From roeysc at gmail.com  Mon Sep  2 16:54:22 2013
From: roeysc at gmail.com (Roey Schurr)
Date: Mon, 2 Sep 2013 17:54:22 +0300
Subject: [FieldTrip] EEG Source Reconstruction - Interpolation by Trial?
Message-ID: <CAHm4wZCmS3DRXeQfQAGg7XwU5PjHB3UjhsSd3FAELLF81J1vpQ@mail.gmail.com>

Hi all,

We are interested in comparing two source reconstruction calculated using
EEG records taken in two different conditions (not ERP), from different
subjects, across the group.

As we see it, what we must do is the following:

1) ft_sourceanalysis (for each condition in each subject, in all trials)
2) ft_sourceinterpolate (the same)
3) ft_volumenormalise (the same)
4) ft_sourcegrandaverage
5) ft_sourcestatistics

The problem is ft_sourceinterpolate will not interpolate each trial
individually, as there is no way to give it the "pow" field per trial.

Is there a way to performd the interpolation over the anatomycal MRI per
trial?

Thank you so much!
Aia and Roey
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From ingenieureniso at gmail.com  Mon Sep  2 17:28:02 2013
From: ingenieureniso at gmail.com (ingenieur eniso)
Date: Mon, 2 Sep 2013 16:28:02 +0100
Subject: [FieldTrip] how to open bdf and rdf files
In-Reply-To: <CAL4kA6dwgo31sL43OMwpruHyOnF5O8MZW0Ha-Z682HfNs8gc=A@mail.gmail.com>
References: <CAPjpx=yj73grOv58wwiLF4Ec2fLGzAiNpy7ziDZGpb+Lphynsg@mail.gmail.com>
	<CAL4kA6dwgo31sL43OMwpruHyOnF5O8MZW0Ha-Z682HfNs8gc=A@mail.gmail.com>
Message-ID: <CAPjpx=ykh+DGDOBWSJQ=oW4sLZrLnKp32uxDyeMevNBcKOuH+g@mail.gmail.com>

Dear Johanna,
Hi Ikaro
Thanks for your  reply.

Best
Ahmed


2013/8/25 Johanna Zumer <johanna.zumer at gmail.com>

> Dear Ahmed,
>
> Does this help?  (http://fieldtrip.fcdonders.nl/getting_started/bdf )
>
> If you are still stuck, maybe try EEGlab import<http://sccn.ucsd.edu/wiki/A01:_Importing_Continuous_and_Epoched_Data> and
> then convert EEGlab format to FieldTrip format (
> http://fieldtrip.fcdonders.nl/integrating_with/integrating_with_eeglab)
>
> Best,
> Johanna
>
>
> 2013/8/23 ingenieur eniso <ingenieureniso at gmail.com>
>
>> Dear all,
>>
>>
>> I have EEG record files in rdf and bdf formats. but I do not know how to
>> open them.
>>
>> Please can anyone send me a matlab function to open these files?
>>
>> I hope you will send me positive and helpful response.
>>
>> Thanks a lot in advance!
>>
>> Best,
>>
>> ahmed
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> 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  Tue Sep  3 12:46:04 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 03 Sep 2013 12:46:04 +0200
Subject: [FieldTrip] EEG Source Reconstruction - Interpolation by Trial?
In-Reply-To: <CAHm4wZCmS3DRXeQfQAGg7XwU5PjHB3UjhsSd3FAELLF81J1vpQ@mail.gmail.com>
References: <CAHm4wZCmS3DRXeQfQAGg7XwU5PjHB3UjhsSd3FAELLF81J1vpQ@mail.gmail.com>
Message-ID: <5225BDEC.5070306@donders.ru.nl>

Dear Roey,

of course there is a way, actual several. I don't see a reason why you 
would want to do that though :) The interpolation purpose is mainly for 
plotting, not for performing fancy statistics or other analyses. In case 
you want to go to a finer spatial resolution, I'd do the reconstruction 
on a finer grid (and there, you will be faced with just physical and 
mathematical constraints in terms of spatial accuracy). That way, your 
reconstruction will be at least based on a physical model, not on some 
'weird' linear interpolation.

Anyway, to answer your question:
First, there is a cfg.parameter field, with which you can specify the 
parameter. If that does not work, the easiest way for you would be to go 
to the code of ft_sourceinterpolate at line 171, copy the lines up to 
184 and put these into your own function. You would need to change them 
appropriately, so that you loop over trials. As I said, there are other 
ways, but that would be the most elegant, fastest (computationally) and 
easiest to understand.

Best,
Jörn

On 9/2/2013 4:54 PM, Roey Schurr wrote:
> Hi all,
>
> We are interested in comparing two source reconstruction calculated 
> using EEG records taken in two different conditions (not ERP), from 
> different subjects, across the group.
>
> As we see it, what we must do is the following:
>
> 1) ft_sourceanalysis (for each condition in each subject, in all trials)
> 2) ft_sourceinterpolate (the same)
> 3) ft_volumenormalise (the same)
> 4) ft_sourcegrandaverage
> 5) ft_sourcestatistics
>
> The problem is ft_sourceinterpolate will not interpolate each trial 
> individually, as there is no way to give it the "pow" field per trial.
>
> Is there a way to performd the interpolation over the anatomycal MRI 
> per trial?
>
> Thank you so much!
> Aia and Roey
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


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

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

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

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

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From guofashou at gmail.com  Tue Sep  3 17:29:46 2013
From: guofashou at gmail.com (guofa shou)
Date: Tue, 3 Sep 2013 10:29:46 -0500
Subject: [FieldTrip] open dataset with both TMS/dDCS and EEG/MEG
Message-ID: <CAC4CbV+M50rutYrWoCqFRuTM7tBqN0XT=5A8zu0Mt-MZtokNbg@mail.gmail.com>

Hi, All,
    I am wondering whether there are some open dataset that was  collected
under one experimental protocol with both TMS/tDCS and EEG/MEG? I mean
TMS+EEG, or tDCS+EEG, or TMS+MEG, or tDCS+MEG in one protocol. Both data
not necessary to be simultaneous, can be separately recorded.
    If anybody happened to know it, please tell me. Or if somebody can
kindly provide me, also please let me know.
Thanks in advance.

-- 
Guofa Shou PhD
Postdoc research associate,
Computational Imaging Laboratory,
University of Oklahoma
3100 Monitor Ave. Suit 280
phone: 405-443-0133
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From guofashou at gmail.com  Tue Sep  3 17:29:46 2013
From: guofashou at gmail.com (guofa shou)
Date: Tue, 3 Sep 2013 10:29:46 -0500
Subject: [FieldTrip] open dataset with both TMS/dDCS and EEG/MEG
Message-ID: <CAC4CbV+M50rutYrWoCqFRuTM7tBqN0XT=5A8zu0Mt-MZtokNbg@mail.gmail.com>

Hi, All,
    I am wondering whether there are some open dataset that was  collected
under one experimental protocol with both TMS/tDCS and EEG/MEG? I mean
TMS+EEG, or tDCS+EEG, or TMS+MEG, or tDCS+MEG in one protocol. Both data
not necessary to be simultaneous, can be separately recorded.
    If anybody happened to know it, please tell me. Or if somebody can
kindly provide me, also please let me know.
Thanks in advance.

-- 
Guofa Shou PhD
Postdoc research associate,
Computational Imaging Laboratory,
University of Oklahoma
3100 Monitor Ave. Suit 280
phone: 405-443-0133
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From M.vanElk at uva.nl  Wed Sep  4 14:50:31 2013
From: M.vanElk at uva.nl (Elk, Michiel van)
Date: Wed, 4 Sep 2013 12:50:31 +0000
Subject: [FieldTrip] PhD Vacancy Cognitive Neuroscience University of
	Amsterdam
Message-ID: <867B60DF-CD51-4AC7-B431-03078D869413@uva.nl>

PhD Vacancy Cognitive Neuroscience
The Social Psychology program of the Faculty of Social and Behavioural Sciences (FMG) is looking for a PhD candidate with a strong background in cognitive neuroscience. This PhD project investigates the neurocognitive mechanisms underlying agency detection and theory-of-mind attributions, by using behavioural, EEG and fMRI experiments. The project is part of a larger research program at the University of Amsterdam, focusing on the psychological and neural basis of religion.

for more information, see:
https://www.academictransfer.com/employer/UVA/vacancy/19839/lang/en/

Michiel van Elk
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From j.herring at fcdonders.ru.nl  Thu Sep  5 11:44:05 2013
From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim))
Date: Thu, 5 Sep 2013 11:44:05 +0200 (CEST)
Subject: [FieldTrip] open dataset with both TMS/dDCS and EEG/MEG
In-Reply-To: <CAC4CbV+M50rutYrWoCqFRuTM7tBqN0XT=5A8zu0Mt-MZtokNbg@mail.gmail.com>
References: <CAC4CbV+M50rutYrWoCqFRuTM7tBqN0XT=5A8zu0Mt-MZtokNbg@mail.gmail.com>
Message-ID: <015b01ceaa1c$76a05bb0$63e11310$@herring@fcdonders.ru.nl>

Dear Guofa,

 

On the FieldTrip website you can now find a tutorial on how to deal with a
TMS-EEG dataset (currently here:
http://fieldtrip.fcdonders.nl/development/eeg_tms). The tutorial includes
a TMS-EEG dataset of a single-pulse study. 

 

TMS+MEG is as far as I know not possible and tDCS+MEG has only recently
been performed successfully
(http://www.nature.com/ncomms/2013/130621/ncomms3032/full/ncomms3032.html)
.

 

Best,

 

Jim 

 

From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of guofa shou
Sent: dinsdag 3 september 2013 17:30
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] open dataset with both TMS/dDCS and EEG/MEG

 

Hi, All, 

    I am wondering whether there are some open dataset that was  collected
under one experimental protocol with both TMS/tDCS and EEG/MEG? I mean
TMS+EEG, or tDCS+EEG, or TMS+MEG, or tDCS+MEG in one protocol. Both data
not necessary to be simultaneous, can be separately recorded.


    If anybody happened to know it, please tell me. Or if somebody can
kindly provide me, also please let me know. 

Thanks in advance.

 

-- 
Guofa Shou PhD
Postdoc research associate,
Computational Imaging Laboratory,
University of Oklahoma
3100 Monitor Ave. Suit 280
phone: 405-443-0133

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From ben.vanlier at bsse.ethz.ch  Thu Sep  5 12:47:07 2013
From: ben.vanlier at bsse.ethz.ch (van Lier  Ben)
Date: Thu, 5 Sep 2013 10:47:07 +0000
Subject: [FieldTrip] setting colormap for ft_multiplotTFR not working + easy
	fix
Message-ID: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A95FA4@MBX13.d.ethz.ch>

Hi all,

I like to have my spectra in the hot colormap instead of the matlab default jet (jet is bad - http://www.jwave.vt.edu/%7Erkriz/Projects/create_color_table/color_07.pdf )

cfg.colormap = hot(256);
works well for all the plots except multiplot. i get this error:

-------------
Error using hg.axes/set
The name 'colormap' is not an accessible property for an instance of class 'axes'.

Error in ft_multiplotTFR (line 501)
  set(gca,'colormap',cfg.colormap);
--------------

gca should be gcf :)

cheers
Ben




From paul.sowman at mq.edu.au  Fri Sep  6 02:56:45 2013
From: paul.sowman at mq.edu.au (Paul Sowman)
Date: Fri, 6 Sep 2013 10:56:45 +1000
Subject: [FieldTrip] MEG job Sydney Australia
Message-ID: <CAOFy9i6YWU-rhDi=F=y_hQ3XWirJ_px9pq-6J4P_X3bWnhfs5Q@mail.gmail.com>

Senior Scientific Advisor

    Located in new state of the art premises, the Australian Hearing Hub
    Working in a leading Research Centre
    Handy to bus, trains, onsite parking available

The Faculty of Human Sciences is a unique and exciting combination of
disciplines across 4 key areas of expertise - Health, Education, Language
and the Mind. The faculty is known for its high calibre professionally
accredited courses and its research excellence across our Departments of
Education and Early Childhood, Linguistics, Psychology, Cognitive Science,
Health Professions and Advanced Medicine.

The Faculty of Human Sciences covers a broad range of disciplines and is
home to the Department of Cognitive Science. The Faculty is building in
health education and healthcare and is investing in the ARC Centre of
Excellence in Cognition and its Disorders as part of their expansion.

The Role

We are seeking a bright, self-motivated person to support research
objectives of the ARC Centre of Excellence and the Department of Cognitive
Science through the provision of scientific and technical support at the
KIT-Macquarie Brain Research Laboratory (Magnetoencephalography (MEG)
laboratory).

The role will involve technical support and logistical planning of the MEG
Laboratory, training staff and students in MEG system hardware and
software, performing routine tests for specific research projects,
providing recommendations and reports to the MEG Committee and advising
them on options for resolution of technical problems. Importantly, the
incumbent will be motivated to develop his/her own research into new
analysis methods and enhanced MEG signal quality.

Selection Criteria:

Please address the following selection criteria and upload as a separate
document as part of the application process. It is recommended that
applicants also attach a covering letter providing a concise overview of
their background, career interests, and suitability for the advertised
position.

Essential:

    Minimum requirement is a Master's degree in Neuroscience, Engineering,
Physics or related field.
    Understanding of the electromagnetic theory needed for signal analysis.
    Knowledge of signal processing techniques/methods.
    Experience with MEG and/or functional neuroimaging acquisition and
analysis.
    Excellent reporting, numerical, statistical and computing skills
(including MATLAB and experimental control software).
    Experience in developing, implementing and maintaining protocols,
polices and procedures
    Good organisational skills including planning, prioritisation, time
management and initiative.

Desirable:

    Ability to design and deliver training
    Ability to communicate and engage with preschool children.

Employment in this position is conditional upon holding a Working with
Children Check Clearance

For full details of the role please view the position description.

http://www.seek.com.au/job/25163778


Package: Level 7, base salary from AUD$79,437 – $86,127 p.a. plus 17%
employer's superannuation and annual leave loading.

Appointment Type: 3 years Full-time, fixed term. Position available
immediately.

Specific Role Enquiries: Specific enquiries related to this position should
be directed to Lesley McKnight on lesley.mcknight at mq.edu.au or
+61-2-9850-9599.

General Recruitment Enquiries: please contact Patsy Moss on
patsy.moss at mq.edu.au or +61-2-9850 9821

Applications Close: 11:55pm22 September 2013 (Australian Eastern Standard
Time)

Macquarie University is an EO Employer committed to diversity and social
inclusion. Applications are encouraged from people with a disability; women
(particularly for senior and non-traditional roles); Indigenous
Australians, people who identify as GLBTIQ; and those from culturally and
linguistically diverse backgrounds.

Applications need to be submitted through the Macquarie University online
recruitment system. Where circumstances such as disability or remote
location prohibit your access to our online system please contact the
enquiries person listed in this advertisement for assistance.

-- 
Paul F Sowman
ARC DECRA Postdoctoral Fellow
Department of Cognitive Science
ARC Centre of Excellence for Cognition and its Disorders (CCD)
MACQUARIE UNIVERSITY NSW 2109
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From jean-michel.badier at univ-amu.fr  Fri Sep  6 15:46:49 2013
From: jean-michel.badier at univ-amu.fr (Jean-Michel Badier)
Date: Fri, 06 Sep 2013 15:46:49 +0200
Subject: [FieldTrip] [Filedtrip] Openmeeg and MEG
Message-ID: <5229DCC9.3080809@univ-amu.fr>


Dear FT and Openmeeg users,

I seems that fieldtrip does not support (anymore ? it seems it was 
possible in the past) Openmeeg for MEG.
Does it means that the Nolte  or the multiple spheres approaches are 
sufficient and do not require extra calculation?
I wonder in some parts of the brain.

Is this integration scheduled sometimes?

Thanks

Jean-Michel
-- 


Jean-Michel Badier

Laboratoire de MagnétoEncéphaloGraphie
Institut de Neurosciences des Systèmes - INSERM UMR 1106
http://ins.medecine.univmed.fr/

Service de Neurophysiologie Clinique.CHU Timone

/Hôpital/de la /Timone/264, rue Saint Pierre 13385 Marseille Cedex 5

33 (0)4 91 38 55 62

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From Ulrich.Pomper at charite.de  Fri Sep  6 16:42:00 2013
From: Ulrich.Pomper at charite.de (Pomper, Ulrich)
Date: Fri, 6 Sep 2013 16:42:00 +0200
Subject: [FieldTrip] Beamforming: Scalp vs. Source mismatch
Message-ID: <C2669B9D730D5C46852FF4877FAD45A90122CFC90967@EXCHANGE31.charite.de>

Dear fieldtrip community,
In my data I found a disconcerting mismatch between EEG scalp topographies and corresponding beamforming solutions, both on the subject and group average level. 
I understand that there might not be a perfect match between source and scalp, but I would expect at least a little resemblance. 

As an example, the link below features topos and source plots from an event-related beta-band decrease after a short tactile stimulation to the left index finger. 
Further below you can find the code I used for the beamforming. (Note that the topos were created from the ft_freqanalysis command within the beamforming script, so baseline and poststimulus data are exactly the same for both source and scalp-level data).

Eight out of 13 subjects show practically no match between source and scalp. On the group average level, the source solution shows a left-anterior decrease which seems not present in the scalp data. Also, the right heispheric decrease at the scalp shifts from central to more posterior sites, which doesn't fit with it beeing of somatosensory origin anymore. 

