only applies the ICA to the blink trials rather than to all the trials.  I myself use EEGlab's infomax implementation in the automatic eyeblink correction tool of my EP Toolkit (http://sourceforge.net/projects/erppcatoolkit/).

Now that said, I should add a little more nuance to my response.  One of the things I observed (or rather, that Tim Curran pointed out to me) is that when you apply ICA to remove eyeblink artifacts in this manner, it can actually substantially increase the noise level in the data, so for the trials without eyeblinks it can have a considerable cost.  So in order to balance the cost/benefit ratio, what I did was to include a trial by trial criterion that the putative eyeblink factors would only be removed if doing so reduced the overall variance of the trial.  This approach does still have some potential for causing the concerns that David raises but not as much as only applying the ICA to blink trials since it does end up getting applied to non-blink trials too.  This does mean that one should be cautious about any apparent effects in the artifact corrected data that are centered around the eyes (that have a blink topography) but that goes without saying in any case.  So anyway, I agree, it's not perfect but seems to be the best available option.

Cheers!

Joe

On May 24, 2011, at 3:11 AM, Stefan Debener wrote:

> Hi Odelia,
> 
> I have a slightly different opinion here. It is certainly true that any filter has the tendency to distort data (with distortion I mean that data consists of a mixture of some wanted, true signal and some unwanted signal, and that the removal of the unwanted part of the signal is neither complete nor specific). In our lab we regularly use ICA for artefact removal (and more), and the benefit/gain is clearly are much larger than the distortion. In fact there are a number of examples out showing that currently only ICA (or related tools) can recover the study of (a substantial fraction of the wanted) EEG signal (but again, it is NOT a perfect tool at all), in particular in cases where other means of SNR enhancement don't work well (averaging, spectral analysis). I am happy to provide references if you are interested...
> 
> For the evaluation of outcome it would be reasonable to not evaluate the ERP alone, as this could be misleading. Better evaluate the sensitivity and specificity of an eye blink attentuation approach on the single trial (and single subject) level, this will give you good insight. And it is worth keeping in mind that the preprocessing of the data (among other issues, like the quality of the recording and so on) largely determines the quality of the output (for some introduction you may look up chapter 3.1 in Ullsperger & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just by a different preprocessing ICA output could vary between crap and excellent unmixing. Thus a poor ICA eye blink attenuation would make me a bit suspicious...
> 
> Best,
> Stefan
> 
> 
> Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman:
>> 
>> And for a related perspective, see 
>> 
>> McMenamin, B. W., Shackman, A. J., Greischar, L. L. & Davidson, R. J. (2011). Electromyogenic artifacts and electroencephalographic inferences revisited, Neuroimage, 54, 4-9. 
>> 
>> http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf
>> 
>> 
>> On Mon, May 23, 2011 at 8:07 PM, Joseph Dien <jdien07 at mac.com> wrote:
>> I agree with David's reasoning.  You may find the following article to be of help as well in understanding the issues involved:
>> 
>> Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763.
>> 
>> Cheers!
>> 
>> Joe
>> 
>> On May 23, 2011, at 11:57 AM, David Groppe wrote:
>> 
>>> Hi Odelia,
>>>   When you use ICA (or any other spatial filter) to correct for EEG
>>> artifacts, you're going to distort your data some by removing true EEG
>>> activity in addition to the artifact (for an explanation, see:
>>> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf).
>>> So to minimize distortion, it would be better not to apply ICA
>>> artifact correction to artifact-free data.  However, if the frequency
>>> of the artifact differs across experimental conditions, it could
>>> confound your analysis.  For example, I suspect people blink more
>>> often to targets in an oddball experiment than standards.  Thus if you
>>> apply ICA only to blinky trials, you could find a difference between
>>> the EEG response to standards and targets that simply reflects the
>>> fact ICA removed more EEG activity in the target trials (i.e., it
>>> wouldn't reflect a true difference in neural processing).
>>>      hope this helps,
>>>         -David
>>> 
>>> On Mon, May 23, 2011 at 1:44 AM, odelia nakar <odidodi at hotmail.com> wrote:
>>>> Hi all,
>>>> 
>>>> I'm troubled by the fact that when I use ICA for blinks\eyes movements
>>>> removal, I remove the relevant components also from trials that do not
>>>> contain blinks\eyes movements. In order to avoid this bias we thought to
>>>> combine the data before ICA ("data" structure) with the data after ICA
>>>> ("dataica" structure), only in specific trials, as follows:
>>>> 
>>>> datall=dataica;
>>>> datall.trial=data.trial;
>>>> datall.time=data.time;
>>>> blinks=[2 4 5 8 bla bla 156];
>>>> for ind=1:length(blinks)
>>>>      datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)};
>>>> end
>>>> 
>>>> To my first question: I just wanted to check that there is no problem with
>>>> that, or any reason not to use it.
>>>> 
>>>> Another issue- I use motor learning task, and I'm trying to understand what
>>>> happens through the process, in terms of power-frequency changes through the
>>>> process. How would you recommend that I'd use the ft_freqanalysis function?
>>>> What method to use (or what do I need to consider when choosing the method
>>>> field)?
>>>> 
>>>> 
>>>> Thanks a lot,
>>>> Odelia.
>>>> 
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>> 
>>> 
>>> 
>>> 
>>> -- 
>>> David Groppe, Ph.D.
>>> Postdoctoral Researcher
>>> Kutaslab
>>> Dept. of Cognitive Science
>>> University of California, San Diego
>>> http://www.cogsci.ucsd.edu/~dgroppe/
>>> 
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> 
>> 
>> --------------------------------------------------------------------------------
>> 
>> Joseph Dien
>> E-mail: jdien07 at mac.com
>> Phone: 301-226-8848
>> Fax: 301-226-8811
>> http://homepage.mac.com/jdien07/
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> 
>> 
>> 
>> 
>> -- 
>> Alexander J. Shackman, Ph.D.
>> Wisconsin Psychiatric Institute & Clinics and
>> Department of Psychology
>> University of Wisconsin-Madison
>> 1202 West Johnson Street
>> Madison, Wisconsin 53706
>> 
>> Telephone: +1 (608) 358-5025
>> Fax: +1 (608) 265-2875
>> Email: shackman at wisc.edu
>> http://psyphz.psych.wisc.edu/~shackman
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> -- 
> Prof. Dr. Stefan Debener
> Neuropsychology	Lab
> Department of Psychology
> University of Oldenburg
> D-26111 Oldenburg
> Germany
> 
> Office: A7 0-038
> Phone: +49-441-798-4271
> Fax:   +49-441-798-5522
> Email: stefan.debener at uni-oldenburg.de
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip










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From yuvharpaz at gmail.com  Fri May 27 05:40:14 2011
From: yuvharpaz at gmail.com (Yuval Harpaz)
Date: Fri, 27 May 2011 06:40:14 +0300
Subject: [FieldTrip] ICA+frqanalysis questions
In-Reply-To: <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com>
References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>
	<543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>
	<BAY162-w15103E26B01D0271AD3F6EAB720@phx.gbl>
	<BANLkTi=YxtpPqFfvORYKmO-23o8zp-Tc3w@mail.gmail.com>
	<09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com>
	<BANLkTikHLHhjes_pF_5wdrF6QjNna3T_Mg@mail.gmail.com>
	<4DDB5A14.3090102@uni-oldenburg.de>
	<34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com>
Message-ID: <BANLkTimvN1B16bHZC=-QxZUNG5b_kF-uGw@mail.gmail.com>

Dear discussion group
Did anybody consider smoothing or filtering the component trace before
rejecting it?
it seems that the added noise to no-blink trials is in a frequency higher
than that typical to blinks. what if we evaluate the component weight,
creating a trace for the eyeblink component for every trial, then bandpass
filter the blink trace , say 0.1-25Hz, and only then remove the component
from the data?
yuval

On 27 May 2011 06:16, Joseph Dien <jdien07 at mac.com> wrote:

> Stefan, just to be clear, I don't think any of us were saying not to use
> ICA to correct blinks.  David was just saying that there are potential
> concerns when one only applies the ICA to the blink trials rather than to
> all the trials.  I myself use EEGlab's infomax implementation in the
> automatic eyeblink correction tool of my EP Toolkit (
> http://sourceforge.net/projects/erppcatoolkit/).
>
> Now that said, I should add a little more nuance to my response.  One of
> the things I observed (or rather, that Tim Curran pointed out to me) is that
> when you apply ICA to remove eyeblink artifacts in this manner, it can
> actually substantially increase the noise level in the data, so for the
> trials without eyeblinks it can have a considerable cost.  So in order to
> balance the cost/benefit ratio, what I did was to include a trial by trial
> criterion that the putative eyeblink factors would only be removed if doing
> so reduced the overall variance of the trial.  This approach does still have
> some potential for causing the concerns that David raises but not as much as
> only applying the ICA to blink trials since it does end up getting applied
> to non-blink trials too.  This does mean that one should be cautious about
> any apparent effects in the artifact corrected data that are centered around
> the eyes (that have a blink topography) but that goes without saying in any
> case.  So anyway, I agree, it's not perfect but seems to be the best
> available option.
>
> Cheers!
>
> Joe
>
> On May 24, 2011, at 3:11 AM, Stefan Debener wrote:
>
>  Hi Odelia,
>
> I have a slightly different opinion here. It is certainly true that any
> filter has the tendency to distort data (with distortion I mean that data
> consists of a mixture of some wanted, true signal and some unwanted signal,
> and that the removal of the unwanted part of the signal is neither complete
> nor specific). In our lab we regularly use ICA for artefact removal (and
> more), and the benefit/gain is clearly are much larger than the distortion.
> In fact there are a number of examples out showing that currently only ICA
> (or related tools) can recover the study of (a substantial fraction of the
> wanted) EEG signal (but again, it is NOT a perfect tool at all), in
> particular in cases where other means of SNR enhancement don't work well
> (averaging, spectral analysis). I am happy to provide references if you are
> interested...
>
> For the evaluation of outcome it would be reasonable to not evaluate the
> ERP alone, as this could be misleading. Better evaluate the sensitivity and
> specificity of an eye blink attentuation approach on the single trial (and
> single subject) level, this will give you good insight. And it is worth
> keeping in mind that the preprocessing of the data (among other issues, like
> the quality of the recording and so on) largely determines the quality of
> the output (for some introduction you may look up chapter 3.1 in Ullsperger
> & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just
> by a different preprocessing ICA output could vary between crap and
> excellent unmixing. Thus a poor ICA eye blink attenuation would make me a
> bit suspicious...
>
> Best,
> Stefan
>
>
> Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman:
>
> And for a related perspective, see
>
> McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. J.
> (2011). Electromyogenic artifacts and electroencephalographic inferences
> revisited, *Neuroimage**, 54*, 4-9.
>
> http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf
>
>
> On Mon, May 23, 2011 at 8:07 PM, Joseph Dien <jdien07 at mac.com> wrote:
>
>>  I agree with David's reasoning.  You may find the following article to
>> be of help as well in understanding the issues involved:
>>
>>  Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of
>> simulated ERPs: Promax versus Infomax rotations. *Human Brain Mapping*,
>> 28(8), 742-763.
>>
>>  Cheers!
>>
>>  Joe
>>
>>  On May 23, 2011, at 11:57 AM, David Groppe wrote:
>>
>>  Hi Odelia,
>>   When you use ICA (or any other spatial filter) to correct for EEG
>> artifacts, you're going to distort your data some by removing true EEG
>> activity in addition to the artifact (for an explanation, see:
>> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf).
>> So to minimize distortion, it would be better not to apply ICA
>> artifact correction to artifact-free data.  However, if the frequency
>> of the artifact differs across experimental conditions, it could
>> confound your analysis.  For example, I suspect people blink more
>> often to targets in an oddball experiment than standards.  Thus if you
>> apply ICA only to blinky trials, you could find a difference between
>> the EEG response to standards and targets that simply reflects the
>> fact ICA removed more EEG activity in the target trials (i.e., it
>> wouldn't reflect a true difference in neural processing).
>>      hope this helps,
>>         -David
>>
>> On Mon, May 23, 2011 at 1:44 AM, odelia nakar <odidodi at hotmail.com>
>> wrote:
>>
>> Hi all,
>>
>>
>>  I'm troubled by the fact that when I use ICA for blinks\eyes movements
>>
>>  removal, I remove the relevant components also from trials that do not
>>
>> contain blinks\eyes movements. In order to avoid this bias we thought to
>>
>>  combine the data before ICA ("data" structure) with the data after ICA
>>
>> ("dataica" structure), only in specific trials, as follows:
>>
>>
>>  datall=dataica;
>>
>> datall.trial=data.trial;
>>
>> datall.time=data.time;
>>
>>  blinks=[2 4 5 8 bla bla 156];
>>
>> for ind=1:length(blinks)
>>
>>      datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)};
>>
>>  end
>>
>>
>>  To my first question: I just wanted to check that there is no problem
>> with
>>
>> that, or any reason not to use it.
>>
>>
>>  Another issue- I use motor learning task, and I'm trying to understand
>> what
>>
>> happens through the process, in terms of power-frequency changes through
>> the
>>
>> process. How would you recommend that I'd use the ft_freqanalysis
>> function?
>>
>> What method to use (or what do I need to consider when choosing the method
>>
>> field)?
>>
>>
>>
>>  Thanks a lot,
>>
>>  Odelia.
>>
>>
>>  _______________________________________________
>>
>> fieldtrip mailing list
>>
>>  fieldtrip at donders.ru.nl
>>
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>>
>>
>> --
>> David Groppe, Ph.D.
>> Postdoctoral Researcher
>> Kutaslab
>> Dept. of Cognitive Science
>> University of California, San Diego
>> http://www.cogsci.ucsd.edu/~dgroppe/
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>>
>> --------------------------------------------------------------------------------
>>
>>  Joseph Dien
>> E-mail: jdien07 at mac.com
>> Phone: 301-226-8848
>> Fax: 301-226-8811
>> http://homepage.mac.com/jdien07/
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>
>
> --
> Alexander J. Shackman, Ph.D.
> Wisconsin Psychiatric Institute & Clinics and
> Department of Psychology
> University of Wisconsin-Madison
> 1202 West Johnson Street
> Madison, Wisconsin 53706
>
> Telephone: +1 (608) 358-5025
> Fax: +1 (608) 265-2875
> Email: shackman at wisc.edu
> http://psyphz.psych.wisc.edu/~shackman
>
>
> _______________________________________________
> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Prof. Dr. Stefan Debener
> Neuropsychology	Lab
> Department of Psychology
> University of Oldenburg
> D-26111 Oldenburg
> Germany
>
> Office: A7 0-038
> Phone: +49-441-798-4271
> Fax:   +49-441-798-5522
> Email: stefan.debener at uni-oldenburg.de
>
>  _______________________________________________
> 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
>



-- 
Y.Harpaz

a link to the BIU MEG lab:
http://faculty.biu.ac.il/~goldsa/index.html

*"Many were increasingly of the opinion that they'd all made a big mistake
in coming down from the trees in the first place. And some said that even
the trees had been a bad move, and that no one should ever have left the
oceans". Douglas Adams
*
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From mahesh.casiraghi at gmail.com  Fri May 27 06:32:01 2011
From: mahesh.casiraghi at gmail.com (Mahesh Casiraghi)
Date: Fri, 27 May 2011 00:32:01 -0400
Subject: [FieldTrip] ICA+frqanalysis questions
In-Reply-To: <BANLkTimvN1B16bHZC=-QxZUNG5b_kF-uGw@mail.gmail.com>
References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>
	<543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>
	<BAY162-w15103E26B01D0271AD3F6EAB720@phx.gbl>
	<BANLkTi=YxtpPqFfvORYKmO-23o8zp-Tc3w@mail.gmail.com>
	<09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com>
	<BANLkTikHLHhjes_pF_5wdrF6QjNna3T_Mg@mail.gmail.com>
	<4DDB5A14.3090102@uni-oldenburg.de>
	<34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com>
	<BANLkTimvN1B16bHZC=-QxZUNG5b_kF-uGw@mail.gmail.com>
Message-ID: <BANLkTinP3RWz2zBq4dsKt5jundLHcNT1PQ@mail.gmail.com>

Dear Yuval and discussion group,


it seems to me that what you are proposing is getting close to what proposed
by the hybrid approach of regica described here:


*Manousos A. Klados, Christos Papadelis, Christoph Braun, Panagiotis D.
Bamidis, REG-ICA: A hybrid methodology combining Blind Source Separation and
regression techniques for the rejection of ocular artifacts, Biomedical
Signal Processing and Control, In Press, Corrected Proof, Available online
16 March 2011, ISSN 1746-8094, DOI: 10.1016/j.bspc.2011.02.001.*

They suggest to selectively run regression based AR only on those components
which correlate with EOG signals. This makes sense to me and I have been
trying to experiment that on some old data, although with no clear
conclusions yet. It may be worth a try for Odelia: Anybody out there with
some insights for this - or maybe a similar - approach?

Cheers,

Mahesh



Mahesh M. Casiraghi
PhD candidate - Cognitive Sciences
Roberto Dell'Acqua Lab, University of Padova
Pierre Jolicoeur Lab, Univesité de Montréal
mahesh.casiraghi at umontreal.ca

I have the conviction that when Physiology will be far enough advanced, the
poet, the philosopher, and the physiologist will all understand each other.
Claude Bernard




On Thu, May 26, 2011 at 11:40 PM, Yuval Harpaz <yuvharpaz at gmail.com> wrote:

> Dear discussion group
> Did anybody consider smoothing or filtering the component trace before
> rejecting it?
> it seems that the added noise to no-blink trials is in a frequency higher
> than that typical to blinks. what if we evaluate the component weight,
> creating a trace for the eyeblink component for every trial, then bandpass
> filter the blink trace , say 0.1-25Hz, and only then remove the component
> from the data?
> yuval
>
> On 27 May 2011 06:16, Joseph Dien <jdien07 at mac.com> wrote:
>
>> Stefan, just to be clear, I don't think any of us were saying not to use
>> ICA to correct blinks.  David was just saying that there are potential
>> concerns when one only applies the ICA to the blink trials rather than to
>> all the trials.  I myself use EEGlab's infomax implementation in the
>> automatic eyeblink correction tool of my EP Toolkit (
>> http://sourceforge.net/projects/erppcatoolkit/).
>>
>> Now that said, I should add a little more nuance to my response.  One of
>> the things I observed (or rather, that Tim Curran pointed out to me) is that
>> when you apply ICA to remove eyeblink artifacts in this manner, it can
>> actually substantially increase the noise level in the data, so for the
>> trials without eyeblinks it can have a considerable cost.  So in order to
>> balance the cost/benefit ratio, what I did was to include a trial by trial
>> criterion that the putative eyeblink factors would only be removed if doing
>> so reduced the overall variance of the trial.  This approach does still have
>> some potential for causing the concerns that David raises but not as much as
>> only applying the ICA to blink trials since it does end up getting applied
>> to non-blink trials too.  This does mean that one should be cautious about
>> any apparent effects in the artifact corrected data that are centered around
>> the eyes (that have a blink topography) but that goes without saying in any
>> case.  So anyway, I agree, it's not perfect but seems to be the best
>> available option.
>>
>> Cheers!
>>
>> Joe
>>
>> On May 24, 2011, at 3:11 AM, Stefan Debener wrote:
>>
>>  Hi Odelia,
>>
>> I have a slightly different opinion here. It is certainly true that any
>> filter has the tendency to distort data (with distortion I mean that data
>> consists of a mixture of some wanted, true signal and some unwanted signal,
>> and that the removal of the unwanted part of the signal is neither complete
>> nor specific). In our lab we regularly use ICA for artefact removal (and
>> more), and the benefit/gain is clearly are much larger than the distortion.
>> In fact there are a number of examples out showing that currently only ICA
>> (or related tools) can recover the study of (a substantial fraction of the
>> wanted) EEG signal (but again, it is NOT a perfect tool at all), in
>> particular in cases where other means of SNR enhancement don't work well
>> (averaging, spectral analysis). I am happy to provide references if you are
>> interested...
>>
>> For the evaluation of outcome it would be reasonable to not evaluate the
>> ERP alone, as this could be misleading. Better evaluate the sensitivity and
>> specificity of an eye blink attentuation approach on the single trial (and
>> single subject) level, this will give you good insight. And it is worth
>> keeping in mind that the preprocessing of the data (among other issues, like
>> the quality of the recording and so on) largely determines the quality of
>> the output (for some introduction you may look up chapter 3.1 in Ullsperger
>> & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just
>> by a different preprocessing ICA output could vary between crap and
>> excellent unmixing. Thus a poor ICA eye blink attenuation would make me a
>> bit suspicious...
>>
>> Best,
>> Stefan
>>
>>
>> Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman:
>>
>> And for a related perspective, see
>>
>> McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. J.
>> (2011). Electromyogenic artifacts and electroencephalographic inferences
>> revisited, *Neuroimage**, 54*, 4-9.
>>
>> http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf
>>
>>
>> On Mon, May 23, 2011 at 8:07 PM, Joseph Dien <jdien07 at mac.com> wrote:
>>
>>>  I agree with David's reasoning.  You may find the following article to
>>> be of help as well in understanding the issues involved:
>>>
>>>  Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA
>>> of simulated ERPs: Promax versus Infomax rotations. *Human Brain Mapping
>>> *, 28(8), 742-763.
>>>
>>>  Cheers!
>>>
>>>  Joe
>>>
>>>  On May 23, 2011, at 11:57 AM, David Groppe wrote:
>>>
>>>  Hi Odelia,
>>>   When you use ICA (or any other spatial filter) to correct for EEG
>>> artifacts, you're going to distort your data some by removing true EEG
>>> activity in addition to the artifact (for an explanation, see:
>>> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf).
>>> So to minimize distortion, it would be better not to apply ICA
>>> artifact correction to artifact-free data.  However, if the frequency
>>> of the artifact differs across experimental conditions, it could
>>> confound your analysis.  For example, I suspect people blink more
>>> often to targets in an oddball experiment than standards.  Thus if you
>>> apply ICA only to blinky trials, you could find a difference between
>>> the EEG response to standards and targets that simply reflects the
>>> fact ICA removed more EEG activity in the target trials (i.e., it
>>> wouldn't reflect a true difference in neural processing).
>>>      hope this helps,
>>>         -David
>>>
>>> On Mon, May 23, 2011 at 1:44 AM, odelia nakar <odidodi at hotmail.com>
>>> wrote:
>>>
>>> Hi all,
>>>
>>>
>>>  I'm troubled by the fact that when I use ICA for blinks\eyes movements
>>>
>>>  removal, I remove the relevant components also from trials that do not
>>>
>>> contain blinks\eyes movements. In order to avoid this bias we thought to
>>>
>>>  combine the data before ICA ("data" structure) with the data after ICA
>>>
>>> ("dataica" structure), only in specific trials, as follows:
>>>
>>>
>>>  datall=dataica;
>>>
>>> datall.trial=data.trial;
>>>
>>> datall.time=data.time;
>>>
>>>  blinks=[2 4 5 8 bla bla 156];
>>>
>>> for ind=1:length(blinks)
>>>
>>>      datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)};
>>>
>>>  end
>>>
>>>
>>>  To my first question: I just wanted to check that there is no problem
>>> with
>>>
>>> that, or any reason not to use it.
>>>
>>>
>>>  Another issue- I use motor learning task, and I'm trying to understand
>>> what
>>>
>>> happens through the process, in terms of power-frequency changes through
>>> the
>>>
>>> process. How would you recommend that I'd use the ft_freqanalysis
>>> function?
>>>
>>> What method to use (or what do I need to consider when choosing the
>>> method
>>>
>>> field)?
>>>
>>>
>>>
>>>  Thanks a lot,
>>>
>>>  Odelia.
>>>
>>>
>>>  _______________________________________________
>>>
>>> fieldtrip mailing list
>>>
>>>  fieldtrip at donders.ru.nl
>>>
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>>
>>>
>>>
>>> --
>>> David Groppe, Ph.D.
>>> Postdoctoral Researcher
>>> Kutaslab
>>> Dept. of Cognitive Science
>>> University of California, San Diego
>>> http://www.cogsci.ucsd.edu/~dgroppe/
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>>
>>>
>>> --------------------------------------------------------------------------------
>>>
>>>  Joseph Dien
>>> E-mail: jdien07 at mac.com
>>> Phone: 301-226-8848
>>> Fax: 301-226-8811
>>> http://homepage.mac.com/jdien07/
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>
>>
>> --
>> Alexander J. Shackman, Ph.D.
>> Wisconsin Psychiatric Institute & Clinics and
>> Department of Psychology
>> University of Wisconsin-Madison
>> 1202 West Johnson Street
>> Madison, Wisconsin 53706
>>
>> Telephone: +1 (608) 358-5025
>> Fax: +1 (608) 265-2875
>> Email: shackman at wisc.edu
>> http://psyphz.psych.wisc.edu/~shackman
>>
>>
>> _______________________________________________
>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> --
>> Prof. Dr. Stefan Debener
>> Neuropsychology	Lab
>> Department of Psychology
>> University of Oldenburg
>> D-26111 Oldenburg
>> Germany
>>
>> Office: A7 0-038
>> Phone: +49-441-798-4271
>> Fax:   +49-441-798-5522
>> Email: stefan.debener at uni-oldenburg.de
>>
>>  _______________________________________________
>> 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
>>
>
>
>
> --
> Y.Harpaz
>
> a link to the BIU MEG lab:
> http://faculty.biu.ac.il/~goldsa/index.html
>
> *"Many were increasingly of the opinion that they'd all made a big mistake
> in coming down from the trees in the first place. And some said that even
> the trees had been a bad move, and that no one should ever have left the
> oceans". Douglas Adams
> *
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From jan.schoffelen at donders.ru.nl  Fri May 27 08:19:02 2011
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Fri, 27 May 2011 08:19:02 +0200
Subject: [FieldTrip] duplicate spm directories
In-Reply-To: <BANLkTinHBVGCGpvRDpAMusbhQF+nLvFY3Q@mail.gmail.com>
References: <BANLkTinHBVGCGpvRDpAMusbhQF+nLvFY3Q@mail.gmail.com>
Message-ID: <6BA914CC-EDD4-4D85-BC49-B790FD08447E@donders.ru.nl>

Dear David,

Yes, you can safely remove the spm2 directory. Unless you rely in your  
analysis pipeline on spm2-specific stuff. The only thing I can think  
of here would be to read in .mnc files.

Cheers,

Jan-Mathijs


On May 27, 2011, at 3:54 AM, David Groppe wrote:

> Hi again,
>   I'm running the March 28th version of Fieldtrip and am getting the
> following warning:
>
> Warning: multiple versions of SPM on your path will confuse FieldTrip
>> In fieldtrip-20110328/private/warning_once at 75
>  In ft_defaults at 45
>  In ft_preprocessing at 179
> Warning: one version of SPM is found here:
> /Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm2/spm.m
>> In ft_defaults at 48
>  In ft_preprocessing at 179
> Warning: one version of SPM is found here:
> /Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm8/spm.m
>
>
> Can I simply remove the spm2 directory?
>      thanks in advance,
>            -D
>
> -- 
> David Groppe, Ph.D.
> Postdoctoral Researcher
> Kutaslab
> Dept. of Cognitive Science
> University of California, San Diego
> http://www.cogsci.ucsd.edu/~dgroppe/
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793



From akademonbrain at gmail.com  Fri May 27 10:43:11 2011
From: akademonbrain at gmail.com (Aka Demon)
Date: Fri, 27 May 2011 11:43:11 +0300
Subject: [FieldTrip] influences between the regions
In-Reply-To: <BANLkTinCqZgQzxQBuAjap5KM4jJ6MnCcEQ@mail.gmail.com>
References: <BANLkTinCqZgQzxQBuAjap5KM4jJ6MnCcEQ@mail.gmail.com>
Message-ID: <BANLkTimvqmmSXt6Tv83nNsZxTZXQ9Fx6LA@mail.gmail.com>

Dear experts

After analyzing memory experiment EEG/MEG and source localization data, i
figured out that there is little I can say about the interactions between
the activated regions as I don’t have any information about the connection
between the activated areas.