I’d appreciate any comments on my data, as well as suggestions on how to proceed  to get a more trustworthy source solution to my beta-band decrease.
Cheers, 
Ulrich


Exemplary plots: https://www.dropbox.com/s/git4w8u3a901l3w/source_vs_scalp.pdf

% Beamforming code %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

foi = 20;
tapsmofreq = 5;
toi_pre = [-.4 -.2];
toi_post = [.15 .35];
lambda = '5%';
        
        %% cut data and append for common filters
        cfg = [];
        cfg.toilim = toi_pre;
        dataPre = ft_redefinetrial(cfg, data);
        
        cfg.toilim = toi_post;
        dataPost = ft_redefinetrial(cfg, data);
        
        dataAll = ft_appenddata([], dataPre, dataPost);
        
        %% Calculate common CSD
        
        cfg = [];
        cfg.method    = 'mtmfft'; 
        cfg.output    = 'powandcsd';
        cfg.tapsmofrq = tapsmofreq;
        cfg.foilim    = [foi foi];
        freqAll = ft_freqanalysis(cfg, dataAll);
        
        %% Calculate CSD for seperate conditions
        
        cfg = [];
        cfg.method    = 'mtmfft';
        cfg.output    = 'powandcsd';
        cfg.tapsmofrq = tapsmofreq;
        cfg.foilim    = [foi foi];
        freqPre = ft_freqanalysis(cfg, dataPre);
        
        cfg = [];
        cfg.method    = 'mtmfft';
        cfg.output    = 'powandcsd';
        cfg.tapsmofrq = tapsmofreq;
        cfg.foilim    = [foi foi];
        freqPost = ft_freqanalysis(cfg, dataPost);
        
        %% Source Analysis
        
        cfg              = [];
        cfg.method       = 'dics';
        cfg.frequency    = foi;
        cfg.grid         = lf_126;
        cfg.vol          = vol;
        cfg.dics.projectnoise = 'no';
        cfg.dics.lambda       = lambda; 
        cfg.dics.keepfilter   = 'yes';
        cfg.dics.realfilter   = 'yes';
        
        sourceAll = ft_sourceanalysis(cfg, freqAll);
        
        %% apply common filter to seperate conditions
        
        cfg.grid.filter = sourceAll.avg.filter;
        
        sourcePre  = ft_sourceanalysis(cfg, freqPre);
        sourcePost = ft_sourceanalysis(cfg, freqPost);
        
        %% Relchange from baseline
        
        sourceDiff = sourcePost;
        sourceDiff.avg.pow = (sourcePost.avg.pow - sourcePre.avg.pow) ./ sourcePre.avg.pow;
        
        



From R.Zimmermann at UKE.Uni-Hamburg.de  Fri Sep  6 17:31:19 2013
From: R.Zimmermann at UKE.Uni-Hamburg.de (Dr. Zimmermann)
Date: Fri, 6 Sep 2013 17:31:19 +0200
Subject: [FieldTrip] acq2ftx - converter thread messages
Message-ID: <5229F547.4020507@UKE.Uni-Hamburg.de>

Hi,

we've got frequent messages from the acq2ftx-program followed by a stop 
of its data transmission:

.............
Data |  70 samples | ID= 397 | slot=596 | dT=  0.0  mT= 51.9  sT=1341.2
Internal converter thread does not keep up with the load.
Data |  70 samples | ID= 398 | slot=597 | dT=  0.0  mT= 51.9  sT=1341.1
Data |  70 samples | ID= 399 | slot=598 | dT=  0.1  mT= 51.9  sT=1341.0
Internal converter thread does not keep up with the load.
Data |  70 samples | ID= 400 | slot=599 | dT=  0.0  mT= 51.9  sT=1340.9
Internal converter thread does not keep up with the load.
Waiting (on 0)
Waiting (on 0)
Waiting (on 0)
...

This sounds as if there is a performance problem, most probably with the 
CPU?

Does / Has this also happen/ed at the Donders? I wonder a bit wether VSM 
has  installed different types of PCs. Our PC has four physical cores 
with 3.4GHz each which should normally be enough for these tasks ...

Regards, Roger
--

Besuchen Sie uns auf: www.uke.de
_____________________________________________________________________

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg
Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik
_____________________________________________________________________

SAVE PAPER - THINK BEFORE PRINTING
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From b.osuagwu.1 at research.gla.ac.uk  Sat Sep  7 15:18:55 2013
From: b.osuagwu.1 at research.gla.ac.uk (Bethel Osuagwu)
Date: Sat, 7 Sep 2013 14:18:55 +0100
Subject: [FieldTrip] sLORETA statistics
Message-ID: <7AB2A399CAFFA442A6262BF9939AC33B5BF1C31D78@CMS07.campus.gla.ac.uk>

Deal Fieldtripers,
Since there is no forum for the software sLORETA (http://www.uzh.ch/keyinst/loreta.htm), I have decided to post here to see if I can get any help.

I am currently processing my data on sLORETA and I have noticed something regarding the statistical significance of my results. The statistical significance of activated regions of the brain depends on how I enter my data into the statistical software  of sLORETA. I put the data in the following two ways.
1)  I computed one cross spectra file with all the trials from one subject. I did this for each subject.  Then I computed sloreta file for each of the subjects' cross spectral file.
2)  I computed one cross spectra file for each trial. So I have trials*subjects number of cross spectral files. I computed the sloreta file for each trials' cross spectra file.

Now, I performed statistics comparing 1) above with its baseline and did the same with 2). I got the same activation pattern for both 1) and 2) but 2) allows more areas of the brain to be significant. To be honest two favours the areas I am interested in but I am not sure if I am deceiving the software with the method in 2). Is the software thinking that each trial in 2) is a unique subject and therefore thinks that I have trials*subjects number of subjects? Is it even a statistical issue if the software is treating my data in this way since each trial could be considered individually anyway? I just want to know why there is a difference between the statistical significance in the two methods and if there is an issue with using method 2).

Thanks for your consideration.
Bethel


From alexandre.gramfort at inria.fr  Sun Sep  8 18:39:07 2013
From: alexandre.gramfort at inria.fr (Alexandre Gramfort)
Date: Sun, 8 Sep 2013 18:39:07 +0200
Subject: [FieldTrip] [Filedtrip] Openmeeg and MEG
In-Reply-To: <5229DCC9.3080809@univ-amu.fr>
References: <5229DCC9.3080809@univ-amu.fr>
Message-ID: <CADeotZpOomN5A+R4K_rVtR-dESFFQeaYTXkPu+A6D5cZdQz9xg@mail.gmail.com>

hi Jean-Michel,

I did not touch the OpenMEEG bindings for a while so it can
have been broken by more recent commits. Nolte's method
is a good alternative.

Best,
Alex


On Fri, Sep 6, 2013 at 3:46 PM, Jean-Michel Badier
<jean-michel.badier at univ-amu.fr> wrote:
>
> Dear FT and Openmeeg users,
>
> I seems that fieldtrip does not support (anymore ? it seems it was possible
> in the past) Openmeeg for MEG.
> Does it means that the Nolte  or the multiple spheres approaches are
> sufficient and do not require extra calculation?
> I wonder in some parts of the brain.
>
> Is this integration scheduled sometimes?
>
> Thanks
>
> Jean-Michel
> --
>
>
> Jean-Michel Badier
>
> Laboratoire de MagnétoEncéphaloGraphie
> Institut de Neurosciences des Systèmes - INSERM UMR 1106
> http://ins.medecine.univmed.fr/
>
>
>
> Service de Neurophysiologie Clinique. CHU Timone
>
> Hôpital de la Timone  264, rue Saint Pierre 13385 Marseille Cedex 5
>
> 33 (0)4 91 38 55 62
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>



From jm.horschig at donders.ru.nl  Mon Sep  9 09:12:54 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 09 Sep 2013 09:12:54 +0200
Subject: [FieldTrip] acq2ftx - converter thread messages
In-Reply-To: <5229F547.4020507@UKE.Uni-Hamburg.de>
References: <5229F547.4020507@UKE.Uni-Hamburg.de>
Message-ID: <522D74F6.8050804@donders.ru.nl>

Dear Roger,

indeed we had this error also the Donders from time to time. We tried to 
figure out where the error comes from, but then were not quite able to 
find the source. However, we were using an older version of acq2ftx back 
then, and with the new version there was no such problem. but also the 
experiment I was running was much shorter than before.
Anyway, for us it helped to restart the computer (to reset the shared 
memory segment) before each experiment and then hope for the best. It 
would be great if you guys could have a closer look at when this error 
shows up and what settings you are using. So, e.g., how long does it 
take until the error shows up? What channels are you streaming and at 
what sampling frequency? Under what circumstances does the error not 
occur? Maybe also check the time when it occurs, we had some trouble 
here once with a cronjob running around noon :)

I am sorry if this all does not really help you much, but I was quite 
satisfied that it did work out for our experiments in the end, so I did 
not spend much more time in investigating those earlier cases were we 
did have this error as well. If you could provide some more information 
though, we can maybe finally find the source of this error.

Best,
Jörn

On 9/6/2013 5:31 PM, Dr. Zimmermann wrote:
> Hi,
>
> we've got frequent messages from the acq2ftx-program followed by a 
> stop of its data transmission:
>
> .............
> Data |  70 samples | ID= 397 | slot=596 | dT=  0.0  mT= 51.9 sT=1341.2
> Internal converter thread does not keep up with the load.
> Data |  70 samples | ID= 398 | slot=597 | dT=  0.0  mT= 51.9 sT=1341.1
> Data |  70 samples | ID= 399 | slot=598 | dT=  0.1  mT= 51.9 sT=1341.0
> Internal converter thread does not keep up with the load.
> Data |  70 samples | ID= 400 | slot=599 | dT=  0.0  mT= 51.9 sT=1340.9
> Internal converter thread does not keep up with the load.
> Waiting (on 0)
> Waiting (on 0)
> Waiting (on 0)
> ...
>
> This sounds as if there is a performance problem, most probably with 
> the CPU?
>
> Does / Has this also happen/ed at the Donders? I wonder a bit wether 
> VSM has  installed different types of PCs. Our PC has four physical 
> cores with 3.4GHz each which should normally be enough for these tasks 
> ...
>
> Regards, Roger
> -- 
>
> Besuchen Sie uns auf: www.uke.de
> _____________________________________________________________________
>
> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen 
> Rechts; Gerichtsstand: Hamburg
> Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. 
> Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik
> _____________________________________________________________________
>
> SAVE PAPER - THINK BEFORE PRINTING
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


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

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

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

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

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From R.Zimmermann at UKE.Uni-Hamburg.de  Mon Sep  9 10:31:41 2013
From: R.Zimmermann at UKE.Uni-Hamburg.de (Dr. Zimmermann)
Date: Mon, 9 Sep 2013 10:31:41 +0200
Subject: [FieldTrip] acq2ftx - converter thread messages
In-Reply-To: <522D74F6.8050804@donders.ru.nl>
References: <5229F547.4020507@UKE.Uni-Hamburg.de>
	<522D74F6.8050804@donders.ru.nl>
Message-ID: <522D876D.9000807@UKE.Uni-Hamburg.de>

Am 09.09.2013 09:12, schrieb "Jörn M. Horschig":
> Dear Roger,

Hi Jören,
>
> indeed we had this error also the Donders from time to time. We tried to
> figure out where the error comes from, but then were not quite able to
> find the source. However, we were using an older version of acq2ftx back
> then, and with the new version there was no such problem. but also the
> experiment I was running was much shorter than before.

what is older, what is new? Does the acq2ftx has a --version like 
option? Were in the sources is the version number? Or shall I test via 
the checksum from the binary?
> Anyway, for us it helped to restart the computer (to reset the shared
> memory segment) before each experiment and then hope for the best. It
> would be great if you guys could have a closer look at when this error
> shows up and what settings you are using. So, e.g., how long does it
> take until the error shows up? What channels are you streaming and at
> what sampling frequency? Under what circumstances does the error not
> occur? Maybe also check the time when it occurs, we had some trouble
> here once with a cronjob running around noon :)

Would You also be interested in system parameters (as load, runnning 
processes etc.?)
>
> I am sorry if this all does not really help you much, but I was quite
> satisfied that it did work out for our experiments in the end, so I did

Indeed that sounds simliar to some windows problems ;-)
> not spend much more time in investigating those earlier cases were we
> did have this error as well. If you could provide some more information
> though, we can maybe finally find the source of this error.

I'll try, shall I send everthing over this mailing list?
>
> Best,
> Jörn

Regards, Roger
>
> On 9/6/2013 5:31 PM, Dr. Zimmermann wrote:
>> Hi,
>>
>> we've got frequent messages from the acq2ftx-program followed by a
>> stop of its data transmission:
>>
>> .............
>> Data |  70 samples | ID= 397 | slot=596 | dT=  0.0  mT= 51.9 sT=1341.2
>> Internal converter thread does not keep up with the load.
>> Data |  70 samples | ID= 398 | slot=597 | dT=  0.0  mT= 51.9 sT=1341.1
>> Data |  70 samples | ID= 399 | slot=598 | dT=  0.1  mT= 51.9 sT=1341.0
>> Internal converter thread does not keep up with the load.
>> Data |  70 samples | ID= 400 | slot=599 | dT=  0.0  mT= 51.9 sT=1340.9
>> Internal converter thread does not keep up with the load.
>> Waiting (on 0)
>> Waiting (on 0)
>> Waiting (on 0)
>> ...
>>
>> This sounds as if there is a performance problem, most probably with
>> the CPU?
>>
>> Does / Has this also happen/ed at the Donders? I wonder a bit wether
>> VSM has  installed different types of PCs. Our PC has four physical
>> cores with 3.4GHz each which should normally be enough for these tasks
>> ...
>>
>> Regards, Roger
>> --
>>
>> Besuchen Sie uns auf: www.uke.de
>> _____________________________________________________________________
>>
>> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen
>> Rechts; Gerichtsstand: Hamburg
>> Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr.
>> Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik
>> _____________________________________________________________________
>>
>> SAVE PAPER - THINK BEFORE PRINTING
>>
>>
>> _______________________________________________
>> 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
>

--

Besuchen Sie uns auf: www.uke.de
_____________________________________________________________________

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg
Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik
_____________________________________________________________________

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From jm.horschig at donders.ru.nl  Mon Sep  9 11:01:09 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 09 Sep 2013 11:01:09 +0200
Subject: [FieldTrip] acq2ftx - converter thread messages
In-Reply-To: <522D876D.9000807@UKE.Uni-Hamburg.de>
References: <5229F547.4020507@UKE.Uni-Hamburg.de>
	<522D74F6.8050804@donders.ru.nl>
	<522D876D.9000807@UKE.Uni-Hamburg.de>
Message-ID: <522D8E55.6040009@donders.ru.nl>

Hi Roger,

> what is older, what is new? Does the acq2ftx has a --version like 
> option? Were in the sources is the version number? Or shall I test via 
> the checksum from the binary?

There's no version option, just the date of the file (revision number of 
fieldtrip). You could indeed do a checksum of the binary and see whether 
it matches the one of the latest FT version.

> Would You also be interested in system parameters (as load, runnning 
> processes etc.?)

Sure, the more butter on the bread the better :)

>>
>> I am sorry if this all does not really help you much, but I was quite
>> satisfied that it did work out for our experiments in the end, so I did
>
> Indeed that sounds simliar to some windows problems ;-)
indeed - but we use linux ;)

>> not spend much more time in investigating those earlier cases were we
>> did have this error as well. If you could provide some more information
>> though, we can maybe finally find the source of this error.
>
> I'll try, shall I send everthing over this mailing list?

maybe use the old bug on bugzilla for communicating further, so that not 
everyone gets spammed ;)
http://bugzilla.fcdonders.nl/show_bug.cgi?id=1370

Thanks for reporting!

Best,
Jörn
>>
>> Best,
>> Jörn
>
> Regards, Roger
>>
>> On 9/6/2013 5:31 PM, Dr. Zimmermann wrote:
>>> Hi,
>>>
>>> we've got frequent messages from the acq2ftx-program followed by a
>>> stop of its data transmission:
>>>
>>> .............
>>> Data |  70 samples | ID= 397 | slot=596 | dT=  0.0  mT= 51.9 sT=1341.2
>>> Internal converter thread does not keep up with the load.
>>> Data |  70 samples | ID= 398 | slot=597 | dT=  0.0  mT= 51.9 sT=1341.1
>>> Data |  70 samples | ID= 399 | slot=598 | dT=  0.1  mT= 51.9 sT=1341.0
>>> Internal converter thread does not keep up with the load.
>>> Data |  70 samples | ID= 400 | slot=599 | dT=  0.0  mT= 51.9 sT=1340.9
>>> Internal converter thread does not keep up with the load.
>>> Waiting (on 0)
>>> Waiting (on 0)
>>> Waiting (on 0)
>>> ...
>>>
>>> This sounds as if there is a performance problem, most probably with
>>> the CPU?
>>>
>>> Does / Has this also happen/ed at the Donders? I wonder a bit wether
>>> VSM has  installed different types of PCs. Our PC has four physical
>>> cores with 3.4GHz each which should normally be enough for these tasks
>>> ...
>>>
>>> Regards, Roger
>>> -- 
>>>
>>> Besuchen Sie uns auf: www.uke.de
>>> _____________________________________________________________________
>>>
>>> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen
>>> Rechts; Gerichtsstand: Hamburg
>>> Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr.
>>> Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik
>>> _____________________________________________________________________
>>>
>>> SAVE PAPER - THINK BEFORE PRINTING
>>>
>>>
>>> _______________________________________________
>>> 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
>>
>
> -- 
>
> Besuchen Sie uns auf: www.uke.de
> _____________________________________________________________________
>
> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen 
> Rechts; Gerichtsstand: Hamburg
> Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. 
> Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik
> _____________________________________________________________________
>
> SAVE PAPER - THINK BEFORE PRINTING
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


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

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

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

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

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From s32334077 at gmail.com  Mon Sep  9 16:20:10 2013
From: s32334077 at gmail.com (Alberto Ghione)
Date: Mon, 9 Sep 2013 16:20:10 +0200
Subject: [FieldTrip] Source reconstruction with MNE solution
Message-ID: <CAN3GWM+ZyBeVm+cq1o+E7KuXcChyWmo6F3s_E6-PhMtH3bNxJQ@mail.gmail.com>

Dear fieldtrippers,
could someone be so kind to please tell me which is the unit of
'source.avg.pow'?

Thanks for your attention,

Alberto Ghione
University of Genoa
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From roeysc at gmail.com  Tue Sep 10 08:51:45 2013
From: roeysc at gmail.com (Roey Schurr)
Date: Tue, 10 Sep 2013 09:51:45 +0300
Subject: [FieldTrip] EEG Source Reconstruction - Interpolation by Trial?
In-Reply-To: <5225BDEC.5070306@donders.ru.nl>
References: <CAHm4wZCmS3DRXeQfQAGg7XwU5PjHB3UjhsSd3FAELLF81J1vpQ@mail.gmail.com>
	<5225BDEC.5070306@donders.ru.nl>
Message-ID: <CAHm4wZDnBHVpMbD_6H14RX8LK3NsossEDPWFKUNpS_sQUbWHig@mail.gmail.com>

Dear Jörn,

Thank you for your kind answer!



>From what we saw on several links it is customary to perform the
interpolation before normalisation, both before statistical analysis (e.g.
http://fieldtrip.fcdonders.nl/tutorial/introduction) or just before
plotting as you mentiones (e.g.
http://fieldtrip.fcdonders.nl/tutorial/beamformer).



The reason we wanted *to interpolate before normalising* is that
interpolation relies on anatomical data, hence it is not possible to use
ft_volumenormalise on pure "source" structure (yet it is possible using it
on "interpolated source" structure).



The reason we wanted to do the *normalisation* *per trial* is the
following: we want to compare the source structure for each condition. In
principle, we could have performed the source analysis over all trials and
get the AVERAGE source per subject per condition, and then compare these
two groups (source condition 1, source condition 2). However, we have too
few subjects, and so we thought it could be best to compare the source
reconstructions of ALL trials over ALL patients in both conditions. Does
this make any sense to you?



Best,

Aia and Roey


On Tue, Sep 3, 2013 at 1:46 PM, "Jörn M. Horschig" <
jm.horschig at donders.ru.nl> wrote:

>  Dear Roey,
>
> of course there is a way, actual several. I don't see a reason why you
> would want to do that though :) The interpolation purpose is mainly for
> plotting, not for performing fancy statistics or other analyses. In case
> you want to go to a finer spatial resolution, I'd do the reconstruction on
> a finer grid (and there, you will be faced with just physical and
> mathematical constraints in terms of spatial accuracy). That way, your
> reconstruction will be at least based on a physical model, not on some
> 'weird' linear interpolation.
>
> Anyway, to answer your question:
> First, there is a cfg.parameter field, with which you can specify the
> parameter. If that does not work, the easiest way for you would be to go to
> the code of ft_sourceinterpolate at line 171, copy the lines up to 184 and
> put these into your own function. You would need to change them
> appropriately, so that you loop over trials. As I said, there are other
> ways, but that would be the most elegant, fastest (computationally) and
> easiest to understand.
>
> Best,
> Jörn
>
>
> On 9/2/2013 4:54 PM, Roey Schurr wrote:
>
>  Hi all,
>
>  We are interested in comparing two source reconstruction calculated
> using EEG records taken in two different conditions (not ERP), from
> different subjects, across the group.
>
>  As we see it, what we must do is the following:
>
>  1) ft_sourceanalysis (for each condition in each subject, in all trials)
> 2) ft_sourceinterpolate (the same)
> 3) ft_volumenormalise (the same)
> 4) ft_sourcegrandaverage
> 5) ft_sourcestatistics
>
>  The problem is ft_sourceinterpolate will not interpolate each trial
> individually, as there is no way to give it the "pow" field per trial.
>
>  Is there a way to performd the interpolation over the anatomycal MRI per
> trial?
>
>  Thank you so much!
> Aia and Roey
>
>
> _______________________________________________
> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> --
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From jm.horschig at donders.ru.nl  Tue Sep 10 17:26:26 2013
From: jm.horschig at donders.ru.nl (=?windows-1252?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 10 Sep 2013 17:26:26 +0200
Subject: [FieldTrip] Beamforming: Scalp vs. Source mismatch
In-Reply-To: <C2669B9D730D5C46852FF4877FAD45A90122CFC90967@EXCHANGE31.charite.de>
References: <C2669B9D730D5C46852FF4877FAD45A90122CFC90967@EXCHANGE31.charite.de>
Message-ID: <522F3A22.8050903@donders.ru.nl>

Dear Ulrich,

as no one dared to respond, yet, I can add my 2 cents. I am afraid they 
won't help much though ;) Also, I am not in expert in EEG source 
reconstruction, so I have no good intuition how EEG activity should 
translate to the source space.

First of all, it might be good to verify the coordinate system you are 
in, i.e. is left in your source plot really left. Next, you could try to 
check whether the coordinate systems are set correctly - if the 
coordinate systems are screwed up, this can result in nasty 90 degrees 
of more complex rotations of your data. This all, however, would not 
explain why the topographies match for some subjects better than for 
others. But maybe you can share part of the pipeline for creating the 
forward model and give us a glimpse of the resulting structures? 
Although it looks like the forward model does line up well, since 
there's nothing else to fuss about, it's the only hunge I got right now. 
Alternatively, maybe parameters for the topo plotting are still 
different from the source plotting, so it might also help to show us the 
calls and cfg-settings for the plotting routine

In addition, I can see that you do not set cfg.keeptrials='yes' when 
computing the FFT of your data. I don't immediately see why that would 
solve the discrepancy between sensor- and source-level, but it might 
help to get a better estimate anyway (so that variance over trials can 
be taken into account). Maybe you just didn't do anything wrong, and 
this is just the step missing to get a more trustworthy result?

I hope any of this helps, and otherwise that someone else is of more help ;)

Best,
Jörn

On 9/6/2013 4:42 PM, Pomper, Ulrich wrote:
> Dear fieldtrip community,
> In my data I found a disconcerting mismatch between EEG scalp topographies and corresponding beamforming solutions, both on the subject and group average level.
> I understand that there might not be a perfect match between source and scalp, but I would expect at least a little resemblance.
>
> As an example, the link below features topos and source plots from an event-related beta-band decrease after a short tactile stimulation to the left index finger.
> Further below you can find the code I used for the beamforming. (Note that the topos were created from the ft_freqanalysis command within the beamforming script, so baseline and poststimulus data are exactly the same for both source and scalp-level data).
>
> Eight out of 13 subjects show practically no match between source and scalp. On the group average level, the source solution shows a left-anterior decrease which seems not present in the scalp data. Also, the right heispheric decrease at the scalp shifts from central to more posterior sites, which doesn't fit with it beeing of somatosensory origin anymore.
>
> I’d appreciate any comments on my data, as well as suggestions on how to proceed  to get a more trustworthy source solution to my beta-band decrease.
> Cheers,
> Ulrich
>
>
> Exemplary plots: https://www.dropbox.com/s/git4w8u3a901l3w/source_vs_scalp.pdf
>
> % Beamforming code %
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> foi = 20;
> tapsmofreq = 5;
> toi_pre = [-.4 -.2];
> toi_post = [.15 .35];
> lambda = '5%';
>          
>          %% cut data and append for common filters
>          cfg = [];
>          cfg.toilim = toi_pre;
>          dataPre = ft_redefinetrial(cfg, data);
>          
>          cfg.toilim = toi_post;
>          dataPost = ft_redefinetrial(cfg, data);
>          
>          dataAll = ft_appenddata([], dataPre, dataPost);
>          
>          %% Calculate common CSD
>          
>          cfg = [];
>          cfg.method    = 'mtmfft';
>          cfg.output    = 'powandcsd';
>          cfg.tapsmofrq = tapsmofreq;
>          cfg.foilim    = [foi foi];
>          freqAll = ft_freqanalysis(cfg, dataAll);
>          
>          %% Calculate CSD for seperate conditions
>          
>          cfg = [];
>          cfg.method    = 'mtmfft';
>          cfg.output    = 'powandcsd';
>          cfg.tapsmofrq = tapsmofreq;
>          cfg.foilim    = [foi foi];
>          freqPre = ft_freqanalysis(cfg, dataPre);
>          
>          cfg = [];
>          cfg.method    = 'mtmfft';
>          cfg.output    = 'powandcsd';
>          cfg.tapsmofrq = tapsmofreq;
>          cfg.foilim    = [foi foi];
>          freqPost = ft_freqanalysis(cfg, dataPost);
>          
>          %% Source Analysis
>          
>          cfg              = [];
>          cfg.method       = 'dics';
>          cfg.frequency    = foi;
>          cfg.grid         = lf_126;
>          cfg.vol          = vol;
>          cfg.dics.projectnoise = 'no';
>          cfg.dics.lambda       = lambda;
>          cfg.dics.keepfilter   = 'yes';
>          cfg.dics.realfilter   = 'yes';
>          
>          sourceAll = ft_sourceanalysis(cfg, freqAll);
>          
>          %% apply common filter to seperate conditions
>          
>          cfg.grid.filter = sourceAll.avg.filter;
>          
>          sourcePre  = ft_sourceanalysis(cfg, freqPre);
>          sourcePost = ft_sourceanalysis(cfg, freqPost);
>          
>          %% Relchange from baseline
>          
>          sourceDiff = sourcePost;
>          sourceDiff.avg.pow = (sourcePost.avg.pow - sourcePre.avg.pow) ./ sourcePre.avg.pow;
>          
>          
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


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

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

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

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



From Keith.McConnell at cchmc.org  Wed Sep 11 19:48:43 2013
From: Keith.McConnell at cchmc.org (McConnell, Keith)
Date: Wed, 11 Sep 2013 17:48:43 +0000
Subject: [FieldTrip] plotting differences in power spectrum
Message-ID: <F8170A13692BD94597081861B03931C62761C05D@MCEXMB1.chmccorp.cchmc.org>

Hello,

I have an MEG experiment in which I expect my stimulus to incite multiple reactions.  I have run the experiment so that the stimulus is applied at two different intensities.  I would like to use the lower intensity stimulus response as a 'mask' for the higher intensity response.

I can calculate the power spectrum for both intensities and find the difference.

Although I can generate an ft_multiplot for each individual power spectrum, I cannot generate a  ft_multiplotTFR of the difference between the two spectra.

I get the following error messages:

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

Error in ft_multiplotTFR (line 135)
data = ft_checkdata(data, 'datatype', 'freq');

Can anyone provide some help?

Thanks,

Keith

Keith McConnell, M.S.

513.636.0739 (desk)
513.504.9907 (cell)

Division of Pulmonary Medicine
Cincinnati Children's Hospital Medical Center
Cincinnati, OH  45229

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From mcantor at umich.edu  Wed Sep 11 20:53:26 2013
From: mcantor at umich.edu (Max Cantor)
Date: Wed, 11 Sep 2013 14:53:26 -0400
Subject: [FieldTrip] cluster based timelock statistics minimum time parameter
Message-ID: <CAFTjRaVWHgWwF4A5J7+EFbxUuAazxd=Fw7B6NCW8u5Dk5igmow@mail.gmail.com>

For a group analysis of ERP data we are interested in limiting cluster size
by temporal extent (E.g. Only consider clusters 20 ms or longer). Is there
a clustering parameter equivalent to minnbchan for time samples? Searching
through the tutorial and help files didn't turn up anything.
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From aaron.schurger at gmail.com  Thu Sep 12 00:32:52 2013
From: aaron.schurger at gmail.com (Aaron Schurger)
Date: Thu, 12 Sep 2013 00:32:52 +0200
Subject: [FieldTrip] cluster based timelock statistics minimum time
	parameter
In-Reply-To: <CAFTjRaVWHgWwF4A5J7+EFbxUuAazxd=Fw7B6NCW8u5Dk5igmow@mail.gmail.com>
References: <CAFTjRaVWHgWwF4A5J7+EFbxUuAazxd=Fw7B6NCW8u5Dk5igmow@mail.gmail.com>
Message-ID: <CALeeyAT4xSTTag6LuiJz4tzeLYXCfxhn9fr0vWCJ=0Q_SFvFjg@mail.gmail.com>

That is a good point. And the choice of min number of time samples
depends heavily on how you have low-pass filtered or smoothed your
data. If you low-pass filter without downsampling, then you've
"artificially" given yourself a much bigger N for a comparison at some
peak in your signal. In general the lower the cutoff frequency of your
low-pass filter (without downsampling), the more time samples (or
lower samplewise p value) you need to make for a significant cluster.
A good rule of thumb is simply to always down-sample to ~ 3 x the
cutoff frequency when you apply a low-pass filter (or smoothing). So
if you low-pass filter at 20 Hz, then downsample to 60 Hz, before
running any permutation test. The permutation test will run a lot
faster too!
Aaron

On Wed, Sep 11, 2013 at 8:53 PM, Max Cantor <mcantor at umich.edu> wrote:
> For a group analysis of ERP data we are interested in limiting cluster size
> by temporal extent (E.g. Only consider clusters 20 ms or longer). Is there a
> clustering parameter equivalent to minnbchan for time samples? Searching
> through the tutorial and help files didn't turn up anything.
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



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


From n.lam at fcdonders.ru.nl  Thu Sep 12 11:25:06 2013
From: n.lam at fcdonders.ru.nl (Lam, N.H.L. (Nietzsche))
Date: Thu, 12 Sep 2013 11:25:06 +0200 (CEST)
Subject: [FieldTrip] plotting differences in power spectrum
In-Reply-To: <F8170A13692BD94597081861B03931C62761C05D@MCEXMB1.chmccorp.cchmc.org>
Message-ID: <419332796.3033469.1378977906912.JavaMail.root@indus.zimbra.ru.nl>

Hi Keith,

I could try to help you (this will be more first attempt with this mailing list...!) 
Could you provide more information about how you calculated the difference between the two spectra, and precisely what 'freq' (your difference spectra) looks like when you feed it as an argument into ft_multiplotTFR?

As a side, I'm aware that there is ft_multiplotXX, where XX can be replaced with "CC", "ER", "TFR", but I haven't seen a function with the name "ft_multiplot" on its own.

Best,
Nietzsche 

----- Original Message -----
> From: "Keith McConnell" <Keith.McConnell at cchmc.org>
> To: fieldtrip at science.ru.nl
> Sent: Wednesday, 11 September, 2013 7:48:43 PM
> Subject: [FieldTrip] plotting differences in power spectrum
> Hello,
> 
> 
> 
> I have an MEG experiment in which I expect my stimulus to incite
> multiple reactions. I have run the experiment so that the stimulus is
> applied at two different intensities. I would like to use the lower
> intensity stimulus response as a 'mask' for the higher intensity
> response.
> 
> 
> 
> I can calculate the power spectrum for both intensities and find the
> difference.
> 
> 
> 
> Although I can generate an ft_multiplot for each individual power
> spectrum, I cannot generate a ft_multiplotTFR of the difference
> between the two spectra.
> 
> 
> 
> I get the following error messages:
> 
> 
> 
> Error using ft_checkdata (line 366)
> 
> This function requires freq data as input.
> 
> 
> 
> Error in ft_multiplotTFR (line 135)
> 
> data = ft_checkdata(data, 'datatype', 'freq');
> 
> 
> 
> Can anyone provide some help?
> 
> 
> 
> Thanks,
> 
> 
> 
> Keith
> 
> 
> 
> Keith McConnell, M.S.
> 
> 
> 
> 513.636.0739 (desk)
> 
> 513.504.9907 (cell)
> 
> 
> 
> Division of Pulmonary Medicine
> 
> Cincinnati Children's Hospital Medical Center
> 
> Cincinnati, OH 45229
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

-- 
Nietzsche H.L. Lam, MSc 
PhD Candidate 

Max Planck Institute for Psycholinguistics 
Wundtlaan 1, 6525 XD Nijmegen, The Netherlands 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging, 
Kapittelweg 29, 6525EN Nijmegen, The Netherlands 

n.lam at fcdonders.ru.nl 
+31-24-3668219 


neurobiologyoflanguage.com 


From politzerahless at gmail.com  Thu Sep 12 12:09:34 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Thu, 12 Sep 2013 14:09:34 +0400
Subject: [FieldTrip] cluster based timelock statistics minimum time
	parameter
Message-ID: <CAJT2k_-+=dRSNH01D08U=RNZ1QXa22EwuWALujf864jP4YdWjg@mail.gmail.com>

Hi Max,

This was recently discussed (see
http://mailman.science.ru.nl/pipermail/fieldtrip/2013-July/006847.html and
following messages), I'm not sure if that will help you or not.

Best,
Steve


Stephen Politzer-Ahles
New York University, Abu Dhabi
Neuroscience of Language Lab
http://www.nyu.edu/projects/politzer-ahles/



>
> ------------------------------
>
> Message: 2
> Date: Wed, 11 Sep 2013 14:53:26 -0400
> From: Max Cantor <mcantor at umich.edu>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] cluster based timelock statistics minimum time
>         parameter
> Message-ID:
>         <CAFTjRaVWHgWwF4A5J7+EFbxUuAazxd=
> Fw7B6NCW8u5Dk5igmow at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> For a group analysis of ERP data we are interested in limiting cluster size
> by temporal extent (E.g. Only consider clusters 20 ms or longer). Is there
> a clustering parameter equivalent to minnbchan for time samples? Searching
> through the tutorial and help files didn't turn up anything.
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130911/c3fa952b/attachment-0001.html
> >
>
> ------------------------------
>
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From Keith.McConnell at cchmc.org  Thu Sep 12 15:05:22 2013
From: Keith.McConnell at cchmc.org (McConnell, Keith)
Date: Thu, 12 Sep 2013 13:05:22 +0000
Subject: [FieldTrip] plotting differences in power spectrum
In-Reply-To: <419332796.3033469.1378977906912.JavaMail.root@indus.zimbra.ru.nl>
References: <F8170A13692BD94597081861B03931C62761C05D@MCEXMB1.chmccorp.cchmc.org>
	<419332796.3033469.1378977906912.JavaMail.root@indus.zimbra.ru.nl>
Message-ID: <F8170A13692BD94597081861B03931C62761C494@MCEXMB1.chmccorp.cchmc.org>

Thank you Nietzsche for your kind offer of help.

First, to your aside, I am trying to use ft_multiplotTFR.  Sorry for my lack of clarity.

Now to the matter:  I have calculated the power spectrum for each level of stimulus intensity using ft_freqanalysis(cfg, data1) and ft_freqanalysis(cfg, data2).  The result is a 3D double precision array arranged (#ChannelsX#FrequencyBinsX#TimeBins).


 I then calculate the difference using 

for i = 1:NUMBER_CHANNELS
    diff(i,:)=(data1.powspctrm(i,:))-(data2.powspctrm(i,:));
end

The result is a 2D double precision array with the form of (#ChannelsX(the product of the number freq bins and the number of time bins))

So, I guess that my problem is that I've gone from a 3D array to a 2D array in the course of the subtraction.  I am not sure how to correct this error.

Thanks again for the help.

Keith

Keith McConnell, M.S.

513.636.0739 (desk)
513.504.9907 (cell)

Division of Pulmonary Medicine
Cincinnati Children's Hospital Medical Center
Cincinnati, OH  45229


-----Original Message-----
From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Lam, N.H.L. (Nietzsche)
Sent: Thursday, September 12, 2013 5:25 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] plotting differences in power spectrum

Hi Keith,

I could try to help you (this will be more first attempt with this mailing list...!) Could you provide more information about how you calculated the difference between the two spectra, and precisely what 'freq' (your difference spectra) looks like when you feed it as an argument into ft_multiplotTFR?