So I was wondering if there are some useful works/tools that I can use to
explorer the influences between the regions (such as information transfer
from one region to the other).

Thanks a lot

Aka
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From drivolta81 at gmail.com  Fri May 27 14:26:28 2011
From: drivolta81 at gmail.com (Davide Rivolta)
Date: Fri, 27 May 2011 14:26:28 +0200
Subject: [FieldTrip] tutorial - ft_volumenormalise
Message-ID: <BANLkTinqaX3UJKw9zmMqTG9NZR69RqM7jg@mail.gmail.com>

Dear Fieldtrippers,

I am running the tutorial on how to localize oscillatory sources using
beamformer techniques.


 It works smooth until I have to normalize the anatomical mri to the
template.

When, after I load the already-segmented subject file, I run
ft_volumenormalise it says the following:

??? Attempted to access V.dim(4); index out of bounds because
numel(V.dim)=3.


Error in ==> spm_create_vol>create_vol at 94
 swapped = spm_type(V.dim(4),'swapped');



 Interestingly this is the same error I get when I try to run
ft_volumesegment both using the tutorial and my anatomical MRIs.

Has someone any idea? Am I doing something silly?

Thank you so much,

Davide
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From rapela at ucsd.edu  Sat May 28 01:13:43 2011
From: rapela at ucsd.edu (=?iso-8859-1?Q?Joaqu=EDn_Rapela?=)
Date: Fri, 27 May 2011 16:13:43 -0700 (PDT)
Subject: [FieldTrip] lead field without with no MRI
Message-ID: <60859.137.110.244.8.1306538023.squirrel@acs-webmail.ucsd.edu>

Dear all,

I want to compute a lead field matrix but I have no MRI scan of my
subjects. I would be happy with a concentric spheres model, or similar,
adjusted to the electrodes locations (modified 10 20 system). I would be
very grateful if somebody directs me to the appropriate functions in
FieldTrip. My apologizes if this is a naive question. I am new to
FieldTrip.

Thanks in advance, Joaquin

-- 
Joaquin Rapela, PhD
Swartz Center for Computational Neuroscience
University of California San Diego
9500 Gilman Drive,
San Diego, CA 92093-0559
tel/fax: (858) 822-7536
http://www-scf.usc.edu/~rapela
----------------------------------

There are men who struggle for a day and they are good.
There are men who struggle for a year and they are better.
There are men who struggle many years, and they are better still.
But there are those who struggle all their lives:
These are the indispensable ones.

                                                                                   Bertolt
Brecht



From michael.wibral at web.de  Sun May 29 09:26:47 2011
From: michael.wibral at web.de (Michael Wibral)
Date: Sun, 29 May 2011 09:26:47 +0200 (CEST)
Subject: [FieldTrip] influences between the regions
Message-ID: <1324085935.896862.1306654007541.JavaMail.fmail@mwmweb084>

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From rapela at ucsd.edu  Sun May 29 21:38:50 2011
From: rapela at ucsd.edu (=?iso-8859-1?Q?Joaqu=EDn_Rapela?=)
Date: Sun, 29 May 2011 12:38:50 -0700 (PDT)
Subject: [FieldTrip] lead field with no MRI
In-Reply-To: <60859.137.110.244.8.1306538023.squirrel@acs-webmail.ucsd.edu>
References: <60859.137.110.244.8.1306538023.squirrel@acs-webmail.ucsd.edu>
Message-ID: <46100.137.110.37.196.1306697930.squirrel@acs-webmail.ucsd.edu>

Below I describe how to compute the leadfield matrix adjusted to a set of
electrodes in an extended 10-20 system, without having an MRI image.

Besides, I have a question: why in the help of the fieldtrip functions
their output is not described?

Cordially, Joaquin

I had to dig into the EEGLAB Dipfit plugin to learn how to do this. I used
the function ft_prepare_leadfield. It requires a head model and the
channel locations. Since I have an extended 10-20 electrode system, I used
a BEM head model that comes with Dipfit, and also uses an extended 10-20
system. This head model is in the plugins directory of dipfit2.2:

hdmFile=/usr/local/eeglab/plugins/dipfit2.2/standard_BEM/standard_vol.mat

and the channel locations for this head model are also in the dipfit2.2
directory:

hmChanfile=/usr/local/eeglab/plugins/dipfit2.2/standard_BEM/elec/standard_1005.elc

It turns out that the previous head model is not ready for
ft_prepare_leadfield,  and I had to use the function ft_prepare_vol_sens
to prepare it. Also, I wanted to compute the leadfield matrix only for the
channels in my data set, whose labels are in the variable dsChanlabels, so
I passed dsChanlabels as the argument 'channel' of ft_prepare_vol_sens.

Finally, I used the head model and sensors prepared by ft_prepare_vol_sens
as input to ft_prepare_headmodel. I append the code that does the job. If
you see any bug, please let me know.

Warmly, Joaquin

###
function grid = joacosPrepareLeadfield(dsChanlabels, hmChanfile, hdmFile)

    cfg = [];
    vol = ft_read_vol(hdmFile);
    sens = ft_read_sens(hmChanfile);

    [vol, sens] = ft_prepare_vol_sens(vol, sens, 'channel', dsChanlabels);

    cfg            = [];
    cfg.elec       = sens;
    cfg.vol        = vol;
    cfg.grid.resolution = 20;

    data = [];

    grid = ft_prepare_leadfield(cfg, data);
###

> Dear all,
>
> I want to compute a lead field matrix but I have no MRI scan of my
> subjects. I would be happy with a concentric spheres model, or similar,
> adjusted to the electrodes locations (modified 10 20 system). I would be
> very grateful if somebody directs me to the appropriate functions in
> FieldTrip. My apologizes if this is a naive question. I am new to
> FieldTrip.
>
> Thanks in advance, Joaquin
>
> --
> Joaquin Rapela, PhD
> Swartz Center for Computational Neuroscience
> University of California San Diego
> 9500 Gilman Drive,
> San Diego, CA 92093-0559
> tel/fax: (858) 822-7536
> http://www-scf.usc.edu/~rapela
> ----------------------------------
>
> There are men who struggle for a day and they are good.
> There are men who struggle for a year and they are better.
> There are men who struggle many years, and they are better still.
> But there are those who struggle all their lives:
> These are the indispensable ones.
>
>                                                                                    Bertolt
> Brecht
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>


-- 
Joaquin Rapela, PhD
Swartz Center for Computational Neuroscience
University of California San Diego
9500 Gilman Drive,
San Diego, CA 92093-0559
tel/fax: (858) 822-7536
http://www-scf.usc.edu/~rapela
----------------------------------

There are men who struggle for a day and they are good.
There are men who struggle for a year and they are better.
There are men who struggle many years, and they are better still.
But there are those who struggle all their lives:
These are the indispensable ones.

                                                                                   Bertolt
Brecht



From Elena.Orekhova at neuro.gu.se  Mon May 30 13:08:29 2011
From: Elena.Orekhova at neuro.gu.se (Elena Orekhova)
Date: Mon, 30 May 2011 11:08:29 +0000
Subject: [FieldTrip] SAM beamformeing on Neuromag data
Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA679@exchccr1.neuro.gu.se>

Dear All,
I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions.

1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data?   It yes, how to  normalize?


2. I would like to do SAM analysis  of evoked field and look at the time courses at ROIs
(virtual channels).  The only tutorial example I have found was for the lcmv-beamformer
(cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure
which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'.



I would be most grateful for any example script of this type analysis!



Regards,

Elena

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From michael.wibral at web.de  Mon May 30 14:08:08 2011
From: michael.wibral at web.de (Michael Wibral)
Date: Mon, 30 May 2011 14:08:08 +0200 (CEST)
Subject: [FieldTrip] SAM beamformeing on Neuromag data
Message-ID: <1443619351.1500061.1306757288215.JavaMail.fmail@mwmweb072>

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From Elena.Orekhova at neuro.gu.se  Mon May 30 16:30:34 2011
From: Elena.Orekhova at neuro.gu.se (Elena Orekhova)
Date: Mon, 30 May 2011 14:30:34 +0000
Subject: [FieldTrip] SAM beamforming on Neuromag data
Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA6D6@exchccr1.neuro.gu.se>

Thank you for this.

I have more concerns.  I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results.
Is it safe to do beamforming with MaxFiltered data?

Elena

________________________________
From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de]
Sent: Monday, May 30, 2011 2:08 PM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data

Hi Elena,

as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed.

There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise:
In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best.
I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..)

What you could do as a first step is to beam separately and compare the results.

Michael


________________________________
Von: "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
Gesendet: May 30, 2011 1:08:29 PM
An: "fieldtrip at donders.ru.nl" <fieldtrip at donders.ru.nl>
Betreff: [FieldTrip] SAM beamformeing on Neuromag data

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Dear All,
I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions.

1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data?   It yes, how to  normalize?


2. I would like to do SAM analysis  of evoked field and look at the time courses at ROIs  (virtual channels).  The only tutorial example I have found was for the lcmv-beamformer
(cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure
which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'.




I would be most grateful for any example script of this type analysis!