As a side, I'm aware that there is ft_multiplotXX, where XX can be replaced with "CC", "ER", "TFR", but I haven't seen a function with the name "ft_multiplot" on its own.

Best,
Nietzsche 

----- Original Message -----
> From: "Keith McConnell" <Keith.McConnell at cchmc.org>
> To: fieldtrip at science.ru.nl
> Sent: Wednesday, 11 September, 2013 7:48:43 PM
> Subject: [FieldTrip] plotting differences in power spectrum Hello,
> 
> 
> 
> I have an MEG experiment in which I expect my stimulus to incite 
> multiple reactions. I have run the experiment so that the stimulus is 
> applied at two different intensities. I would like to use the lower 
> intensity stimulus response as a 'mask' for the higher intensity 
> response.
> 
> 
> 
> I can calculate the power spectrum for both intensities and find the 
> difference.
> 
> 
> 
> Although I can generate an ft_multiplot for each individual power 
> spectrum, I cannot generate a ft_multiplotTFR of the difference 
> between the two spectra.
> 
> 
> 
> I get the following error messages:
> 
> 
> 
> Error using ft_checkdata (line 366)
> 
> This function requires freq data as input.
> 
> 
> 
> Error in ft_multiplotTFR (line 135)
> 
> data = ft_checkdata(data, 'datatype', 'freq');
> 
> 
> 
> Can anyone provide some help?
> 
> 
> 
> Thanks,
> 
> 
> 
> Keith
> 
> 
> 
> Keith McConnell, M.S.
> 
> 
> 
> 513.636.0739 (desk)
> 
> 513.504.9907 (cell)
> 
> 
> 
> Division of Pulmonary Medicine
> 
> Cincinnati Children's Hospital Medical Center
> 
> Cincinnati, OH 45229
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

--
Nietzsche H.L. Lam, MSc
PhD Candidate 

Max Planck Institute for Psycholinguistics Wundtlaan 1, 6525 XD Nijmegen, The Netherlands 

Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Kapittelweg 29, 6525EN Nijmegen, The Netherlands 

n.lam at fcdonders.ru.nl 
+31-24-3668219


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




From Keith.McConnell at cchmc.org  Thu Sep 12 15:45:41 2013
From: Keith.McConnell at cchmc.org (McConnell, Keith)
Date: Thu, 12 Sep 2013 13:45:41 +0000
Subject: [FieldTrip] plotting differences in power spectrum
In-Reply-To: <419332796.3033469.1378977906912.JavaMail.root@indus.zimbra.ru.nl>
References: <F8170A13692BD94597081861B03931C62761C05D@MCEXMB1.chmccorp.cchmc.org>
	<419332796.3033469.1378977906912.JavaMail.root@indus.zimbra.ru.nl>
Message-ID: <F8170A13692BD94597081861B03931C62761C4E7@MCEXMB1.chmccorp.cchmc.org>

Hello Nietzche,

I have solved the problem.  Thenak you for you're offer to help.  Explaining the problem in detail was what led me to the solution.

Have a great day,

Keith

Keith McConnell, M.S.

513.636.0739 (desk)
513.504.9907 (cell)

Division of Pulmonary Medicine
Cincinnati Children's Hospital Medical Center
Cincinnati, OH  45229


-----Original Message-----
From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Lam, N.H.L. (Nietzsche)
Sent: Thursday, September 12, 2013 5:25 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] plotting differences in power spectrum

Hi Keith,

I could try to help you (this will be more first attempt with this mailing list...!) Could you provide more information about how you calculated the difference between the two spectra, and precisely what 'freq' (your difference spectra) looks like when you feed it as an argument into ft_multiplotTFR?

As a side, I'm aware that there is ft_multiplotXX, where XX can be replaced with "CC", "ER", "TFR", but I haven't seen a function with the name "ft_multiplot" on its own.

Best,
Nietzsche 

----- Original Message -----
> From: "Keith McConnell" <Keith.McConnell at cchmc.org>
> To: fieldtrip at science.ru.nl
> Sent: Wednesday, 11 September, 2013 7:48:43 PM
> Subject: [FieldTrip] plotting differences in power spectrum Hello,
> 
> 
> 
> I have an MEG experiment in which I expect my stimulus to incite 
> multiple reactions. I have run the experiment so that the stimulus is 
> applied at two different intensities. I would like to use the lower 
> intensity stimulus response as a 'mask' for the higher intensity 
> response.
> 
> 
> 
> I can calculate the power spectrum for both intensities and find the 
> difference.
> 
> 
> 
> Although I can generate an ft_multiplot for each individual power 
> spectrum, I cannot generate a ft_multiplotTFR of the difference 
> between the two spectra.
> 
> 
> 
> I get the following error messages:
> 
> 
> 
> Error using ft_checkdata (line 366)
> 
> This function requires freq data as input.
> 
> 
> 
> Error in ft_multiplotTFR (line 135)
> 
> data = ft_checkdata(data, 'datatype', 'freq');
> 
> 
> 
> Can anyone provide some help?
> 
> 
> 
> Thanks,
> 
> 
> 
> Keith
> 
> 
> 
> Keith McConnell, M.S.
> 
> 
> 
> 513.636.0739 (desk)
> 
> 513.504.9907 (cell)
> 
> 
> 
> Division of Pulmonary Medicine
> 
> Cincinnati Children's Hospital Medical Center
> 
> Cincinnati, OH 45229
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

--
Nietzsche H.L. Lam, MSc
PhD Candidate 

Max Planck Institute for Psycholinguistics Wundtlaan 1, 6525 XD Nijmegen, The Netherlands 

Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Kapittelweg 29, 6525EN Nijmegen, The Netherlands 

n.lam at fcdonders.ru.nl 
+31-24-3668219


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




From Izabela.Mikula at mpi.nl  Thu Sep 12 15:48:56 2013
From: Izabela.Mikula at mpi.nl (Izabela Mikula)
Date: Thu, 12 Sep 2013 15:48:56 +0200
Subject: [FieldTrip] plotting differences in power spectrum
In-Reply-To: <F8170A13692BD94597081861B03931C62761C494@MCEXMB1.chmccorp.cchmc.org>
References: <F8170A13692BD94597081861B03931C62761C05D@MCEXMB1.chmccorp.cchmc.org>
	<419332796.3033469.1378977906912.JavaMail.root@indus.zimbra.ru.nl>
	<F8170A13692BD94597081861B03931C62761C494@MCEXMB1.chmccorp.cchmc.org>
Message-ID: <8920B8D343C27B46B5BEDB8BFA8B2657477D73A5E1@MAILER.mpi.nl>

Hi Keith,

The diff object that you created only contains powspctrm field, so it doesn't have freq data structure anymore.
I would suggest using:

cfg=[];
cfg.operation='subtract'
cfg.parameter = 'powspctrm';
diff=ft_math(cfg, data1,data2)

Hope that helps.

Best,
Izabela

-----Original Message-----
From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of McConnell, Keith
Sent: Thursday, September 12, 2013 3:05 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] plotting differences in power spectrum

Thank you Nietzsche for your kind offer of help.

First, to your aside, I am trying to use ft_multiplotTFR.  Sorry for my lack of clarity.

Now to the matter:  I have calculated the power spectrum for each level of stimulus intensity using ft_freqanalysis(cfg, data1) and ft_freqanalysis(cfg, data2).  The result is a 3D double precision array arranged (#ChannelsX#FrequencyBinsX#TimeBins).


 I then calculate the difference using 

for i = 1:NUMBER_CHANNELS
    diff(i,:)=(data1.powspctrm(i,:))-(data2.powspctrm(i,:));
end

The result is a 2D double precision array with the form of (#ChannelsX(the product of the number freq bins and the number of time bins))

So, I guess that my problem is that I've gone from a 3D array to a 2D array in the course of the subtraction.  I am not sure how to correct this error.

Thanks again for the help.

Keith

Keith McConnell, M.S.

513.636.0739 (desk)
513.504.9907 (cell)

Division of Pulmonary Medicine
Cincinnati Children's Hospital Medical Center Cincinnati, OH  45229


-----Original Message-----
From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Lam, N.H.L. (Nietzsche)
Sent: Thursday, September 12, 2013 5:25 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] plotting differences in power spectrum

Hi Keith,

I could try to help you (this will be more first attempt with this mailing list...!) Could you provide more information about how you calculated the difference between the two spectra, and precisely what 'freq' (your difference spectra) looks like when you feed it as an argument into ft_multiplotTFR?

As a side, I'm aware that there is ft_multiplotXX, where XX can be replaced with "CC", "ER", "TFR", but I haven't seen a function with the name "ft_multiplot" on its own.

Best,
Nietzsche 

----- Original Message -----
> From: "Keith McConnell" <Keith.McConnell at cchmc.org>
> To: fieldtrip at science.ru.nl
> Sent: Wednesday, 11 September, 2013 7:48:43 PM
> Subject: [FieldTrip] plotting differences in power spectrum Hello,
> 
> 
> 
> I have an MEG experiment in which I expect my stimulus to incite 
> multiple reactions. I have run the experiment so that the stimulus is 
> applied at two different intensities. I would like to use the lower 
> intensity stimulus response as a 'mask' for the higher intensity 
> response.
> 
> 
> 
> I can calculate the power spectrum for both intensities and find the 
> difference.
> 
> 
> 
> Although I can generate an ft_multiplot for each individual power 
> spectrum, I cannot generate a ft_multiplotTFR of the difference 
> between the two spectra.
> 
> 
> 
> I get the following error messages:
> 
> 
> 
> Error using ft_checkdata (line 366)
> 
> This function requires freq data as input.
> 
> 
> 
> Error in ft_multiplotTFR (line 135)
> 
> data = ft_checkdata(data, 'datatype', 'freq');
> 
> 
> 
> Can anyone provide some help?
> 
> 
> 
> Thanks,
> 
> 
> 
> Keith
> 
> 
> 
> Keith McConnell, M.S.
> 
> 
> 
> 513.636.0739 (desk)
> 
> 513.504.9907 (cell)
> 
> 
> 
> Division of Pulmonary Medicine
> 
> Cincinnati Children's Hospital Medical Center
> 
> Cincinnati, OH 45229
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

--
Nietzsche H.L. Lam, MSc
PhD Candidate 

Max Planck Institute for Psycholinguistics Wundtlaan 1, 6525 XD Nijmegen, The Netherlands 

Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Kapittelweg 29, 6525EN Nijmegen, The Netherlands 

n.lam at fcdonders.ru.nl 
+31-24-3668219


neurobiologyoflanguage.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 Keith.McConnell at cchmc.org  Thu Sep 12 15:51:28 2013
From: Keith.McConnell at cchmc.org (McConnell, Keith)
Date: Thu, 12 Sep 2013 13:51:28 +0000
Subject: [FieldTrip] plotting differences in power spectrum
In-Reply-To: <8920B8D343C27B46B5BEDB8BFA8B2657477D73A5E1@MAILER.mpi.nl>
References: <F8170A13692BD94597081861B03931C62761C05D@MCEXMB1.chmccorp.cchmc.org>
	<419332796.3033469.1378977906912.JavaMail.root@indus.zimbra.ru.nl>
	<F8170A13692BD94597081861B03931C62761C494@MCEXMB1.chmccorp.cchmc.org>
	<8920B8D343C27B46B5BEDB8BFA8B2657477D73A5E1@MAILER.mpi.nl>
Message-ID: <F8170A13692BD94597081861B03931C62761C515@MCEXMB1.chmccorp.cchmc.org>

Thank you, Izabela.  Your solution is much more efficient than my own!

Keith McConnell, M.S.

513.636.0739 (desk)
513.504.9907 (cell)

Division of Pulmonary Medicine
Cincinnati Children's Hospital Medical Center
Cincinnati, OH  45229


-----Original Message-----
From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Izabela Mikula
Sent: Thursday, September 12, 2013 9:49 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] plotting differences in power spectrum

Hi Keith,

The diff object that you created only contains powspctrm field, so it doesn't have freq data structure anymore.
I would suggest using:

cfg=[];
cfg.operation='subtract'
cfg.parameter = 'powspctrm';
diff=ft_math(cfg, data1,data2)

Hope that helps.

Best,
Izabela

-----Original Message-----
From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of McConnell, Keith
Sent: Thursday, September 12, 2013 3:05 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] plotting differences in power spectrum

Thank you Nietzsche for your kind offer of help.

First, to your aside, I am trying to use ft_multiplotTFR.  Sorry for my lack of clarity.

Now to the matter:  I have calculated the power spectrum for each level of stimulus intensity using ft_freqanalysis(cfg, data1) and ft_freqanalysis(cfg, data2).  The result is a 3D double precision array arranged (#ChannelsX#FrequencyBinsX#TimeBins).


 I then calculate the difference using 

for i = 1:NUMBER_CHANNELS
    diff(i,:)=(data1.powspctrm(i,:))-(data2.powspctrm(i,:));
end

The result is a 2D double precision array with the form of (#ChannelsX(the product of the number freq bins and the number of time bins))

So, I guess that my problem is that I've gone from a 3D array to a 2D array in the course of the subtraction.  I am not sure how to correct this error.

Thanks again for the help.

Keith

Keith McConnell, M.S.

513.636.0739 (desk)
513.504.9907 (cell)

Division of Pulmonary Medicine
Cincinnati Children's Hospital Medical Center Cincinnati, OH  45229


-----Original Message-----
From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Lam, N.H.L. (Nietzsche)
Sent: Thursday, September 12, 2013 5:25 AM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] plotting differences in power spectrum

Hi Keith,

I could try to help you (this will be more first attempt with this mailing list...!) Could you provide more information about how you calculated the difference between the two spectra, and precisely what 'freq' (your difference spectra) looks like when you feed it as an argument into ft_multiplotTFR?

As a side, I'm aware that there is ft_multiplotXX, where XX can be replaced with "CC", "ER", "TFR", but I haven't seen a function with the name "ft_multiplot" on its own.

Best,
Nietzsche 

----- Original Message -----
> From: "Keith McConnell" <Keith.McConnell at cchmc.org>
> To: fieldtrip at science.ru.nl
> Sent: Wednesday, 11 September, 2013 7:48:43 PM
> Subject: [FieldTrip] plotting differences in power spectrum Hello,
> 
> 
> 
> I have an MEG experiment in which I expect my stimulus to incite 
> multiple reactions. I have run the experiment so that the stimulus is 
> applied at two different intensities. I would like to use the lower 
> intensity stimulus response as a 'mask' for the higher intensity 
> response.
> 
> 
> 
> I can calculate the power spectrum for both intensities and find the 
> difference.
> 
> 
> 
> Although I can generate an ft_multiplot for each individual power 
> spectrum, I cannot generate a ft_multiplotTFR of the difference 
> between the two spectra.
> 
> 
> 
> I get the following error messages:
> 
> 
> 
> Error using ft_checkdata (line 366)
> 
> This function requires freq data as input.
> 
> 
> 
> Error in ft_multiplotTFR (line 135)
> 
> data = ft_checkdata(data, 'datatype', 'freq');
> 
> 
> 
> Can anyone provide some help?
> 
> 
> 
> Thanks,
> 
> 
> 
> Keith
> 
> 
> 
> Keith McConnell, M.S.
> 
> 
> 
> 513.636.0739 (desk)
> 
> 513.504.9907 (cell)
> 
> 
> 
> Division of Pulmonary Medicine
> 
> Cincinnati Children's Hospital Medical Center
> 
> Cincinnati, OH 45229
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

--
Nietzsche H.L. Lam, MSc
PhD Candidate 

Max Planck Institute for Psycholinguistics Wundtlaan 1, 6525 XD Nijmegen, The Netherlands 

Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Kapittelweg 29, 6525EN Nijmegen, The Netherlands 

n.lam at fcdonders.ru.nl 
+31-24-3668219


neurobiologyoflanguage.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 n.lam at fcdonders.ru.nl  Thu Sep 12 15:53:14 2013
From: n.lam at fcdonders.ru.nl (Lam, N.H.L. (Nietzsche))
Date: Thu, 12 Sep 2013 15:53:14 +0200 (CEST)
Subject: [FieldTrip] plotting differences in power spectrum
In-Reply-To: <8920B8D343C27B46B5BEDB8BFA8B2657477D73A5E1@MAILER.mpi.nl>
Message-ID: <175390384.3043142.1378993994588.JavaMail.root@indus.zimbra.ru.nl>

Hi Keith,

In addition, it is helpful for future questions if you include a display of the fields in your data structure.  As Izabela pointed out, it looked lke you were missing all the other necessary fields in order for ft_multiplotTFR to recognise the data as freq data:

e.g., on the fieldtrip website we show the data as follows:

TFRhann = 

        label: {149x1 cell}
       dimord: 'chan_freq_time'
         freq: [2 4 6 8 10 12 14 16 18 20 22 24 26 28 30]
         time: [1x41 double]
    powspctrm: [149x15x41 double]
    cumtapcnt: [77x15 double]
         grad: [1x1 struct]
          cfg: [1x1 struct]