Regards,

Elena

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From tobiasnavarroschroeder at googlemail.com  Mon May 30 17:58:32 2011
From: tobiasnavarroschroeder at googlemail.com (Tobias Navarro Schroeder)
Date: Mon, 30 May 2011 17:58:32 +0200
Subject: [FieldTrip] Beamforming on resting state data
In-Reply-To: <BANLkTi=hF3XzG-COK0E9SfviYnZxRLkHgA@mail.gmail.com>
References: <BANLkTi=hF3XzG-COK0E9SfviYnZxRLkHgA@mail.gmail.com>
Message-ID: <BANLkTimoY1F-WD2NP8_1C+7=c+w0cQV7NQ@mail.gmail.com>

Hi Fieldtrippers,

I performed DICS beamforming on resting-state data (i.e. no task, no
baseline, eyes closed) of a clinical population and controls.
According to the sensor data the patients have more gamma-band (60-90
Hz) activity over temporal areas (somewhat spread-out).
Curiously, after beamforming and group comparisons with 'indepsamplesT'
permutation statistics the difference map shows more gamma-band (60-90
Hz) activity for controls in the left, middle-temporal gyrus.
Hence, the source-level results are opposite to the sensor-level results
(although more spatially confined). This is *not* a problem of the design
matrix, or confusing the groups.

Question 1: Does anybody have experience with opposite results on source and
sensor level?

The individual raw beamforming results (interpolated on the subjects' MRIs)
look suspicios as well. Due to the 'unit gain constraint' there should be an
overestimation of power in the center of the head, but only a minority of
subjects show that. Often I see temporal or parietal activity.

Question 2:

Would a lack of a blob in the center of the head in individual,
raw, beamforming data indicate an erroneous source analysis?

Thanks a lot for help and suggestions.

Best, Tobias Navarro Schröder

ps: The configurations for calculating the covariance and the beamforming is
added below:


1) % Compute the covariance matrices

cfg.output =
'powandcsd';

cfg.foi = 75;

cfg.foilim = [75 75];

cfg.tapsmofrq = 15; % 75 +- 15 = 60 - 90 Hz

cfg.pad =
'maxperlen'; % default

cfg.method =
'wltconvol'; % wavelet analysis

cfg.width = 5;
% Width of the wavelet. Determines the temporal and spectral resolution of
the analysis constant.



2) % Perform the actual beamforming

% load grids of MRI volume

fullnameGrid = [ CurSubject.mripath CurSubject.MRIModel];

cfg = load(fullnameGrid);

cfg.vol = cfg.hdm;

 cfg.frequency = 75;

cfg.method =
'dics';

cfg.keepfilter =
'yes'; % keep the beamformer filters (virtual electrodes) for later use

cfg.keeptrial =
'no';

cfg.keepmom =
'yes'; % useful for connectivity calculations. Dipole moments..

cfg.projectmom =
'yes';

cfg.projectnoise =
'yes';

cfg.latency = 1;
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From michael.wibral at web.de  Mon May 30 17:58:47 2011
From: michael.wibral at web.de (Michael Wibral)
Date: Mon, 30 May 2011 17:58:47 +0200 (CEST)
Subject: [FieldTrip] SAM beamforming on Neuromag data
Message-ID: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072>

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From Tim.Bardouille at nrc-cnrc.gc.ca  Mon May 30 18:23:22 2011
From: Tim.Bardouille at nrc-cnrc.gc.ca (Bardouille, Tim)
Date: Mon, 30 May 2011 12:23:22 -0400
Subject: [FieldTrip] SAM beamforming on Neuromag data
In-Reply-To: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072>
References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072>
Message-ID: <AF07BA1AFA000448A60FB8EBAAE338E796BBDD7F@NRCCENMB2.nrc.ca>

Hi Michael, Elena,

If it becomes a sticking point, you could also run MaxFilter with the -nosss option. I don't have any experience with how this would affect the beamformer output, but it would at least resolve the rank issue.

Tim.

---------------------------------------------------------
Timothy Bardouille, PhD, Research Officer
Laboratory for Clinical MEG
NRC Institute for Biodiagnostics (Atlantic)
Office: Halifax Infirmary
3900 - 1796 Summer Street
Halifax, Nova Scotia B3H 3A7
Phone: 902-473-1865
Lab: 902-470-3936
Fax: 902-473-1851
---------------------------------------------------------
________________________________
From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Michael Wibral [michael.wibral at web.de]
Sent: May 30, 2011 12:58 PM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] SAM beamforming on Neuromag data


Hi Elena,

as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update.
If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this.
(Note: If someone who reads this is of a different opinion, please let me know!)


Michael

________________________________
Von: "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
Gesendet: May 30, 2011 4:30:34 PM
An: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data

Thank you for this.

I have more concerns.  I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results.
Is it safe to do beamforming with MaxFiltered data?

Elena

________________________________
From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de]
Sent: Monday, May 30, 2011 2:08 PM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data


Hi Elena,

as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed.

There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise:
In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best.
I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..)

What you could do as a first step is to beam separately and compare the results.

Michael


________________________________
Von: "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
Gesendet: May 30, 2011 1:08:29 PM
An: "fieldtrip at donders.ru.nl" <fieldtrip at donders.ru.nl>
Betreff: [FieldTrip] SAM beamformeing on Neuromag data

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Dear All,
I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions.

1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data?   It yes, how to  normalize?


2. I would like to do SAM analysis  of evoked field and look at the time courses at ROIs  (virtual channels).  The only tutorial example I have found was for the lcmv-beamformer
(cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure
which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'.





I would be most grateful for any example script of this type analysis!



Regards,

Elena

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From smoratti at psi.ucm.es  Mon May 30 21:27:13 2011
From: smoratti at psi.ucm.es (Stephan Moratti)
Date: Mon, 30 May 2011 21:27:13 +0200
Subject: [FieldTrip] SAM beamforming on Neuromag data
In-Reply-To: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072>
References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072>
Message-ID: <985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es>

Hi Michael,

Thanks for your comments! We have just started with a Neuromag system  
in Madrid and we ran into the same questions. Thanks for posting your  
comments. Could you tell me where I can find the Neuromag discussion  
list, please?

Best,

Stephan

El 30/05/2011, a las 17:58, Michael Wibral escribió:

>
> Hi Elena,
>
> as far as I can see from the neuromeg discussion list and the  
> maxfilter papers the properties of the components removed by the  
> maxfilter do not require a leadfield update.
> If you run into rank-deficiency issue with the covariance matrix a  
> tiny amount of regularization should fix this.
> (Note: If someone who reads this is of a different opinion, please  
> let me know!)
>
>
> Michael
>
> Von: "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
> Gesendet: May 30, 2011 4:30:34 PM
> An: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl 
> >
> Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data
>
> Thank you for this.
>
> I have more concerns.  I applied MaxFilter to the data. Since  
> MaxFilter reduces the rank of the covariance matrix by removing  
> noisy components, it may influence the beamformer results.
> Is it safe to do beamforming with MaxFiltered data?
>
> Elena
>
> From: fieldtrip-bounces at donders.ru.nl [fieldtrip- 
> bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de 
> ]
> Sent: Monday, May 30, 2011 2:08 PM
> To: Email discussion list for the FieldTrip project
> Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data
>
>
> Hi Elena,
>
> as far as I know, the leadfield computation should be aware of the  
> different UNITS (not only scales) of gradiometers and magnetometers.  
> There was a problem with the sign of the leadfields but that should  
> have been fixed.
>
> There is one more fundamental problem however, that you should be  
> aware of (doesn't invalidate your source analysis but bears  
> potential for fine-tuning), which is the projection of noise:
> In beamforming the unit gain constraint guarantees that you get your  
> source signal back with unit gain. Added on top however is  
> neurophysiological crosstalk (minimized) and sensor noise of the  
> sensors with the largest weights in your Beamformer (not reducible).  
> So different sensor types willhave different (inverse) leadfield  
> strengths, theerfore also fiofefrent source noise levels. the  
> relative benefits of each sensor type changes from location to  
> location, so a location (and data) dependend weighting would in  
> principle be best.
> I am not sure if and how this is implemented if FT (Bayesian  
> weighting would be optimal here..)
>
> What you could do as a first step is to beam separately and compare  
> the results.
>
> Michael
>
>
> Von: "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
> Gesendet: May 30, 2011 1:08:29 PM
> An: "fieldtrip at donders.ru.nl" <fieldtrip at donders.ru.nl>
> Betreff: [FieldTrip] SAM beamformeing on Neuromag data
>
> @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face  
> { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font- 
> family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal  
> { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family:  
> Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font- 
> family: Courier; }span.HTMLPreformattedChar { font-family:  
> Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1  
> { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E  
> \671D "; }@font-face { font-family: "Cambria Math"; }@font-face  
> { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal  
> { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family:  
> Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font- 
> family: Courier; }span.HTMLPreformattedChar { font-family:  
> Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1  
> { page: WordSection1; }
> Dear All,
>
> I try to run beamformer analysis on the auditory MEG data (Neuromag)  
> and have basic questions.
>
>
> 1.Magnetometers and gradiometers Neuromag sensors have different  
> scales. Does the Fieldtrip take care of this difference or should I  
> normalize the data?   It yes, how to  normalize?
>
>
> 2. I would like to do SAM analysis  of evoked field and look at the  
> time courses at ROIs  (virtual channels).  The only tutorial example  
> I have found was for the lcmv-beamformer
> (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer) 
> . I am not sure
> which parameters should I specify in ft_sourceanalysis if cfg.method  
> = 'sam'.
>
>
> I would be most grateful for any example script of this type analysis!
>
> Regards,
> Elena
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


________________________________________________________
Stephan Moratti, PhD

see also: http://web.me.com/smoratti/

Department of Basic Psychology
Universidad Complutense de Madrid

Centro de Tecnología Biomédica CBT,
Universidad Politécnica de Madrid,

en la actualidad (currently at) en el
Centro de Magnetoencefalografía Dr. Perez Modrego,
Universidad Complutense de Madrid,
Faculdad de Medicina,
Pabellón 8,
Avda. Complutense, s/n,
28040 Madrid,
Spain,

email: smoratti at psi.ucm.es
Tel.:    +34 91 394 2186
Fax.:   +34 91 394 2294

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From jstout211 at yahoo.com  Mon May 30 23:28:16 2011
From: jstout211 at yahoo.com (Jeff Stout)
Date: Mon, 30 May 2011 14:28:16 -0700 (PDT)
Subject: [FieldTrip] MEGRealign channel
Message-ID: <365289.7941.qm@web113516.mail.gq1.yahoo.com>

Hi All,
I am having trouble using the ft_megrealign command with a 4D Magnes 3600 system.  I am trying to use this command to interpolate bad channels that have been removed in preprocessing.  When I view the output of megrealign using ft_plot_sens, sensor 'A229' is badly misplaced (approximately 10 cm above the top of the sensor array), but all the other sensors appear appropriate.  In the dataset A229 has not been labelled as a bad channel, nor any of its neighboring channels. The location of A229 is significant in that it is the most inferior/anterior channel on the left side.  I am using the original grad file as a template input using ft_read_sens('c,rfDC') and scaling the MEG channels to cm.  I am not sure how helpful the code is - below is my input and some of the output.  I can provide an image if this would be helpful.

temp = ft_read_sens(subjectdata.FA_dataset);
temp.pnt = temp.pnt*100;
temp.unit  = 'cm';

cfg = [];
cfg.inwardshift = 1;
cfg.vol=vol;
cfg.template{1}= temp;
cfg.channel={'MEG'};
con.grad.pnt = con.grad.pnt*100;
con.grad.unit = 'cm';
con = ft_megrealign(cfg, con)

computing surface normals
mean distance towards template gradiometers is 0.00 cm
creating dipole grid based on inward-shifted brain surface from volume conductor model
Warning: the normals of the surface triangulation are inward oriented 
> In fieldtrip-20110507/private/headsurface at 211
  In ft_prepare_sourcemodel at 492
 
 In ft_megrealign at 245
642 dipoles inside, 0 dipoles outside brain
computing forward model for 642 dipoles
pruning 122 from 246, i.e. removing the 122 smallest spatial components
computing interpolation matrix #1
computing interpolation matrix #2
computing interpolation matrix #3
pruning 124 from 248, i.e. removing the 124 smallest spatial components
realigning trial 1
original -> template             RV 14.42 %
original             -> original RV 14.42 %
original -> template -> original RV 14.44 % ....................


Does anyone know why this would be occurring and how to fix it?
Thanks,
Jeff Stout
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From jan.schoffelen at donders.ru.nl  Tue May 31 09:04:26 2011
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Tue, 31 May 2011 09:04:26 +0200
Subject: [FieldTrip] MEGRealign channel
In-Reply-To: <365289.7941.qm@web113516.mail.gq1.yahoo.com>
References: <365289.7941.qm@web113516.mail.gq1.yahoo.com>
Message-ID: <012FDE87-5002-4626-B821-D83AAC043C59@donders.ru.nl>

Hi Jeff,

Thanks for reporting this. We'll look into it as soon as possible.

Best wishes,

Jan-Mathijs


On May 30, 2011, at 11:28 PM, Jeff Stout wrote:

>
> Hi All,
>
> I am having trouble using the ft_megrealign command with a 4D Magnes  
> 3600 system.  I am trying to use this command to interpolate bad  
> channels that have been removed in preprocessing.  When I view the  
> output of megrealign using ft_plot_sens, sensor 'A229' is badly  
> misplaced (approximately 10 cm above the top of the sensor array),  
> but all the other sensors appear appropriate.  In the dataset A229  
> has not been labelled as a bad channel, nor any of its neighboring  
> channels. The location of A229 is significant in that it is the most  
> inferior/anterior channel on the left side.  I am using the original  
> grad file as a template input using ft_read_sens('c,rfDC') and  
> scaling the MEG channels to cm.  I am not sure how helpful the code  
> is - below is my input and some of the output.  I can provide an  
> image if this would be helpful.
>
>
> temp = ft_read_sens(subjectdata.FA_dataset);
> temp.pnt = temp.pnt*100;
> temp.unit  = 'cm';
>
> cfg = [];
> cfg.inwardshift = 1;
> cfg.vol=vol;
> cfg.template{1}= temp;
> cfg.channel={'MEG'};
> con.grad.pnt = con.grad.pnt*100;
> con.grad.unit = 'cm';
> con = ft_megrealign(cfg, con)
>
> computing surface normals
> mean distance towards template gradiometers is 0.00 cm
> creating dipole grid based on inward-shifted brain surface from  
> volume conductor model
> Warning: the normals of the surface triangulation are inward oriented
> > In fieldtrip-20110507/private/headsurface at 211
>   In ft_prepare_sourcemodel at 492
>   In ft_megrealign at 245
> 642 dipoles inside, 0 dipoles outside brain
> computing forward model for 642 dipoles
> pruning 122 from 246, i.e. removing the 122 smallest spatial  
> components
> computing interpolation matrix #1
> computing interpolation matrix #2
> computing interpolation matrix #3
> pruning 124 from 248, i.e. removing the 124 smallest spatial  
> components
> realigning trial 1
> original -> template             RV 14.42 %
> original             -> original RV 14.42 %
> original -> template -> original RV 14.44 % ....................
>
>
> Does anyone know why this would be occurring and how to fix it?
>
> Thanks,
> Jeff Stout
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793

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From Nina.Kahlbrock at uni-duesseldorf.de  Tue May 31 09:23:51 2011
From: Nina.Kahlbrock at uni-duesseldorf.de (Nina Kahlbrock)
Date: Tue, 31 May 2011 09:23:51 +0200
Subject: [FieldTrip] SAM beamforming on Neuromag data
In-Reply-To: <985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es>
References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072>
	<985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es>
Message-ID: <001301cc1f63$b0faedc0$cd136386@VMED.UKD>

Hi Stephan,

 

you can find the discussion list at:

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=NEUROMEG

 

Best,

Nina

 

  _____  

Von: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] Im Auftrag von Stephan Moratti
Gesendet: Montag, 30. Mai 2011 21:27
An: Email discussion list for the FieldTrip project
Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data

 

Hi Michael,

 

Thanks for your comments! We have just started with a Neuromag system in
Madrid and we ran into the same questions. Thanks for posting your comments.
Could you tell me where I can find the Neuromag discussion list, please?

 

Best,

 

Stephan

 

El 30/05/2011, a las 17:58, Michael Wibral escribió:






Hi Elena,

as far as I can see from the neuromeg discussion list and the maxfilter
papers the properties of the components removed by the maxfilter do not
require a leadfield update.
If you run into rank-deficiency issue with the covariance matrix a tiny
amount of regularization should fix this.
(Note: If someone who reads this is of a different opinion, please let me
know!)


Michael

  _____  

Von: "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
Gesendet: May 30, 2011 4:30:34 PM
An: "Email discussion list for the FieldTrip project"
<fieldtrip at donders.ru.nl>
Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data

Thank you for this.

I have more concerns.  I applied MaxFilter to the data. Since MaxFilter
reduces the rank of the covariance matrix by removing noisy components, it
may influence the beamformer results.
Is it safe to do beamforming with MaxFiltered data?

Elena

  _____  

From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on
behalf of Michael Wibral [michael.wibral at web.de]
Sent: Monday, May 30, 2011 2:08 PM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data
 

 

Hi Elena,

as far as I know, the leadfield computation should be aware of the different
UNITS (not only scales) of gradiometers and magnetometers. There was a
problem with the sign of the leadfields but that should have been fixed.

There is one more fundamental problem however, that you should be aware of
(doesn't invalidate your source analysis but bears potential for
fine-tuning), which is the projection of noise:
In beamforming the unit gain constraint guarantees that you get your source
signal back with unit gain. Added on top however is neurophysiological
crosstalk (minimized) and sensor noise of the sensors with the largest
weights in your Beamformer (not reducible). So different sensor types
willhave different (inverse) leadfield strengths, theerfore also fiofefrent
source noise levels. the relative benefits of each sensor type changes from
location to location, so a location (and data) dependend weighting would in
principle be best.
I am not sure if and how this is implemented if FT (Bayesian weighting would
be optimal here..)

What you could do as a first step is to beam separately and compare the
results.

Michael



  _____  

Von: "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
Gesendet: May 30, 2011 1:08:29 PM
An: "fieldtrip at donders.ru.nl" <fieldtrip at donders.ru.nl>
Betreff: [FieldTrip] SAM beamformeing on Neuromag data

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}span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault {
font-family: Cambria; }div.WordSection1 { page: WordSection1; }

Dear All,

I try to run beamformer analysis on the auditory MEG data (Neuromag) and
have basic questions.

 

1.Magnetometers and gradiometers Neuromag sensors have different scales.
Does the Fieldtrip take care of this difference or should I normalize the
data?   It yes, how to  normalize?

 

2. I would like to do SAM analysis  of evoked field and look at the time
courses at ROIs  (virtual channels).  The only tutorial example I have found
was for the lcmv-beamformer 
(cfg.method = 'lcmv';
http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure 
which parameters should I specify in ft_sourceanalysis if cfg.method =
'sam'.   
 