Best,
Nietzsche 

----- Original Message -----
> From: "Izabela Mikula" <Izabela.Mikula at mpi.nl>
> To: "FieldTrip discussion list" <fieldtrip at science.ru.nl>
> Sent: Thursday, 12 September, 2013 3:48:56 PM
> Subject: Re: [FieldTrip] plotting differences in power spectrum
> Hi Keith,
> 
> The diff object that you created only contains powspctrm field, so it
> doesn't have freq data structure anymore.
> I would suggest using:
> 
> cfg=[];
> cfg.operation='subtract'
> cfg.parameter = 'powspctrm';
> diff=ft_math(cfg, data1,data2)
> 
> Hope that helps.
> 
> Best,
> Izabela
> 
> -----Original Message-----
> From: fieldtrip-bounces at science.ru.nl
> [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of McConnell, Keith
> Sent: Thursday, September 12, 2013 3:05 PM
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] plotting differences in power spectrum
> 
> Thank you Nietzsche for your kind offer of help.
> 
> First, to your aside, I am trying to use ft_multiplotTFR. Sorry for my
> lack of clarity.
> 
> Now to the matter: I have calculated the power spectrum for each level
> of stimulus intensity using ft_freqanalysis(cfg, data1) and
> ft_freqanalysis(cfg, data2). The result is a 3D double precision array
> arranged (#ChannelsX#FrequencyBinsX#TimeBins).
> 
> 
> I then calculate the difference using
> 
> for i = 1:NUMBER_CHANNELS
> diff(i,:)=(data1.powspctrm(i,:))-(data2.powspctrm(i,:));
> end
> 
> The result is a 2D double precision array with the form of
> (#ChannelsX(the product of the number freq bins and the number of time
> bins))
> 
> So, I guess that my problem is that I've gone from a 3D array to a 2D
> array in the course of the subtraction. I am not sure how to correct
> this error.
> 
> Thanks again for the help.
> 
> Keith
> 
> Keith McConnell, M.S.
> 
> 513.636.0739 (desk)
> 513.504.9907 (cell)
> 
> Division of Pulmonary Medicine
> Cincinnati Children's Hospital Medical Center Cincinnati, OH 45229
> 
> 
> -----Original Message-----
> From: fieldtrip-bounces at science.ru.nl
> [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Lam, N.H.L.
> (Nietzsche)
> Sent: Thursday, September 12, 2013 5:25 AM
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] plotting differences in power spectrum
> 
> Hi Keith,
> 
> I could try to help you (this will be more first attempt with this
> mailing list...!) Could you provide more information about how you
> calculated the difference between the two spectra, and precisely what
> 'freq' (your difference spectra) looks like when you feed it as an
> argument into ft_multiplotTFR?
> 
> As a side, I'm aware that there is ft_multiplotXX, where XX can be
> replaced with "CC", "ER", "TFR", but I haven't seen a function with
> the name "ft_multiplot" on its own.
> 
> Best,
> Nietzsche
> 
> ----- Original Message -----
> > From: "Keith McConnell" <Keith.McConnell at cchmc.org>
> > To: fieldtrip at science.ru.nl
> > Sent: Wednesday, 11 September, 2013 7:48:43 PM
> > Subject: [FieldTrip] plotting differences in power spectrum Hello,
> >
> >
> >
> > I have an MEG experiment in which I expect my stimulus to incite
> > multiple reactions. I have run the experiment so that the stimulus
> > is
> > applied at two different intensities. I would like to use the lower
> > intensity stimulus response as a 'mask' for the higher intensity
> > response.
> >
> >
> >
> > I can calculate the power spectrum for both intensities and find the
> > difference.
> >
> >
> >
> > Although I can generate an ft_multiplot for each individual power
> > spectrum, I cannot generate a ft_multiplotTFR of the difference
> > between the two spectra.
> >
> >
> >
> > I get the following error messages:
> >
> >
> >
> > Error using ft_checkdata (line 366)
> >
> > This function requires freq data as input.
> >
> >
> >
> > Error in ft_multiplotTFR (line 135)
> >
> > data = ft_checkdata(data, 'datatype', 'freq');
> >
> >
> >
> > Can anyone provide some help?
> >
> >
> >
> > Thanks,
> >
> >
> >
> > Keith
> >
> >
> >
> > Keith McConnell, M.S.
> >
> >
> >
> > 513.636.0739 (desk)
> >
> > 513.504.9907 (cell)
> >
> >
> >
> > Division of Pulmonary Medicine
> >
> > Cincinnati Children's Hospital Medical Center
> >
> > Cincinnati, OH 45229
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> --
> Nietzsche H.L. Lam, MSc
> PhD Candidate
> 
> Max Planck Institute for Psycholinguistics Wundtlaan 1, 6525 XD
> Nijmegen, The Netherlands
> 
> Donders Institute for Brain, Cognition and Behaviour, Centre for
> Cognitive Neuroimaging, Kapittelweg 29, 6525EN Nijmegen, The
> Netherlands
> 
> n.lam at fcdonders.ru.nl
> +31-24-3668219
> 
> 
> neurobiologyoflanguage.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

-- 
Nietzsche H.L. Lam, MSc 
PhD Candidate 

Max Planck Institute for Psycholinguistics 
Wundtlaan 1, 6525 XD Nijmegen, The Netherlands 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging, 
Kapittelweg 29, 6525EN Nijmegen, The Netherlands 

n.lam at fcdonders.ru.nl 
+31-24-3668219 


neurobiologyoflanguage.com 


From tzvetan.popov at uni-konstanz.de  Thu Sep 12 15:52:49 2013
From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov)
Date: Thu, 12 Sep 2013 15:52:49 +0200
Subject: [FieldTrip] plotting differences in power spectrum
In-Reply-To: <F8170A13692BD94597081861B03931C62761C494@MCEXMB1.chmccorp.cchmc.org>
References: <F8170A13692BD94597081861B03931C62761C05D@MCEXMB1.chmccorp.cchmc.org>
	<419332796.3033469.1378977906912.JavaMail.root@indus.zimbra.ru.nl>
	<F8170A13692BD94597081861B03931C62761C494@MCEXMB1.chmccorp.cchmc.org>
Message-ID: <DA40F33E-7DCE-413A-BDEA-D6B37B34135D@uni-konstanz.de>


Dear Keith,

could you type
diff=freqdata1;
diff.powspctrm=freqdata1.powspctrm-freqdata2.powspctrm;

and plot diff? Maybe that would suffice your needs.
best
tzvetan




*******************************************
Tzvetan Popov  
Clinical Psychology       
University of Konstanz
Box 23
78457 Konstanz, GERMANY
Phone: 0049-7531-883086
Fax:      0049-7531-884601
Email:  tzvetan.popov at uni-konstanz.de
*******************************************

> Thank you Nietzsche for your kind offer of help.
> 
> First, to your aside, I am trying to use ft_multiplotTFR.  Sorry for my lack of clarity.
> 
> Now to the matter:  I have calculated the power spectrum for each level of stimulus intensity using ft_freqanalysis(cfg, data1) and ft_freqanalysis(cfg, data2).  The result is a 3D double precision array arranged (#ChannelsX#FrequencyBinsX#TimeBins).
> 
> 
> I then calculate the difference using 
> 
> for i = 1:NUMBER_CHANNELS
>    diff(i,:)=(data1.powspctrm(i,:))-(data2.powspctrm(i,:));
> end
> 
> The result is a 2D double precision array with the form of (#ChannelsX(the product of the number freq bins and the number of time bins))
> 
> So, I guess that my problem is that I've gone from a 3D array to a 2D array in the course of the subtraction.  I am not sure how to correct this error.
> 
> Thanks again for the help.
> 
> Keith
> 
> Keith McConnell, M.S.
> 
> 513.636.0739 (desk)
> 513.504.9907 (cell)
> 
> Division of Pulmonary Medicine
> Cincinnati Children's Hospital Medical Center
> Cincinnati, OH  45229
> 
> 
> -----Original Message-----
> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Lam, N.H.L. (Nietzsche)
> Sent: Thursday, September 12, 2013 5:25 AM
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] plotting differences in power spectrum
> 
> Hi Keith,
> 
> I could try to help you (this will be more first attempt with this mailing list...!) Could you provide more information about how you calculated the difference between the two spectra, and precisely what 'freq' (your difference spectra) looks like when you feed it as an argument into ft_multiplotTFR?
> 
> As a side, I'm aware that there is ft_multiplotXX, where XX can be replaced with "CC", "ER", "TFR", but I haven't seen a function with the name "ft_multiplot" on its own.
> 
> Best,
> Nietzsche 
> 
> ----- Original Message -----
>> From: "Keith McConnell" <Keith.McConnell at cchmc.org>
>> To: fieldtrip at science.ru.nl
>> Sent: Wednesday, 11 September, 2013 7:48:43 PM
>> Subject: [FieldTrip] plotting differences in power spectrum Hello,
>> 
>> 
>> 
>> I have an MEG experiment in which I expect my stimulus to incite 
>> multiple reactions. I have run the experiment so that the stimulus is 
>> applied at two different intensities. I would like to use the lower 
>> intensity stimulus response as a 'mask' for the higher intensity 
>> response.
>> 
>> 
>> 
>> I can calculate the power spectrum for both intensities and find the 
>> difference.
>> 
>> 
>> 
>> Although I can generate an ft_multiplot for each individual power 
>> spectrum, I cannot generate a ft_multiplotTFR of the difference 
>> between the two spectra.
>> 
>> 
>> 
>> I get the following error messages:
>> 
>> 
>> 
>> Error using ft_checkdata (line 366)
>> 
>> This function requires freq data as input.
>> 
>> 
>> 
>> Error in ft_multiplotTFR (line 135)
>> 
>> data = ft_checkdata(data, 'datatype', 'freq');
>> 
>> 
>> 
>> Can anyone provide some help?
>> 
>> 
>> 
>> Thanks,
>> 
>> 
>> 
>> Keith
>> 
>> 
>> 
>> Keith McConnell, M.S.
>> 
>> 
>> 
>> 513.636.0739 (desk)
>> 
>> 513.504.9907 (cell)
>> 
>> 
>> 
>> Division of Pulmonary Medicine
>> 
>> Cincinnati Children's Hospital Medical Center
>> 
>> Cincinnati, OH 45229
>> 
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> --
> Nietzsche H.L. Lam, MSc
> PhD Candidate 
> 
> Max Planck Institute for Psycholinguistics Wundtlaan 1, 6525 XD Nijmegen, The Netherlands 
> 
> Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Kapittelweg 29, 6525EN Nijmegen, The Netherlands 
> 
> n.lam at fcdonders.ru.nl 
> +31-24-3668219
> 
> 
> neurobiologyoflanguage.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 jean-michel.badier at univ-amu.fr  Thu Sep 12 15:51:43 2013
From: jean-michel.badier at univ-amu.fr (Jean-Michel Badier)
Date: Thu, 12 Sep 2013 15:51:43 +0200
Subject: [FieldTrip] [Filedtrip] Openmeeg and MEG
In-Reply-To: <CADeotZpOomN5A+R4K_rVtR-dESFFQeaYTXkPu+A6D5cZdQz9xg@mail.gmail.com>
References: <5229DCC9.3080809@univ-amu.fr>
	<CADeotZpOomN5A+R4K_rVtR-dESFFQeaYTXkPu+A6D5cZdQz9xg@mail.gmail.com>
Message-ID: <5231C6EF.4070102@univ-amu.fr>

Thanks Alex,

/cfg = [];//
//cfg.method = 'singleshell';//
//cfg.method = 'openmeeg';//
//vol = ft_prepare_headmodel(cfg, segmentedmri);//
/
Will work fine but and make the calls to openmeeg but:

/cfg                 = [];//
//cfg.grad            = grad;//
//cfg.vol             = vol;//
//cfg.reducerank      = 'no';//
//cfg.channel         = SELECTED_CHANNELS;//
//cfg.grid.resolution = 1.0;   % use a 3-D grid with a 1 cm resolution//
//[grid] = ft_prepare_leadfield(cfg);//
/
will generate the following errors:

/Error using ft_prepare_vol_sens (line 296)//
//MEG not yet supported with openmeeg//
//
//Error in prepare_headmodel (line 79)//
//[vol, sens] = ft_prepare_vol_sens(vol, sens, 'channel', cfg.channel, 
'order', cfg.order);//
//
//Error in ft_prepare_leadfield (line 123)//
//[vol, sens, cfg] = prepare_headmodel(cfg, data);/

Your example code in the openmeeg page will generate the same error.

The reason I am asking (beside the fact I like openmeeg ;-) ) is the 
fact that found differences in some results that I tried to reproduce 
with the Nolte method. I need to look at that more in more details.

Thanks again

Jean-Michel



Le 08/09/13 18:39, Alexandre Gramfort a écrit :
> hi Jean-Michel,
>
> I did not touch the OpenMEEG bindings for a while so it can
> have been broken by more recent commits. Nolte's method
> is a good alternative.
>
> Best,
> Alex
>
>
> On Fri, Sep 6, 2013 at 3:46 PM, Jean-Michel Badier
> <jean-michel.badier at univ-amu.fr> wrote:
>> Dear FT and Openmeeg users,
>>
>> I seems that fieldtrip does not support (anymore ? it seems it was possible
>> in the past) Openmeeg for MEG.
>> Does it means that the Nolte  or the multiple spheres approaches are
>> sufficient and do not require extra calculation?
>> I wonder in some parts of the brain.
>>
>> Is this integration scheduled sometimes?
>>
>> Thanks
>>
>> Jean-Michel
>> --
>>
>>
>> Jean-Michel Badier
>>
>> Laboratoire de MagnétoEncéphaloGraphie
>> Institut de Neurosciences des Systèmes - INSERM UMR 1106
>> http://ins.medecine.univmed.fr/
>>
>>
>>
>> Service de Neurophysiologie Clinique. CHU Timone
>>
>> Hôpital de la Timone  264, rue Saint Pierre 13385 Marseille Cedex 5
>>
>> 33 (0)4 91 38 55 62
>>
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 


Jean-Michel Badier

Laboratoire de MagnétoEncéphaloGraphie
Institut de Neurosciences des Systèmes - INSERM UMR 1106
http://ins.medecine.univmed.fr/

Service de Neurophysiologie Clinique.CHU Timone

/Hôpital/de la /Timone/264, rue Saint Pierre 13385 Marseille Cedex 5

33 (0)4 91 38 55 62

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From mcantor at umich.edu  Thu Sep 12 17:52:00 2013
From: mcantor at umich.edu (Max Cantor)
Date: Thu, 12 Sep 2013 11:52:00 -0400
Subject: [FieldTrip] cluster based timelock statistics minimum time
	parameter
In-Reply-To: <CAJT2k_-+=dRSNH01D08U=RNZ1QXa22EwuWALujf864jP4YdWjg@mail.gmail.com>
References: <CAJT2k_-+=dRSNH01D08U=RNZ1QXa22EwuWALujf864jP4YdWjg@mail.gmail.com>
Message-ID: <CAFTjRaUqwRySN5ytMtJM2oUMM-YibgGVDC3U_VzHYKt=YsWjgw@mail.gmail.com>

Thanks Aaron and Stephen, I think this will really help us. We're going to
try using a low pass filter to effect the minimum cluster window.


On Thu, Sep 12, 2013 at 6:09 AM, Stephen Politzer-Ahles <
politzerahless at gmail.com> wrote:

>
> Hi Max,
>
> This was recently discussed (see
> http://mailman.science.ru.nl/pipermail/fieldtrip/2013-July/006847.html and
> following messages), I'm not sure if that will help you or not.
>
> Best,
> Steve
>
>
> Stephen Politzer-Ahles
> New York University, Abu Dhabi
> Neuroscience of Language Lab
> http://www.nyu.edu/projects/politzer-ahles/
>
>
>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Wed, 11 Sep 2013 14:53:26 -0400
>> From: Max Cantor <mcantor at umich.edu>
>> To: fieldtrip at science.ru.nl
>> Subject: [FieldTrip] cluster based timelock statistics minimum time
>>         parameter
>> Message-ID:
>>         <CAFTjRaVWHgWwF4A5J7+EFbxUuAazxd=
>> Fw7B6NCW8u5Dk5igmow at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>
>> For a group analysis of ERP data we are interested in limiting cluster
>> size
>> by temporal extent (E.g. Only consider clusters 20 ms or longer). Is there
>> a clustering parameter equivalent to minnbchan for time samples? Searching
>> through the tutorial and help files didn't turn up anything.
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>> ------------------------------
>>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From reyesale at usc.edu  Thu Sep 12 17:54:38 2013
From: reyesale at usc.edu (Alexander Reyes)
Date: Thu, 12 Sep 2013 08:54:38 -0700
Subject: [FieldTrip] generic data format
Message-ID: <CAOGmYv8TyuKX-to-dTbAJd7O4Oxx57uSaZM1_5z2hdiT1KSu1Q@mail.gmail.com>

Hello,

I am having some difficulty getting my data into a format that can be read
by FieldTrip correctly. I apologize in advance for the length of this e
mail. This is actually a two part question.

1. The data I am trying to analyze consists of electrocorticography (ECoG)
data rather than EEG or MEG and was collected with a system not supported
by FieldTrip. My raw data are segmented into 30 second trials (22 in total)
and arranged into columns representing 76 ECoG and 8 EMG channels and
sampled at 500 Hz. There are no markers or triggers in my data as of now
since this is preliminary data. Additionally, I have not removed any
artifacts from the data nor have I redefined any trials.

Following the FAQ for importing a generic data format, I have successfully
created the following structure:

data.label =          subjectData.Labels;
data.fsample =     subjectData.Fs;
data.trial =         subjectData.TrialData;
data.time =          subjectData.Ref;

I have fed this data into the ft_preprocessing.m function with the
configuration shown below.

cfg = [];
cfg.channel       = 'C*';
cfg.lpfilter      = 'yes';
cfg.hpfilter      = 'yes';
cfg.bsfilter      = 'yes';
cfg.lpfreq        = 100/data.fsample;
cfg.hpfreq        = 10/data.fsample;
cfg.bsfreq        = [59 61]/data.fsample;
cfg.lpfiltord     = 4;
cfg.hpfiltord     = 4;
cfg.bpfiltord     = 4;
cfg.lpfilttype    = 'but';
cfg.hpfilttype    = 'but';
ecog = ft_preprocessing(cfg,data);

The generated file filters the data correctly, but there are edge effects
so I would like to pad the data. However, when I insert the two extra lines
shown below and then run ft_preprocessing, I get the error that follows.

cfg.padding       = 200;
cfg.padtype       = 'data';


Error using butter (line 83)
butter: critical frequencies must be in (0 1)

Error in ft_preproc_lowpassfilter (line 93)
    [B, A] = butter(N, max(Flp)/Fn);

Error in preproc (line 297)
if strcmp(cfg.lpfilter, 'yes'),     dat = ft_preproc_lowpassfilter(dat,
fsample, cfg.lpfreq, cfg.lpfiltord, cfg.lpfilttype,
cfg.lpfiltdir, cfg.lpinstabilityfix); end

Error in ft_preprocessing (line 323)
    [dataout.trial{i}, dataout.label, dataout.time{i}, cfg] =
preproc(data.trial{i}(rawindx,:), data.label(rawindx),  data.time{i},
    cfg, begpadding, endpadding);

I would appreciate some help as to why the padding does not work for my
data set.