 
I would be most grateful for any example script of this type analysis!
 
Regards, 
Elena

 

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

 


________________________________________________________

Stephan Moratti, PhD

see also: http://web.me.com/smoratti/

Department of Basic Psychology

Universidad Complutense de Madrid

 

Centro de Tecnología Biomédica CBT,
Universidad Politécnica de Madrid,

en la actualidad (currently at) en el
Centro de Magnetoencefalografía Dr. Perez Modrego,
Universidad Complutense de Madrid,
Faculdad de Medicina,
Pabellón 8,
Avda. Complutense, s/n,
28040 Madrid,
Spain,

email: smoratti at psi.ucm.es
Tel.:    +34 91 394 2186
Fax.:   +34 91 394 2294

 

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From smoratti at psi.ucm.es  Tue May 31 11:42:21 2011
From: smoratti at psi.ucm.es (Stephan Moratti)
Date: Tue, 31 May 2011 11:42:21 +0200
Subject: [FieldTrip] SAM beamforming on Neuromag data
In-Reply-To: <001301cc1f63$b0faedc0$cd136386@VMED.UKD>
References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072>
	<985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es>
	<001301cc1f63$b0faedc0$cd136386@VMED.UKD>
Message-ID: <BA177811-9E8B-4B23-8005-6A16528DD17E@psi.ucm.es>

Hallo Nina,

Vielen Dank !!!

Stephan

El 31/05/2011, a las 09:23, Nina Kahlbrock escribió:

> Hi Stephan,
>  
> you can find the discussion list at:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=NEUROMEG
>  
> Best,
> Nina
>  
> Von: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] Im Auftrag von Stephan Moratti
> Gesendet: Montag, 30. Mai 2011 21:27
> An: Email discussion list for the FieldTrip project
> Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data
>  
> Hi Michael,
>  
> Thanks for your comments! We have just started with a Neuromag system in Madrid and we ran into the same questions. Thanks for posting your comments. Could you tell me where I can find the Neuromag discussion list, please?
>  
> Best,
>  
> Stephan
>  
> El 30/05/2011, a las 17:58, Michael Wibral escribió:
> 
> 
> 
> Hi Elena,
> 
> as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update.
> If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this.
> (Note: If someone who reads this is of a different opinion, please let me know!)
> 
> 
> Michael
> 
> Von: "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
> Gesendet: May 30, 2011 4:30:34 PM
> An: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
> Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data
> 
> Thank you for this.
> 
> I have more concerns.  I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results.
> Is it safe to do beamforming with MaxFiltered data?
> 
> Elena
> 
> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de]
> Sent: Monday, May 30, 2011 2:08 PM
> To: Email discussion list for the FieldTrip project
> Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data
>  
>  
> Hi Elena,
> 
> as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed.
> 
> There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise:
> In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best.
> I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..)
> 
> What you could do as a first step is to beam separately and compare the results.
> 
> Michael
> 
> 
> Von: "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
> Gesendet: May 30, 2011 1:08:29 PM
> An: "fieldtrip at donders.ru.nl" <fieldtrip at donders.ru.nl>
> Betreff: [FieldTrip] SAM beamformeing on Neuromag data
> 
> @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }
> Dear All,
> I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions.
>  
> 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data?   It yes, how to  normalize?
>  
> 2. I would like to do SAM analysis  of evoked field and look at the time courses at ROIs  (virtual channels).  The only tutorial example I have found was for the lcmv-beamformer 
> (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure 
> which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'.   
>  
>  
> I would be most grateful for any example script of this type analysis!
>  
> Regards, 
> Elena
>  
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>  
> 
> ________________________________________________________
> Stephan Moratti, PhD
> 
> see also: http://web.me.com/smoratti/
> 
> Department of Basic Psychology
> Universidad Complutense de Madrid
>  
> Centro de Tecnología Biomédica CBT,
> Universidad Politécnica de Madrid,
> 
> en la actualidad (currently at) en el
> Centro de Magnetoencefalografía Dr. Perez Modrego,
> Universidad Complutense de Madrid,
> Faculdad de Medicina,
> Pabellón 8,
> Avda. Complutense, s/n,
> 28040 Madrid,
> Spain,
> 
> email: smoratti at psi.ucm.es
> Tel.:    +34 91 394 2186
> Fax.:   +34 91 394 2294
>  
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


________________________________________________________
Stephan Moratti, PhD

see also: http://web.me.com/smoratti/

Department of Basic Psychology
Universidad Complutense de Madrid

Centro de Tecnología Biomédica CBT,
Universidad Politécnica de Madrid,

en la actualidad (currently at) en el
Centro de Magnetoencefalografía Dr. Perez Modrego,
Universidad Complutense de Madrid,
Faculdad de Medicina,
Pabellón 8,
Avda. Complutense, s/n,
28040 Madrid,
Spain,

email: smoratti at psi.ucm.es
Tel.:    +34 91 394 2186
Fax.:   +34 91 394 2294

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From Elena.Orekhova at neuro.gu.se  Tue May 31 12:06:40 2011
From: Elena.Orekhova at neuro.gu.se (Elena Orekhova)
Date: Tue, 31 May 2011 10:06:40 +0000
Subject: [FieldTrip] SAM beamforming on Neuromag data
In-Reply-To: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072>
References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072>
Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA7E7@exchccr1.neuro.gu.se>

Hi Michael,

> If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this.

What lambda you would recommend?

Elena


________________________________
From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de]
Sent: Monday, May 30, 2011 5:58 PM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] SAM beamforming on Neuromag data


Hi Elena,

as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update.
If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this.
(Note: If someone who reads this is of a different opinion, please let me know!)


Michael

________________________________
Von: "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
Gesendet: May 30, 2011 4:30:34 PM
An: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data

Thank you for this.

I have more concerns.  I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results.
Is it safe to do beamforming with MaxFiltered data?

Elena

________________________________
From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de]
Sent: Monday, May 30, 2011 2:08 PM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data


Hi Elena,

as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed.

There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise:
In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best.
I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..)

What you could do as a first step is to beam separately and compare the results.

Michael


________________________________
Von: "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
Gesendet: May 30, 2011 1:08:29 PM
An: "fieldtrip at donders.ru.nl" <fieldtrip at donders.ru.nl>
Betreff: [FieldTrip] SAM beamformeing on Neuromag data

@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }
Dear All,
I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions.

1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data?   It yes, how to  normalize?


2. I would like to do SAM analysis  of evoked field and look at the time courses at ROIs  (virtual channels).  The only tutorial example I have found was for the lcmv-beamformer
(cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure
which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'.





I would be most grateful for any example script of this type analysis!



Regards,

Elena

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From yuvharpaz at gmail.com  Tue May 31 12:42:53 2011
From: yuvharpaz at gmail.com (Yuval Harpaz)
Date: Tue, 31 May 2011 13:42:53 +0300
Subject: [FieldTrip] SAM beamforming on Neuromag data
In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03ECA7E7@exchccr1.neuro.gu.se>
References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072>
	<32CC77C0C8A7AD4B9410934642608E1F03ECA7E7@exchccr1.neuro.gu.se>
Message-ID: <BANLkTi=nTktweiV3CVPva=gF_85y8zVLow@mail.gmail.com>

Dear Elena and group
it basically depends on how much co-variability there is. if you use a large
frequency range and a large strech of time you need to correct little if
any. if you use averaged data and say from 50 to 120ms from target onset you
need more regularization. I used 5% even for relatively short time interval
(but large freq. range) and found it reasonable.
yuval
On 31 May 2011 13:06, Elena Orekhova <Elena.Orekhova at neuro.gu.se> wrote:

>  Hi Michael,
>
>
> > If you run into rank-deficiency issue with the covariance matrix a tiny
> amount of regularization should fix this.
>
> What lambda you would recommend?
>
> Elena
>
>
>  ------------------------------
> *From:* fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]
> on behalf of Michael Wibral [michael.wibral at web.de]
> *Sent:* Monday, May 30, 2011 5:58 PM
>
> *To:* Email discussion list for the FieldTrip project
> *Subject:* Re: [FieldTrip] SAM beamforming on Neuromag data
>
>
> Hi Elena,
>
> as far as I can see from the neuromeg discussion list and the maxfilter
> papers the properties of the components removed by the maxfilter do not
> require a leadfield update.
> If you run into rank-deficiency issue with the covariance matrix a tiny
> amount of regularization should fix this.
> (Note: If someone who reads this is of a different opinion, please let me
> know!)
>
>
> Michael
>
>  ------------------------------
> *Von:* "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
> *Gesendet:* May 30, 2011 4:30:34 PM
> *An:* "Email discussion list for the FieldTrip project" <
> fieldtrip at donders.ru.nl>
> *Betreff:* Re: [FieldTrip] SAM beamforming on Neuromag data
>
>  Thank you for this.
>
> I have more concerns.  I applied MaxFilter to the data. Since MaxFilter
> reduces the rank of the covariance matrix by removing noisy components, it
> may influence the beamformer results.
> Is it safe to do beamforming with MaxFiltered data?
>
> Elena
>
>  ------------------------------
> *From:* fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]
> on behalf of Michael Wibral [michael.wibral at web.de]
> *Sent:* Monday, May 30, 2011 2:08 PM
> *To:* Email discussion list for the FieldTrip project
> *Subject:* Re: [FieldTrip] SAM beamformeing on Neuromag data
>
>
> Hi Elena,
>
> as far as I know, the leadfield computation should be aware of the
> different UNITS (not only scales) of gradiometers and magnetometers. There
> was a problem with the sign of the leadfields but that should have been
> fixed.
>
> There is one more fundamental problem however, that you should be aware of
> (doesn't invalidate your source analysis but bears potential for
> fine-tuning), which is the projection of noise:
> In beamforming the unit gain constraint guarantees that you get your source
> signal back with unit gain. Added on top however is neurophysiological
> crosstalk (minimized) and sensor noise of the sensors with the largest
> weights in your Beamformer (not reducible). So different sensor types
> willhave different (inverse) leadfield strengths, theerfore also fiofefrent
> source noise levels. the relative benefits of each sensor type changes from
> location to location, so a location (and data) dependend weighting would in
> principle be best.
> I am not sure if and how this is implemented if FT (Bayesian weighting
> would be optimal here..)
>
> What you could do as a first step is to beam separately and compare the
> results.
>
> Michael
>
>
>  ------------------------------
> *Von:* "Elena Orekhova" <Elena.Orekhova at neuro.gu.se>
> *Gesendet:* May 30, 2011 1:08:29 PM
> *An:* "fieldtrip at donders.ru.nl" <fieldtrip at donders.ru.nl>
> *Betreff:* [FieldTrip] SAM beamformeing on Neuromag data
>
>  @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face {
> font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family:
> "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm
> 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm
> 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar
> { font-family: Courier; }.MsoChpDefault { font-family: Cambria;
> }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D
> \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face
> { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal {
> margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre {
> margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier;
> }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault {
> font-family: Cambria; }div.WordSection1 { page: WordSection1; }
>
> Dear All,
>
> I try to run beamformer analysis on the auditory MEG data (Neuromag) and
> have basic questions.
>
>
>
> 1.Magnetometers and gradiometers Neuromag sensors have different scales.
> Does the Fieldtrip take care of this difference or should I normalize the
> data?   It yes, how to  normalize?
>
>
>
> 2. I would like to do SAM analysis  of evoked field and look at the time courses at ROIs  (virtual channels).  The only tutorial example I have found was for the lcmv-beamformer
> (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure
> which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'.
>
>
>
> I would be most grateful for any example script of this type analysis!
>
>
>
> Regards,
>
> Elena
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
sent from my 4-year-old PC. poor fellow, only ipod classic, no mail there.

Y.Harpaz

a link to the BIU MEG lab:
http://faculty.biu.ac.il/~goldsa/index.html

*"Many were increasingly of the opinion that they'd all made a big mistake
in coming down from the trees in the first place. And some said that even
the trees had been a bad move, and that no one should ever have left the
oceans". Douglas Adams
*
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From michael.wibral at web.de  Tue May 31 12:44:50 2011
From: michael.wibral at web.de (Michael Wibral)
Date: Tue, 31 May 2011 12:44:50 +0200 (CEST)
Subject: [FieldTrip] Beamforming on resting state data
Message-ID: <2026821476.1720343.1306838690403.JavaMail.fmail@mwmweb074>

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From tobiasnavarroschroeder at googlemail.com  Tue May 31 14:12:48 2011
From: tobiasnavarroschroeder at googlemail.com (Tobias Navarro Schroeder)
Date: Tue, 31 May 2011 14:12:48 +0200
Subject: [FieldTrip] Beamforming on resting state data
In-Reply-To: <2026821476.1720343.1306838690403.JavaMail.fmail@mwmweb074>
References: <2026821476.1720343.1306838690403.JavaMail.fmail@mwmweb074>
Message-ID: <BANLkTikoNmrH4Mb-WwFOJs+b8eGW19+HUg@mail.gmail.com>

Hi Michael,

thanks a lot for that suggestion.
The gamma activity at the sensor level might indeed be of muscular origin
and this would explain why it doesn't show up inside the head.
Even after automatic & manual artifact rejection the patients were left with
more gamma activity. To my 'untrained eye' the sensor topographies suggested
that the activity would come from the brain. It didn't extend to the
boundaries of the Topoplot, at least in the 60-90 Hz range. However, this
was the case for other parts of the gamma-band.

Greetings, Tobias


On Tue, May 31, 2011 at 12:44 PM, Michael Wibral <michael.wibral at web.de>wrote:

> Hi Tobias,
>
> it could be that the temporal activity at the sensor level is of muscular
> origin. Given all runs well in beamforming you shouldn't see too much of
> that insode the head - have you considered this possibility?
>
> Michael
>
>
>
>  ------------------------------
> *Von:* "Tobias Navarro Schroeder" <tobiasnavarroschroeder at googlemail.com>
> *Gesendet:* May 30, 2011 5:58:32 PM
> *An:* fieldtrip at donders.ru.nl
> *Betreff:* [FieldTrip] Beamforming on resting state data
>
>
>  Hi Fieldtrippers,
>
> I performed DICS beamforming on resting-state data (i.e. no task, no
> baseline, eyes closed) of a clinical population and controls.
> According to the sensor data the patients have more gamma-band (60-90
> Hz) activity over temporal areas (somewhat spread-out).
> Curiously, after beamforming and group comparisons with 'indepsamplesT'
> permutation statistics the difference map shows more gamma-band (60-90
> Hz) activity for controls in the left, middle-temporal gyrus.
> Hence, the source-level results are opposite to the sensor-level results
> (although more spatially confined). This is *not* a problem of the design
> matrix, or confusing the groups.
>
> Question 1: Does anybody have experience with opposite results on source
> and sensor level?
>
> The individual raw beamforming results (interpolated on the subjects' MRIs)
> look suspicios as well. Due to the 'unit gain constraint' there should be an
> overestimation of power in the center of the head, but only a minority of
> subjects show that. Often I see temporal or parietal activity.
>
> Question 2:
>
> Would a lack of a blob in the center of the head in individual,
> raw, beamforming data indicate an erroneous source analysis?
>
> Thanks a lot for help and suggestions.
>
> Best, Tobias Navarro Schröder
>
> ps: The configurations for calculating the covariance and the beamforming
> is added below:
>
>
>
> 1) % Compute the covariance matrices
>
>
>
> cfg.output =
> 'powandcsd';
>
> cfg.foi = 75;
>
> cfg.foilim = [75 75];
>
> cfg.tapsmofrq = 15; % 75 +- 15 = 60 - 90 Hz
>
> cfg.pad =
> 'maxperlen'; % default
>
> cfg.method =
> 'wltconvol'; % wavelet analysis
>
> cfg.width = 5;
> % Width of the wavelet. Determines the temporal and spectral resolution of
> the analysis constant.
>
>
>
> 2) % Perform the actual beamforming
>
> % load grids of MRI volume
>
> fullnameGrid = [ CurSubject.mripath CurSubject.MRIModel];
>
> cfg = load(fullnameGrid);
>
> cfg.vol = cfg.hdm;
>
>
>
>
>
> cfg.frequency = 75;
>
> cfg.method =
> 'dics';
>
> cfg.keepfilter =
> 'yes'; % keep the beamformer filters (virtual electrodes) for later use
>
> cfg.keeptrial =
> 'no';
>
> cfg.keepmom =
> 'yes'; % useful for connectivity calculations. Dipole moments..
>
> cfg.projectmom =
> 'yes';
>
> cfg.projectnoise =
> 'yes';
>
> cfg.latency = 1;
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From michael.wibral at web.de  Tue May 31 15:36:46 2011
From: michael.wibral at web.de (Michael Wibral)
Date: Tue, 31 May 2011 15:36:46 +0200 (CEST)
Subject: [FieldTrip] SAM beamforming on Neuromag data
Message-ID: <1271334421.1768792.1306849006599.JavaMail.fmail@mwmweb074>

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From valentin.umbach at hu-berlin.de  Tue May 31 18:51:17 2011
From: valentin.umbach at hu-berlin.de (Valentin J. Umbach)
Date: Tue, 31 May 2011 18:51:17 +0200
Subject: [FieldTrip] Emotiv headset realtime capture
Message-ID: <BANLkTimJngfWWopu4ezeuamV4JS7xUCKgw@mail.gmail.com>

Hi, I'm new to FieldTrip and I'm interested in using it to capture
realtime data from the Emotiv headset using this interface:
http://fieldtrip.fcdonders.nl/development/realtime/emotiv
I'm not clear about how to make calls to this interface from within
Matlab. Also, I would like to know if it's possible to access not just
the raw EEG, but also the API output of the detection libraries
(Affectiv Suite...).
Any help is greatly appreciated!

Best, Valentin

-- 
Dipl.-Psych. Valentin J. Umbach
Institut für Psychologie
Humboldt-Universität zu Berlin
Rudower Chaussee 18
12489 Berlin
Tel. +49 30 2093 9438
E-Mail: valentin.umbach at hu-berlin.de



From mcoskun at mail.uh.edu  Tue May 31 23:09:13 2011
From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun)
Date: Tue, 31 May 2011 16:09:13 -0500
Subject: [FieldTrip] Dipole Fitting Algorithm
Message-ID: <726086fb76fc3.4de512a9@mail.uh.edu>


Dear Fieldtrippers,


I am having little trouble understanding the dipole fitting algorithm. Any comments will be greatly appreciated.


1) During dipole fitting, a model data (Vmodel) is created using the computed leadfield. How exactly this model data is computed? Is it simply the projection of the pinv'ed leadfield to the true data (Vdata)? 


2) The error is computed between the model data and true data for the best dipole. Is this RMS error?


3) The last part of dipole fitting is a non-linear search. I really wonder what is the algorithm, what exactly non-linear search is doing?


Thanks in advance
Mehmet


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