2. In an attempt to keep moving forward, I have bypassed the padding and
tried to do a simple frequency analysis using the following configuration:

cfg = [];
cfg.method = 'mtmfft';
cfg.output = 'pow';
cfg.foi = [1:30];
cfg.taper = 'hanning';
cfg.t_ftimwin = 4./cfg.foi;
cfg.toi = 0:0.5:30;
cfg.tapsmofrq = 4;
freq = ft_freqanalysis (cfg,ecog);

But I get the following error:

Error using ft_specest_mtmfft (line 75)
the padding that you specified is shorter than the data

Error in ft_freqanalysis (line 503)
      [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper',
cfg.taper, options{:}, 'feedback', fbopt);

I was wondering if I could get some help decrypting this error message.

Thank you in advance.

Alex.
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From pgoodin at swin.edu.au  Thu Sep 12 23:49:33 2013
From: pgoodin at swin.edu.au (Peter Goodin)
Date: Thu, 12 Sep 2013 21:49:33 +0000
Subject: [FieldTrip] 3d sensor space plots?
Message-ID: <A55BBE5A90EFC441A6FE147DF0DFE26EBCDAA1@gsp-ex02.ds.swin.edu.au>

Hi Fieldtrippers,

Does Fieldtrip have a native option to plot data to a 3d sensor space (so something like https://wiki.umd.edu/meglab/images/0/0f/MEG160_M100.jpg)? If not, have others found work arounds and managed to produce these plots (so either constructing your own scripts or importing your data into other software or the like)?

Thanks,

Peter

__________________________
Peter Goodin,
BSc (Hons), Ph.D Candidate.

Brain and Psychological Sciences Research Centre (BPsych)
Swinburne University,
Hawthorn, Vic, 3122

Monash Alfred Psychiatry Research Centre (MAPrc)
Level 4, 607 St Kilda Road,
Melbourne 3004
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From jochem.rieger at uni-oldenburg.de  Fri Sep 13 03:20:07 2013
From: jochem.rieger at uni-oldenburg.de (Jochem Rieger)
Date: Thu, 12 Sep 2013 18:20:07 -0700
Subject: [FieldTrip] Post-doctoral position with a focus on speech coding in
 the human brain.
Message-ID: <52326847.3020509@uni-oldenburg.de>

The Department of Applied Neurocognitive Psychology at Oldenburg
University, Germany, offers a

Post-doctoral position (salary level E13 TVL, 3 years)

with a focus on signal processing / statistical learning for analysis of
speech coding in the human brain. 

The position is linked to the collaborative research center "The Active
Auditory System" SFB-TR 31. The research center aims to characterize and
model mechanism of auditory object formation and scene analysis by
combining psychophysical, neurophysiological, and quantitative modelling.

The post-doctoral position is situated in a project that applies
statistical learning methods to human intracranial recordings (ECoG) and
fMRI to derive and test quantitative statistical models of speech coding
in the human brain. The experiments are performed in a highly
interdisciplinary lab environment and in close collaboration with the
University of California Berkeley and Stanford University.

The quantitative nature of the research project will require highly
motivated candidates with strong quantitative and experimental skills.
Successful candidates will perform cutting edge research and should have
a background in one or more of the following fields: signal processing,
statistical learning, brain-machine-interfacing, non-invasive or
invasive human neurophysiology of the auditory system. Applicants must
have an academic university degree (Master or equivalent) and a PhD (or
equivalent).

Successful candidates will work in an interdisciplinary network with
opportunities for international exchange.

The post-doctoral position is initially limited to three years, with an
option for extension, and can be split.

Applications should include your CV, a list of most recent publications,
two recommendation letters, and a research statement (max. 3 pages). The
University of Oldenburg is an equal opportunity employer. To increase
the proportion of women and non-disqualifying handicapped, they will be
preferred among candidates with equal qualifications.

Please send inquiries and electronic applications per email (preferred)
to Professor Dr. Jochem Rieger: Jochem.rieger at uni-oldenburg.de
<mailto:Jochem.rieger at uni-oldenburg.de>

or paper applications per regular mail to:

Margrit Jung
Dept. of Applied Neurocognitive Psychology
Institute of Psychology
Oldenburg University
26111 Oldenburg
Germany

Application deadline is October 6^th , 2013.

-- 
Prof. Dr. rer. nat. Jochem Rieger

Applied Neurocognitive         Knight Lab
Psychology                     Helen Wills Neuroscience Institute
Faculty V                      University of California
Carl-von-Ossietzky University  132 Barker Hall
26111 Oldenburg                Berkeley, CA 94720-3192
Germany                        USA

Phone: +49(0)4417984533
Fax:   +49(0)4417983865

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From roeysc at gmail.com  Mon Sep 16 13:14:12 2013
From: roeysc at gmail.com (Roey Schurr)
Date: Mon, 16 Sep 2013 14:14:12 +0300
Subject: [FieldTrip] Source Analysis Normalisation in-subject and
	in-group
In-Reply-To: <CAHm4wZAWwHisWEPd41qxe6EiNAgkh_vqv2eMWvaGpNWdRQ1xww@mail.gmail.com>
References: <CAHm4wZAWwHisWEPd41qxe6EiNAgkh_vqv2eMWvaGpNWdRQ1xww@mail.gmail.com>
Message-ID: <CAHm4wZAiwd-eC3ODVr=xf_gTyW3PjBCNvg4wMn+gFqdsRiRWgA@mail.gmail.com>

Dear all,

This is a reminder regardig our question about nomralisation of EEG in
source reconstruction analysis.

Thank you all in advance!
Aia and Roey

On Mon, Aug 26, 2013 at 1:08 AM, Roey Schurr <roeysc at gmail.com> wrote:

> Hi all,
>
> We have a question regarding normalisation of EEG signals for source
> reconstruction analysis.
>
> We have EEG records (not ERP) of a few patients in two different
> conditions (each condition consists of several 2 seconds segments/trials).
> Each recording was done over a period of a few days, and in different
> sessions. We also have anatomycal MRI scans for each patient (subject).
>
> We would like to make two statistic comparisons:
>
> 1.    Compare the source analysis of the two conditions in each subject.
>
> 2.    Compare the source analysis of the two conditions, based upon all
> subjects.
>
> For the first comparison, we are puzzled about the appropriate way to
> normalise and standardize our data, since each EEG segment was recorded at
> a different time, and hence may be affected by different electrode
> conductivity, for example. How would you normalise the data?
>
> For the second comparison, of course, we would like to normalise the
> source analysis results in the anatomycal level using ft_volumenormalise.
>
> However, we are puzzled about the appropriate way to normalise and
> standardize our data, since subjects differ from each other (for example,
> anatomycally, resulting in changes of power spectrum).
>
> How would you standartize the data between subjects?
>
>
>
> Thank you very much,
>
> best regards,
>
> Aia and Roey
>
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From ajaymaddirala at gmail.com  Mon Sep 16 14:03:45 2013
From: ajaymaddirala at gmail.com (ajay maddirala)
Date: Mon, 16 Sep 2013 17:33:45 +0530
Subject: [FieldTrip] Downloading Problem-REG
Message-ID: <CAJa6ZTbJXFoy+qeRcS1H2=Q8KUurKmSTJiuOnu_q8v08Z1hNnw@mail.gmail.com>

Respected Sir,

I am Research Scholar working on M/EEG. Recently i have seen  a tutorial
on  "Dealing With TMS-EEG dataset". In that tutorial, to download the data
one link is given, when i click on that link i am unable to download the
data. Please tell me what is the problem.

                                  Thank You Sir.


-- 
AJAY KUMAR.MADDIRALA,
Research Scholar,
Department of Electronics & Electrical Engg (EEE),
Indian Institute of Technology Guwahati (IITG),
Guwahati,
Assam State,
India.
cell +918011212952
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From j.herring at fcdonders.ru.nl  Mon Sep 16 15:22:54 2013
From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim))
Date: Mon, 16 Sep 2013 15:22:54 +0200 (CEST)
Subject: [FieldTrip] Downloading Problem-REG
In-Reply-To: <CAJa6ZTbJXFoy+qeRcS1H2=Q8KUurKmSTJiuOnu_q8v08Z1hNnw@mail.gmail.com>
References: <CAJa6ZTbJXFoy+qeRcS1H2=Q8KUurKmSTJiuOnu_q8v08Z1hNnw@mail.gmail.com>
Message-ID: <007e01ceb2df$daa2da40$8fe88ec0$@herring@fcdonders.ru.nl>

Dear Ajay,

 

Do you get a specific error? I have checked the link to the dataset and it
seems to work.

 

Best,

 

Jim

 

From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of ajay maddirala
Sent: maandag 16 september 2013 14:04
To: fieldtrip at donders.ru.nl
Subject: [FieldTrip] Downloading Problem-REG

 

Respected Sir,

I am Research Scholar working on M/EEG. Recently i have seen  a tutorial
on  "Dealing With TMS-EEG dataset". In that tutorial, to download the data
one link is given, when i click on that link i am unable to download the
data. Please tell me what is the problem. 

                                  Thank You Sir.


 


-- 

AJAY KUMAR.MADDIRALA,

Research Scholar,

Department of Electronics & Electrical Engg (EEE),

Indian Institute of Technology Guwahati (IITG),

Guwahati,

Assam State,

India.

cell +918011212952

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From jan.schoffelen at donders.ru.nl  Mon Sep 16 16:12:30 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Mon, 16 Sep 2013 16:12:30 +0200
Subject: [FieldTrip] setting colormap for ft_multiplotTFR not working +
	easy fix
In-Reply-To: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A95FA4@MBX13.d.ethz.ch>
References: <DC66D6ECA4FEFA4BBEE185B117D1DA6613A95FA4@MBX13.d.ethz.ch>
Message-ID: <02B6BF3A-896A-480A-A04E-227CD0AA29DF@donders.ru.nl>

Hi Ben,

Thanks for letting us know, and for providing the fix ;-). I updated the code, and it should be available in tonight's download, or otherwise by doing ft_version update.

Best wishes,

Jan-Mathijs


On Sep 5, 2013, at 12:47 PM, van Lier Ben wrote:

> Hi all,
> 
> I like to have my spectra in the hot colormap instead of the matlab default jet (jet is bad - http://www.jwave.vt.edu/%7Erkriz/Projects/create_color_table/color_07.pdf )
> 
> cfg.colormap = hot(256);
> works well for all the plots except multiplot. i get this error:
> 
> -------------
> Error using hg.axes/set
> The name 'colormap' is not an accessible property for an instance of class 'axes'.
> 
> Error in ft_multiplotTFR (line 501)
>  set(gca,'colormap',cfg.colormap);
> --------------
> 
> gca should be gcf :)
> 
> cheers
> Ben
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

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

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

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

http://www.hettaligebrein.nl

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From deleted  Mon Sep 16 17:12:53 2013
From: deleted (deleted)
Date: Mon, 16 Sep 2013 17:12:53 +0200
Subject: [FieldTrip] ft_singleplotTFR seems broken
Message-ID: <CAJ7RtRGw_o4pO5tR8RFWJad4K32pArxMXRJcXnOp5irtEcOxOA@mail.gmail.com>

Dear Fieldtrippers,

I've been doing some exploratory plotting of a dataset where several
subjects were exposed to a continuous stimulus (CPM) over the course of
three minutes. One of the things that was asked was a time-frequency plot,
over those three minutes. While I'm not quite sure a TFR can be used on
that scale without problems, I went ahead with it just to see what
Fieldtrip would do. What I got, was this:
http://tinypic.com/r/zx2tqs/5|
And I have no idea what went wrong (note that this specific subject only
got a 60s stimulus). Quality of the picture and the validity of the
analysis aside, I have a severe problem with the axes, which seem to be all
over the place.

I simply read the data using ft_preprocessing (no filters or anything,
since the student in charge already used a 10Hz high-pass and a 150Hz
low-pass filter).
The only field in 'cfg' is 'headerfile'.

Next, I call ft_freqanalysis with:
*    cfg.output = 'pow';*
*    cfg.method = 'wavelet'; % default; Morlet wavelet*
*    cfg.taper = 'hanning';
*
*    cfg.tapsmofrq = 4;*
*    cfg.channel = 'Cz';*
*    cfg.foi = [20:0.5:30];*
*    cfg.t_ftimwin = ones(length(cfg.foi),1).*0.25;*
*    cfg.toi = 0:0.5:60;*

And finally, I end up with the monstrocity shown earlier. This problem only
presents itself with Fieldtrip-related functions, the normal Matlab-plots
work as well as they've ever done, so I'm thinking it's something in
Fieldtrip that's causing this.

My hope is that someone has encountered this problem before, and knows how
to solve it...

Sincerely,

Casper
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From max-philipp.stenner at med.ovgu.de  Mon Sep 16 18:36:08 2013
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Mon, 16 Sep 2013 16:36:08 +0000
Subject: [FieldTrip] Imaginary coherence and planar gradients
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58831FAD3649@esen3.imed.uni-magdeburg.de>

Dear fieldtrippers,

is it problematic to use ft_megplanar and ft_combineplanar (with cfg.combinemethod = 'svd') before computing phase-coupling, e.g. the imaginary part of coherency? Any help is much appreciated,

thanks!,

best wishes

Max



From Keith.McConnell at cchmc.org  Mon Sep 16 21:24:34 2013
From: Keith.McConnell at cchmc.org (McConnell, Keith)
Date: Mon, 16 Sep 2013 19:24:34 +0000
Subject: [FieldTrip] ft_rejectvisual question
Message-ID: <F8170A13692BD94597081861B03931C62761CFBF@MCEXMB1.chmccorp.cchmc.org>

Hello,

When using the cfg.method 'summary' are there a 'rules of thumb' for deciding what channels to reject for each of the parameters (var, min, max, etc.)?

Thank you,

Keith McConnell, M.S.

513.636.0739 (desk)
513.504.9907 (cell)

Division of Pulmonary Medicine
Cincinnati Children's Hospital Medical Center
Cincinnati, OH  45229

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From aaron.schurger at gmail.com  Mon Sep 16 22:37:04 2013
From: aaron.schurger at gmail.com (Aaron Schurger)
Date: Mon, 16 Sep 2013 22:37:04 +0200
Subject: [FieldTrip] ft_rejectvisual question
In-Reply-To: <F8170A13692BD94597081861B03931C62761CFBF@MCEXMB1.chmccorp.cchmc.org>
References: <F8170A13692BD94597081861B03931C62761CFBF@MCEXMB1.chmccorp.cchmc.org>
Message-ID: <CALeeyAQz4SXM=53KnRZ8R=n9R6tMBh-PpJdkdXFg8pWrkicNeQ@mail.gmail.com>

Reject trials before you reject channels. Sometimes a channel looks
bad just because of one bad trial. The way the data are presented, you
can spot this by eye.
Aaron

On Mon, Sep 16, 2013 at 9:24 PM, McConnell, Keith
<Keith.McConnell at cchmc.org> wrote:
> Hello,
>
>
>
> When using the cfg.method 'summary' are there a 'rules of thumb' for
> deciding what channels to reject for each of the parameters (var, min, max,
> etc.)?
>
>
>
> Thank you,
>
>
>
> Keith McConnell, M.S.
>
>
>
> 513.636.0739 (desk)
>
> 513.504.9907 (cell)
>
>
>
> Division of Pulmonary Medicine
>
> Cincinnati Children's Hospital Medical Center
>
> Cincinnati, OH  45229
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



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


From felix.lucka at uni-muenster.de  Tue Sep 17 10:39:03 2013
From: felix.lucka at uni-muenster.de (Felix Lucka)
Date: Tue, 17 Sep 2013 10:39:03 +0200
Subject: [FieldTrip] ft_rejectvisual question
In-Reply-To: <CALeeyAQz4SXM=53KnRZ8R=n9R6tMBh-PpJdkdXFg8pWrkicNeQ@mail.gmail.com>
References: <F8170A13692BD94597081861B03931C62761CFBF@MCEXMB1.chmccorp.cchmc.org>
	<CALeeyAQz4SXM=53KnRZ8R=n9R6tMBh-PpJdkdXFg8pWrkicNeQ@mail.gmail.com>
Message-ID: <52381527.8000805@uni-muenster.de>

Hi!
In addition to what Aaron said, if you want to reject channels, make 
sure that you do not reject them based on the activity you're actually 
looking for. For example, if you analyze stimulus evoked activity, do 
NOT reject channels based on the summary of the full trial data but only 
based on the summary of the pre stimulus interval...otherwise you'll 
delete the most important channels to analyze your data ;)
Best, Felix

Am 16.09.2013 22:37, schrieb Aaron Schurger:
> Reject trials before you reject channels. Sometimes a channel looks
> bad just because of one bad trial. The way the data are presented, you
> can spot this by eye.
> Aaron
>
> On Mon, Sep 16, 2013 at 9:24 PM, McConnell, Keith
> <Keith.McConnell at cchmc.org> wrote:
>> Hello,
>>
>>
>>
>> When using the cfg.method 'summary' are there a 'rules of thumb' for
>> deciding what channels to reject for each of the parameters (var, min, max,
>> etc.)?
>>
>>
>>
>> Thank you,
>>
>>
>>
>> Keith McConnell, M.S.
>>
>>
>>
>> 513.636.0739 (desk)
>>
>> 513.504.9907 (cell)
>>
>>
>>
>> Division of Pulmonary Medicine
>>
>> Cincinnati Children's Hospital Medical Center
>>
>> Cincinnati, OH  45229
>>
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>

-- 
  Dipl.-Math. Felix Lucka
  e-mail: felix.lucka at uni-muenster.de

  Workgroup Imaging, Prof. Dr. Martin Burger
  Institute for Computational and Applied Mathematics, University of 
Muenster
  www: http://wwwmath.uni-muenster.de/num/burger/organization/lucka

  Workgroup Methods in Bioelectromagnetism, PD. Dr. Carsten Wolters	
  Institute for Biomagnetism and Biosignalanalysis, University of Muenster
  www: http://campus.uni-muenster.de/index.php?id=919&L=1


From Keith.McConnell at cchmc.org  Tue Sep 17 17:10:12 2013
From: Keith.McConnell at cchmc.org (McConnell, Keith)
Date: Tue, 17 Sep 2013 15:10:12 +0000
Subject: [FieldTrip] ft_rejectvisual question #2
Message-ID: <F8170A13692BD94597081861B03931C62761D1EE@MCEXMB1.chmccorp.cchmc.org>

Hello,

Having run ft_rejectvisual with cfg.method = 'sumary' I don't see where the list of trials/channels marked BAD is stored.

I think I need that list for further analysis, no?

Keith McConnell, M.S.

513.636.0739 (desk)
513.504.9907 (cell)

Division of Pulmonary Medicine
Cincinnati Children's Hospital Medical Center
Cincinnati, OH  45229

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From aaron.schurger at gmail.com  Tue Sep 17 23:37:52 2013
From: aaron.schurger at gmail.com (Aaron Schurger)
Date: Tue, 17 Sep 2013 23:37:52 +0200
Subject: [FieldTrip] ft_rejectvisual question #2
In-Reply-To: <F8170A13692BD94597081861B03931C62761D1EE@MCEXMB1.chmccorp.cchmc.org>
References: <F8170A13692BD94597081861B03931C62761D1EE@MCEXMB1.chmccorp.cchmc.org>
Message-ID: <CALeeyAR+A_-fS7+nNRG2BfMZKqn4qO=6d-q7i4zGy5fOnrkhWA@mail.gmail.com>

I had always wondered about that. It simply returns a new data
structure with the bad trials and channels either excluded or replaced
with nan's. Maybe the list of excluded channels and trials is somehow
stored in the new data structure, but you can easily modify the code
so that it returns the variables chansel and trlsel. Just replace the
first line of ft_rejectvisual with

function [data,trlsel,chansel] = ft_rejectvisual(cfg, data)

Then you call the function like this:

[~,trlsel,chansel] = ft_rejectvisual(cfg,data);

So this way you keep you data structure as it was, but you now have
two indexes, one with the bad trials and one with the bad channels.

Aaron

On Tue, Sep 17, 2013 at 5:10 PM, McConnell, Keith
<Keith.McConnell at cchmc.org> wrote:
> Hello,
>
>
>
> Having run ft_rejectvisual with cfg.method = 'sumary' I don't see where the
> list of trials/channels marked BAD is stored.
>
>
>
> I think I need that list for further analysis, no?
>
>
>
> Keith McConnell, M.S.
>
>
>
> 513.636.0739 (desk)
>
> 513.504.9907 (cell)
>
>
>
> Division of Pulmonary Medicine
>
> Cincinnati Children's Hospital Medical Center
>
> Cincinnati, OH  45229
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



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


From s.rombetto at cib.na.cnr.it  Wed Sep 18 10:36:43 2013
From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it)
Date: Wed, 18 Sep 2013 10:36:43 +0200
Subject: [FieldTrip] synchronization likelihood
Message-ID: <20130918103643.0xkfrms2ogwk8848@arco.cib.na.cnr.it>

Dear Fieldtrip users,

I'd like to implement the synchronization likelihood algorithm in
matlab, in order to analyze data with Fieldtrip.
Do you know if anybody has already implemented it? Or maybe do you  
have any hint for me?

I am considering the paper written by CJ Stam et al., "Synchronization  
likelihood: an unbiased measure of generalized synchronization in  
multivariate data sets" as a guideline.
I know that Prof.Stam developed an instrument to evaluate  
synchronization, but my data (MEG data) are too big to be analyzed.

Thanks and best regards
-------------------------
   Dott.ssa Sara Rombetto
   Istituto di Cibernetica
   "E. Caianiello"
   Via Campi Flegrei, 34
   80078 Pozzuoli (NA)
   Italy
   mob +39 3401689815
   tel +39 0818675361
   fax +39 0818675128
--------------------------
"I disapprove of what you say, but I will defend to the death your
right to say
it." [Evelyn Beatrice Hall, The Friends Of Voltaire]


----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.





From eelke.spaak at donders.ru.nl  Wed Sep 18 13:25:32 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Wed, 18 Sep 2013 13:25:32 +0200
Subject: [FieldTrip] ft_singleplotTFR seems broken
In-Reply-To: <CAJ7RtRGw_o4pO5tR8RFWJad4K32pArxMXRJcXnOp5irtEcOxOA@mail.gmail.com>
References: <CAJ7RtRGw_o4pO5tR8RFWJad4K32pArxMXRJcXnOp5irtEcOxOA@mail.gmail.com>
Message-ID: <CABPNLUo5=dHpPA8JER_7yLg5YPM1qCcjkCXm11imJ-rGvEt_ew@mail.gmail.com>

Dear Casper,

Could you maybe post a snippet online somewhere (e.g. dropbox) of data
corresponding to this plot (i.e. the output of ft_freqanalysis that
you input to ft_singleplotTFR, assuming that it's averaged over trials
and therefore small)? Then we can see whether this is reproducable on
our systems.

Best,
Eelke

On 16 September 2013 17:12, deleted <deleted> wrote:
> Dear Fieldtrippers,
>
> I've been doing some exploratory plotting of a dataset where several
> subjects were exposed to a continuous stimulus (CPM) over the course of
> three minutes. One of the things that was asked was a time-frequency plot,
> over those three minutes. While I'm not quite sure a TFR can be used on that
> scale without problems, I went ahead with it just to see what Fieldtrip
> would do. What I got, was this:
> http://tinypic.com/r/zx2tqs/5|
> And I have no idea what went wrong (note that this specific subject only got
> a 60s stimulus). Quality of the picture and the validity of the analysis
> aside, I have a severe problem with the axes, which seem to be all over the
> place.
>
> I simply read the data using ft_preprocessing (no filters or anything, since
> the student in charge already used a 10Hz high-pass and a 150Hz low-pass
> filter).
> The only field in 'cfg' is 'headerfile'.
>
> Next, I call ft_freqanalysis with:
>     cfg.output = 'pow';
>     cfg.method = 'wavelet'; % default; Morlet wavelet
>     cfg.taper = 'hanning';
>     cfg.tapsmofrq = 4;
>     cfg.channel = 'Cz';
>     cfg.foi = [20:0.5:30];
>     cfg.t_ftimwin = ones(length(cfg.foi),1).*0.25;
>     cfg.toi = 0:0.5:60;
>
> And finally, I end up with the monstrocity shown earlier. This problem only
> presents itself with Fieldtrip-related functions, the normal Matlab-plots
> work as well as they've ever done, so I'm thinking it's something in
> Fieldtrip that's causing this.
>
> My hope is that someone has encountered this problem before, and knows how
> to solve it...
>
> Sincerely,
>
> Casper
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From Keith.McConnell at cchmc.org  Fri Sep 20 17:01:45 2013
From: Keith.McConnell at cchmc.org (McConnell, Keith)
Date: Fri, 20 Sep 2013 15:01:45 +0000
Subject: [FieldTrip] event re-labeling
Message-ID: <F8170A13692BD94597081861B03931C62761FD9F@MCEXMB1.chmccorp.cchmc.org>

Hello,

I have an data for which the events are inconsistently mislabeled.

Can/should I make the corrections using ft_write_event or,

can/should I make the correction at ft_read_event and redirect the function from the file to a corrected event structure?

Thanks,

Keith

Keith McConnell, M.S.

513.636.0739 (desk)
513.504.9907 (cell)

Division of Pulmonary Medicine
Cincinnati Children's Hospital Medical Center
Cincinnati, OH  45229

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From laura.marzetti at gmail.com  Sat Sep 21 10:13:00 2013
From: laura.marzetti at gmail.com (Laura Marzetti)
Date: Sat, 21 Sep 2013 10:13:00 +0200
Subject: [FieldTrip] Classification for comp structure
Message-ID: <CALyuhN2=TfYDV+B4K_0divkSC_XZqT6EV+-Vd_jPhectCSRrJw@mail.gmail.com>

Hi all,
I found a reference to the function ft_componentclassification in the wiki
documentation:
http://fieldtrip.fcdonders.nl/reference/ft_componentclassification
but apparently there is no function named after
ft_componentclassification.m in fieldtrip. Can anyone clarify the situation
to me?
Is there any tool to classify ICs?

Best,
Laura
-- 
Laura Marzetti, PhD
Istituto di Tecnologie Avanzate Biomediche
Università di Chieti "G. D'Annunzio"
Via dei Vestini - Campus Universitario
66013 Chieti - ITALY

phone: 0039-0871-3556944
fax: 0039-0871-3556930
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From jan.schoffelen at donders.ru.nl  Sat Sep 21 10:50:12 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Sat, 21 Sep 2013 10:50:12 +0200
Subject: [FieldTrip] Classification for comp structure
In-Reply-To: <CALyuhN2=TfYDV+B4K_0divkSC_XZqT6EV+-Vd_jPhectCSRrJw@mail.gmail.com>
References: <CALyuhN2=TfYDV+B4K_0divkSC_XZqT6EV+-Vd_jPhectCSRrJw@mail.gmail.com>
Message-ID: <E0D42417-F311-4EF1-A32D-4BC146449DF9@donders.ru.nl>

Hi Laura,

The clarification would be that this 'function' has been added as a place-holder to incorporate the classification strategies that are employed by for example the Chieti team. I'd say if you have any code to contribute: please knock yourself out, and feel free to do so.

Best wishes,

Jan-Mathijs


On Sep 21, 2013, at 10:13 AM, Laura Marzetti wrote:

> Hi all,
> I found a reference to the function ft_componentclassification in the wiki documentation:
> http://fieldtrip.fcdonders.nl/reference/ft_componentclassification
> but apparently there is no function named after ft_componentclassification.m in fieldtrip. Can anyone clarify the situation to me?
> Is there any tool to classify ICs?
> 
> Best,
> Laura
> -- 
> Laura Marzetti, PhD 
> Istituto di Tecnologie Avanzate Biomediche
> Università di Chieti "G. D'Annunzio"
> Via dei Vestini - Campus Universitario
> 66013 Chieti - ITALY
>  
> phone: 0039-0871-3556944
> fax: 0039-0871-3556930
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

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

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

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

http://www.hettaligebrein.nl

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From laura.marzetti at gmail.com  Sat Sep 21 12:03:22 2013
From: laura.marzetti at gmail.com (Laura Marzetti)
Date: Sat, 21 Sep 2013 12:03:22 +0200
Subject: [FieldTrip] Classification for comp structure
In-Reply-To: <E0D42417-F311-4EF1-A32D-4BC146449DF9@donders.ru.nl>
References: <CALyuhN2=TfYDV+B4K_0divkSC_XZqT6EV+-Vd_jPhectCSRrJw@mail.gmail.com>
	<E0D42417-F311-4EF1-A32D-4BC146449DF9@donders.ru.nl>
Message-ID: <CALyuhN36h1Q_LHKiV01On+6LpxrxTQKx0VUAurqrA6f=-3ARjQ@mail.gmail.com>

Let's see. Thanks
Laura


On Sat, Sep 21, 2013 at 10:50 AM, jan-mathijs schoffelen <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Laura,
>
> The clarification would be that this 'function' has been added as a
> place-holder to incorporate the classification strategies that are employed
> by for example the Chieti team. I'd say if you have any code to contribute:
> please knock yourself out, and feel free to do so.
>
> Best wishes,
>
> Jan-Mathijs
>
>
> On Sep 21, 2013, at 10:13 AM, Laura Marzetti wrote:
>
> Hi all,
> I found a reference to the function ft_componentclassification in the wiki
> documentation:
> http://fieldtrip.fcdonders.nl/reference/ft_componentclassification
> but apparently there is no function named after
> ft_componentclassification.m in fieldtrip. Can anyone clarify the situation
> to me?
> Is there any tool to classify ICs?
>
> Best,
> Laura
> --
> Laura Marzetti, PhD
> Istituto di Tecnologie Avanzate Biomediche
> Università di Chieti "G. D'Annunzio"
> Via dei Vestini - Campus Universitario
> 66013 Chieti - ITALY
>
> phone: 0039-0871-3556944
> fax: 0039-0871-3556930
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> Jan-Mathijs Schoffelen, MD PhD
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
>
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
>
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
>
> http://www.hettaligebrein.nl
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Laura Marzetti, PhD
Istituto di Tecnologie Avanzate Biomediche
Università di Chieti "G. D'Annunzio"
Via dei Vestini - Campus Universitario
66013 Chieti - ITALY

phone: 0039-0871-3556944
fax: 0039-0871-3556930
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From r.vandermeij at donders.ru.nl  Mon Sep 23 14:48:57 2013
From: r.vandermeij at donders.ru.nl (Roemer van der Meij)
Date: Mon, 23 Sep 2013 14:48:57 +0200
Subject: [FieldTrip] generic data format
In-Reply-To: <CAOGmYv8TyuKX-to-dTbAJd7O4Oxx57uSaZM1_5z2hdiT1KSu1Q@mail.gmail.com>
References: <CAOGmYv8TyuKX-to-dTbAJd7O4Oxx57uSaZM1_5z2hdiT1KSu1Q@mail.gmail.com>
Message-ID: <CA+WpQ36sCPL=kA1jjyXEHXjn+Ni-G9_UR6xCfC5c+OFf32mEDg@mail.gmail.com>

Hi Alex,

Sorry for the late response.
With regards to the first question, all filtering frequencies should be
specified in Hz. So, if you want a low pass at 10Hz, a high pass at 100Hz,
and a band-stop between 59 and 61 Hz, you should specify (which likely
fixes the error):
cfg.lpfreq        = 100
cfg.hpfreq        = 10
cfg.bsfreq        = [59 61]
Padding should be specified as the total number of seconds of each trial,
and (200-30)/2 seconds on each side seems a bit rigorous for removing
filtering artifacts ;). Unless you were intentionally using a low pass of
10/500 = 0.02 Hz. The longer the impulse response of the filter, the more
padding is needed to remove edge artifacts. (A 4th order butt of a very low
low-pass would have the IIR's filters version of an impulse response that
is very very long). In general, when using the above suggested filtering
frequencies and a 4th order butterworth and a sampling of 500Hz, a few
seconds of padding on both sides of the trial will likely be enough to
prevent edge artifacts.

However, when importing an unsupported data format, you cannot make use of
data-padding, which is the most optimal one. You could opt for
zero/mean/mirror padding, but they add transition artifacts, which might be
even worse than your edge-artifacts. Don't use these unless it's really the
only option, and be careful when doing so. My suggestion in your case would
be to segment the data (during importing) with additional data, and remove
this data after filtering, by hand (take care to adjust not only
data.trial, but also data.time). So, if trial #2 would last from 30 to 60
seconds, segment it from 25 to 65, filter it, and remove the first 5 and
the last 5 seconds. This will, of course, create issues if you want to use
the first 5 seconds of data.

With regards to your second question, the error suggests you used an
improper cfg.pad option. I don't see this in your code though, are you
absolutely sure you didn't include a cfg.pad? This should be specified in
seconds, which is the total length of each trial + padding. If left out,
this defaults to the length of the largest trial. Note though, this refers
to zero padding for spectral interpolation. Also, the option cfg.tapsmofrq
is only used if you specifiy cfg.taper = 'dpss'. It isn't used when using
cfg.taper = 'hanning'.

Cheers,
Roemer




On Thu, Sep 12, 2013 at 5:54 PM, Alexander Reyes <reyesale at usc.edu> wrote:

> Hello,
>
> I am having some difficulty getting my data into a format that can be read
> by FieldTrip correctly. I apologize in advance for the length of this e
> mail. This is actually a two part question.
>
> 1. The data I am trying to analyze consists of electrocorticography (ECoG)
> data rather than EEG or MEG and was collected with a system not supported
> by FieldTrip. My raw data are segmented into 30 second trials (22 in total)
> and arranged into columns representing 76 ECoG and 8 EMG channels and
> sampled at 500 Hz. There are no markers or triggers in my data as of now
> since this is preliminary data. Additionally, I have not removed any
> artifacts from the data nor have I redefined any trials.
>
> Following the FAQ for importing a generic data format, I have successfully
> created the following structure:
>
> data.label =          subjectData.Labels;
> data.fsample =     subjectData.Fs;
> data.trial =         subjectData.TrialData;
> data.time =          subjectData.Ref;
>
> I have fed this data into the ft_preprocessing.m function with the
> configuration shown below.
>
> cfg = [];
> cfg.channel       = 'C*';
> cfg.lpfilter      = 'yes';
> cfg.hpfilter      = 'yes';
> cfg.bsfilter      = 'yes';
> cfg.lpfreq        = 100/data.fsample;
> cfg.hpfreq        = 10/data.fsample;
> cfg.bsfreq        = [59 61]/data.fsample;
> cfg.lpfiltord     = 4;
> cfg.hpfiltord     = 4;
> cfg.bpfiltord     = 4;
> cfg.lpfilttype    = 'but';
> cfg.hpfilttype    = 'but';
> ecog = ft_preprocessing(cfg,data);
>
> The generated file filters the data correctly, but there are edge effects
> so I would like to pad the data. However, when I insert the two extra lines
> shown below and then run ft_preprocessing, I get the error that follows.
>
> cfg.padding       = 200;
> cfg.padtype       = 'data';
>
>
> Error using butter (line 83)
> butter: critical frequencies must be in (0 1)
>
> Error in ft_preproc_lowpassfilter (line 93)
>     [B, A] = butter(N, max(Flp)/Fn);
>
> Error in preproc (line 297)
> if strcmp(cfg.lpfilter, 'yes'),     dat = ft_preproc_lowpassfilter(dat,
> fsample, cfg.lpfreq, cfg.lpfiltord, cfg.lpfilttype,
> cfg.lpfiltdir, cfg.lpinstabilityfix); end
>
> Error in ft_preprocessing (line 323)
>     [dataout.trial{i}, dataout.label, dataout.time{i}, cfg] =
> preproc(data.trial{i}(rawindx,:), data.label(rawindx),  data.time{i},
>     cfg, begpadding, endpadding);
>
> I would appreciate some help as to why the padding does not work for my
> data set.
>
> 2. In an attempt to keep moving forward, I have bypassed the padding and
> tried to do a simple frequency analysis using the following configuration:
>
> cfg = [];
> cfg.method = 'mtmfft';
> cfg.output = 'pow';
> cfg.foi = [1:30];
> cfg.taper = 'hanning';
> cfg.t_ftimwin = 4./cfg.foi;
> cfg.toi = 0:0.5:30;
> cfg.tapsmofrq = 4;
> freq = ft_freqanalysis (cfg,ecog);
>
> But I get the following error:
>
> Error using ft_specest_mtmfft (line 75)
> the padding that you specified is shorter than the data
>
> Error in ft_freqanalysis (line 503)
>       [spectrum,ntaper,foi] = ft_specest_mtmfft(dat, time, 'taper',
> cfg.taper, options{:}, 'feedback', fbopt);
>
> I was wondering if I could get some help decrypting this error message.
>
> Thank you in advance.
>
> Alex.
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Roemer van der Meij M.Sc.
PhD Candidate
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognition
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 r.vandermeij at donders.ru.nl  Mon Sep 23 14:57:09 2013
From: r.vandermeij at donders.ru.nl (Roemer van der Meij)
Date: Mon, 23 Sep 2013 14:57:09 +0200
Subject: [FieldTrip] event re-labeling
In-Reply-To: <F8170A13692BD94597081861B03931C62761FD9F@MCEXMB1.chmccorp.cchmc.org>
References: <F8170A13692BD94597081861B03931C62761FD9F@MCEXMB1.chmccorp.cchmc.org>
Message-ID: <CA+WpQ36CsQuT9j=ePT49Fq06v1th=zzSkAvS3TEx2C+0L9K90A@mail.gmail.com>

Hi Keith,

You could fix the low level files that contain the event labels like you
suggested. However, I would advise you to just make an exception for this
specific dataset in your reading function, i.e. the function where you call
ft_definetrial in. A lot easier and much less error prone.

Best,
Roemer



On Fri, Sep 20, 2013 at 5:01 PM, McConnell, Keith <Keith.McConnell at cchmc.org
> wrote:

>  Hello,****
>
> ** **
>
> I have an data for which the events are inconsistently mislabeled.****
>
> ** **
>
> Can/should I make the corrections using ft_write_event or,****
>
> ** **
>
> can/should I make the correction at ft_read_event and redirect the
> function from the file to a corrected event structure?****
>
> ** **
>
> Thanks,****
>
> ** **
>
> Keith****
>
> ** **
>
> Keith McConnell, M.S.****
>
> ** **
>
> 513.636.0739 (desk)****
>
> 513.504.9907 (cell)****
>
> ** **
>
> Division of Pulmonary Medicine****
>
> Cincinnati Children's Hospital Medical Center****
>
> Cincinnati, OH  45229****
>
> ** **
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Roemer van der Meij M.Sc.
PhD Candidate
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognition
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 dave at davebritton.com  Tue Sep 24 00:57:47 2013
From: dave at davebritton.com (Dave Britton)
Date: Mon, 23 Sep 2013 18:57:47 -0400
Subject: [FieldTrip] Events in ANT data files
Message-ID: <5240C76B.5000302@davebritton.com>

How are events properly accessed in ANT eep_cnt files? There are three 
file types generated by the ANT data acquisition system, .cnt (the 
continuous data), .trg (the triggers) and .evt (events?) I am having a 
problem with missing entries in the trg files, and I wondered if the 
problem is just the trg file or if the data are also missing in the cnt 
or evt files. Is there a way to access the evt files to check this out? 
I notice that when I use the ft_databrowser routine, I will see vertical 
separators labelled with trigger codes (sometimes in unexpected places), 
so I suspect that the read_eep routine is able to get these codes from 
somewhere other than the trg files. Is this so?
-Dave


From r.oostenveld at donders.ru.nl  Tue Sep 24 09:25:04 2013
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Tue, 24 Sep 2013 09:25:04 +0200
Subject: [FieldTrip] Fwd: University of Kent,
	UK - PhD studentship on EEG-based mental fatigue study
References: <E4B0D1813025A74E9F36E85EE715E4EBBE9DDAAE@EX10-LIVE-MBN1.ad.kent.ac.uk>
Message-ID: <91DD1A49-3A7B-4F03-9BD3-2EFBDCC5D77E@donders.ru.nl>

FYI

Begin forwarded message:

> From: Caroline Li <C.Li at kent.ac.uk>
> Date: 23 September 2013 16:59:05 CEST
>  
> PhD Scholarship available Brain Signal Analysis using EEG
>  
> Research Theme              : This project aims to perform analysis on EEG (Electroencephalography) data to investigate mental fatigue. More generally, we aim to find an indicator for the identification of brain states (i.e. fatigue, non-fatigue) using novel methods. It might have a wide range of applications (i.e. military, sports and medical applications).
>  
> Key words                   : EEG, time-frequency analysis, phase synchrony, machine learning, pattern recognition, general linear model
>  
> Location                      : University of Kent at Medway, UK (40-50 mins from London by train)
> Supervisor                  : Dr. Caroline Ling Li
> Co-supervisors           : Prof. Samuele Marcora, Prof. Howard Bowman
>  
> Funding
> Three-year PhD scholarship is available to UK, EU and overseas students and will cover home tuition fees plus a maintenance grant equivalent to the full UK Research Council rate.
>  
> Criteria 
> Applicant must have a good first degree or good Master’s level degree. Ideally at Master level with relevant research experience. Strong programming or/and math skill is preferred. Previous research experience leading to publications would be an advantage.
>  
> How to apply 
> Send covering letter and CV together with contacts of two referees to c.li at kent.ac.uk, including contact detail, research interest and your suitability for this award. Please also include experience, if any, of academic or professional research; experience, if any, of teaching or mentoring.
>  
> You must also complete the online form for making a formal application for a PhD (Doctor of Philosophy Research) in Computer Science at the University of Kent via
> http://www.kent.ac.uk/courses/postgrad/apply/index.html
>  
> Successful candidate will be based at Medway Campus. Information about Medway Campus can be found here:http://www.kent.ac.uk/locations/medway/campus/index.html
>  
> For more information, please go to: http://www.cs.kent.ac.uk/people/staff/cl339 or contact c.li at kent.ac.uk
> Kent provides a dynamic and challenging academic environment and has an excellent reputation for collaborative research with universities around the world. For more information about Kent’s research portfolio see: www.kent.ac.uk/pg
>  
> ====================================================================================
> Caroline Li (Ph.D)| Lecturer |School of Computing |University of Kent
> Founder of Brain|Cognition|Computing Lab 
> M-318, Medway Building, University of Kent, Chatham, ME4 4AG
> Tel: +44(0)1634 202987 | Mobile: +44 (0) 79355 75488 | Skype: llwelcome921
>  
> Web: http://www.cs.kent.ac.uk/people/staff/cl339/index.html | E-Mail : c.li at kent.ac.uk
> ====================================================================================
>  
>  
>  

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From jm.horschig at donders.ru.nl  Tue Sep 24 14:49:04 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 24 Sep 2013 14:49:04 +0200
Subject: [FieldTrip] Events in ANT data files
In-Reply-To: <5240C76B.5000302@davebritton.com>
References: <5240C76B.5000302@davebritton.com>
Message-ID: <52418A40.8090708@donders.ru.nl>

Hi Dave,

at least for my data, the events are stored in a separate trigger 
channel stored with the .trg file. Also, I don't have a .evt-file. The 
ft_read_events code reads in the name of the .cnt file and then searches 
for the corresponding .trg file to read in the trigger values and 
events. If no .trg file exists, it throws a warning. I don't think these 
triggers are read in from somewhere else. Maybe you can debug 
ft_read_events to find out what is happening in your case (open Matlab, 
type in 'edit ft_read_events', go to line 599 and add a breakpoint 
there, then execture your code)/

Best,
Jörn


On 9/24/2013 12:57 AM, Dave Britton wrote:
> How are events properly accessed in ANT eep_cnt files? There are three 
> file types generated by the ANT data acquisition system, .cnt (the 
> continuous data), .trg (the triggers) and .evt (events?) I am having a 
> problem with missing entries in the trg files, and I wondered if the 
> problem is just the trg file or if the data are also missing in the 
> cnt or evt files. Is there a way to access the evt files to check this 
> out? I notice that when I use the ft_databrowser routine, I will see 
> vertical separators labelled with trigger codes (sometimes in 
> unexpected places), so I suspect that the read_eep routine is able to 
> get these codes from somewhere other than the trg files. Is this so?
> -Dave
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


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

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

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

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



From maximilien.chaumon at gmail.com  Tue Sep 24 15:45:23 2013
From: maximilien.chaumon at gmail.com (Maximilien Chaumon)
Date: Tue, 24 Sep 2013 15:45:23 +0200
Subject: [FieldTrip] Fwd: BERLIN: Cutting EEG Symposium - February 2014
In-Reply-To: <CAFU3-hE0ysEaf-E-TMaBrP=1s3n3TXE8GHrNUidY+0tPM-D=QA@mail.gmail.com>
References: <CAFU3-hE0ysEaf-E-TMaBrP=1s3n3TXE8GHrNUidY+0tPM-D=QA@mail.gmail.com>
Message-ID: <CAFU3-hGYOz1M4ApW4zec4Wem-7JrP6dc7VjiMzfyiRXZ0y6Vug@mail.gmail.com>

Dear EEGLAB and FIELDTRIP community,
We are pleased to announce our symposium on EEG analysis methods. Bellow is
the announcement.


*************************************************************

                                 Berlin School of Mind and Brain****

http://www.mind-and-brain.de/postdoctoral-program/scientific-events/cutting-eeg
****************************************************************************
****

*Cutting EEG 2014
**Symposium on cutting-edge methods in EEG research for the study of
cognition
*


******

*Date: 19-21 February 2014*
*Venue: Berlin School of Mind and Brain, Luisenstraße 56, Festsaal, 10117
Berlin*

This symposium will be at the same time a forum for leading researchers to
exchange their latest findings, as well as a thorough introduction to
cutting-edge EEG analysis methods for young researchers and students.****

Topics include advanced statistical analysis such as general linear
modeling of single trial EEG data, non-linear optimisation and model driven
inference, source localization, multimodal imaging, measuring information
flow, brain computer interfaces and mobile EEG recording.
More information, including the complete list of invited speakers and
abstracts is available at ****

http://www.mind-and-brain.de/postdoctoral-program/scientific-events/cutting-eeg
.****

** **

*Registration* is compulsory due to limited number of places.
Please *send an email* with your Name, Degree and Affiliation to
cuttingeeg at gmail.com. *

Call for posters*: Submissions for posters are invited.
*Deadline: November 30*. *Apply by email* with Title, Author(s),
Affiliations and Abstract (200 words max.) to cuttingeeg at gmail.com.
Incomplete submissions will be discarded.
The abstract and poster should clearly relate to the topic of the
symposium. The abstract should present work with electroencephalography;
experimental work on cognition, and the use of advanced analysis methods is
preferred.
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From pierre.megevand at gmail.com  Wed Sep 25 04:37:50 2013
From: pierre.megevand at gmail.com (=?ISO-8859-1?Q?Pierre_M=E9gevand?=)
Date: Tue, 24 Sep 2013 22:37:50 -0400
Subject: [FieldTrip] tests of uniformity for circular data (intertrial
 coherence / phase-locking value)
Message-ID: <CANFe_cifRD+ZbQeDcaajEUo+iPNnJzyeKAKrd-OSLMzF+3vK+Q@mail.gmail.com>

Dear Fieldtrip users,

I have a question regarding tests of uniformity for circular data.

In essence, I am looking for a one-sample permutation test of the null
hypothesis that there is no phase concentration at a given electrode and
timepoint, that controls for the repetition of testing over electrodes and
timepoints (family-wise type I error rate).

I am working with intracranial EEG data. If I want to assess which brain
regions respond to an external stimulus, a possible approach is to extract
the high-gamma power for each electrode at each trial following stimulus
presentation, normalize it against a suitable baseline (e.g. before
stimulus presentation), and then compute a one-sample permutation test
based on the tmax statistic. The null hypothesis assessed by this test is
that there is no change in high-gamma power following stimulus
presentation. Such an approach provides strong control for the family-wise
type I error rate (otherwise, the repetition of statistical testing at each
electrode and timeframe would give rise to an unacceptably high risk of
falsely rejecting the null hypothesis) (Groppe et al., Psychophysiology
2011).

Now, I am wondering whether something similar exists for phase
concentration. In my experiment, there is a cue that signals imminent
stimulus presentation (the cue is non-informative as to which condition the
stimulus actually belongs to), and I am looking for signs that phase
concentration (reflected by an increase in the intertrial coherence or
phase-locking value) happened at some electrodes following the cue and
before the actual stimulus was presented. If I have a strong prior
hypothesis on the timing of the effect of the cue (as well as the frequency
band that will undergo phase reset or concentration, and the electrode
location), I can select a timepoint and electrode and use the Rayleigh test
or the omnibus test for circular data (see e.g. Fisher, Statistical
Analysis of Circular Data, 1993; a MATLAB toolbox implementing some of
these tests has been developed:
http://www.mathworks.com/matlabcentral/fileexchange/10676-circular-statistics-toolbox-directional-statistics).
These tests assess the null hypothesis that a sample of circular data (such
as phase angles of brain oscillations) come from a circular uniform
distribution (the alternative hypothesis differs somewhat between these
tests).

But, what if I don't have such a strong a priori hypothesis? Is there a way
for me to compute the intertrial coherence at each timepoint and each
electrode (similar to the high-gamma power), and then perform some sort of
statistical test against a null hypothesis of uniformity, all the while
correcting for multiple comparisons?

Specifically, bearing in mind the one-sample tmax statistic-based
permutation test for changes in high-gamma power mentioned above: is there
a way to design a permutation test for circular data that assesses the null
hypothesis that the data do come from a circular uniform distribution?

I am aware that Fieldtrip includes an option to assess differences in
intertrial coherence across experimental conditions (a 2-sample test), but
here I am specifically looking for a 1-sample test.

Thank you for your thoughts, comments and advice!

Pierre
--
Pierre Mégevand, MD, PhD
Post-doctoral research fellow
Laboratory for Multimodal Human Brain Mapping
Feinstein Institute for Medical Research
Manhasset, NY, USA
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From nina.merkel at brain.mpg.de  Wed Sep 25 09:15:53 2013
From: nina.merkel at brain.mpg.de (Merkel, Nina)
Date: Wed, 25 Sep 2013 07:15:53 +0000
Subject: [FieldTrip] Mapping headmodel voxels to brain regions
Message-ID: <E6B37E8C99E7B14BA78AB32130F6D4D03042BF26@UM-EXCDAG-A01.um.gwdg.de>

Dear Fieltrip users,

I am looking for a nice and easy way to map the headmodel voxels to brain areas. If there are any solutions around, you could let me know?

Thank you,
Nina
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From a.stolk8 at gmail.com  Wed Sep 25 09:20:19 2013
From: a.stolk8 at gmail.com (Arjen Stolk)
Date: Wed, 25 Sep 2013 09:20:19 +0200
Subject: [FieldTrip] Mapping headmodel voxels to brain regions
In-Reply-To: <E6B37E8C99E7B14BA78AB32130F6D4D03042BF26@UM-EXCDAG-A01.um.gwdg.de>
References: <E6B37E8C99E7B14BA78AB32130F6D4D03042BF26@UM-EXCDAG-A01.um.gwdg.de>
Message-ID: <CAAiwptSKQCvzPJFkZXFwEDbjgdi3p-=vqsDbW=pwiB1VoXJH_Q@mail.gmail.com>

Hi Nina,

Perhaps you might want to have a look at 'ft_volumelookup', and this page:

http://fieldtrip.fcdonders.nl/faq/how_can_i_determine_the_anatomical_label_of_a_source
?

best wishes,
Arjen


2013/9/25 Merkel, Nina <nina.merkel at brain.mpg.de>

>  Dear Fieltrip users,
>
> I am looking for a nice and easy way to map the headmodel voxels to brain
> areas. If there are any solutions around, you could let me know?
>
> Thank you,
> Nina
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From eelke.spaak at donders.ru.nl  Wed Sep 25 09:28:34 2013
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Wed, 25 Sep 2013 09:28:34 +0200
Subject: [FieldTrip] tests of uniformity for circular data (intertrial
 coherence / phase-locking value)
In-Reply-To: <CANFe_cifRD+ZbQeDcaajEUo+iPNnJzyeKAKrd-OSLMzF+3vK+Q@mail.gmail.com>
References: <CANFe_cifRD+ZbQeDcaajEUo+iPNnJzyeKAKrd-OSLMzF+3vK+Q@mail.gmail.com>
Message-ID: <CABPNLUoxjHS-vmT5j4n6X4F7=Ti5aL4-jTL2xPj_nM4xdHzt3Q@mail.gmail.com>

Dear Pierre,

As you are probably aware, FieldTrip's cluster-corrected statistics
routines rely on permutation of condition labels. If there are no
condition labels, there is basically nothing to permute. So it is not
straightforward to use the default statistics routines for 1-sample
testing.

I think there are three options. First, you could do a 2-sample test
against artificial data. You could generate a data set of the exact
same dimensions as your real data, but with a phase distribution that
is uniform over trials. Then you can use ft_statfun_diff_itc to tell
you whether your observed data has a significantly difference ITC from
this artificial data. Since you know the latter has zero ITC, this
will in effect be a 1-sample test (analogous to doing a paired-sample
t-test against all zero data). At least, I am quite sure that per
time-frequency-channel point the test should be valid, but I am not
entirely sure the cluster correction still is valid with this
approach.

Second, you could generate surrogate data by destroying the ITC in
your observed data. This would entail something like shifting the time
course in each trial by a random amount (with rollover), then
computing the ITC for all points, finding cluster candidates,
computing each cluster's ITC, and adding this to a reference
distribution. Then you apply the same cluster-candidate-finding
algorithm to your observed data and compare the observed clusters'
pooled ITC to your cluster reference distribution. Note that this
essentially means implementing your own cluster permutation routines,
where not the conditions are permuted but the time courses. This is
not a trivial problem, because the neighbourhood structure across
electrodes is typically not regular (time and frequency are easy
because they form straightforward matrices).

Third, perhaps the most elegant, and certainly the easiest option, is
to look at event-related potentials :) If you filter your raw data in
the frequency band of interest (and thus remove the DC component),
then if there is no phase concentration in the data, the averaged ERP
will be zero. If the ERP is significantly non-zero at a given time
point and electrode, this means that there is phase concentration
across trials in the frequency band you filtered in at that point.
Note that for this approach to work, it is probably wise to
(iteratively) filter in relatively narrow frequency bands (using a FIR
filter). This will also allow you to construct a time-frequency plot.

Hope this helps!

Best,
Eelke



On 25 September 2013 04:37, Pierre Mégevand <pierre.megevand at gmail.com> wrote:
> Dear Fieldtrip users,
>
> I have a question regarding tests of uniformity for circular data.
>
> In essence, I am looking for a one-sample permutation test of the null
> hypothesis that there is no phase concentration at a given electrode and
> timepoint, that controls for the repetition of testing over electrodes and
> timepoints (family-wise type I error rate).
>
> I am working with intracranial EEG data. If I want to assess which brain
> regions respond to an external stimulus, a possible approach is to extract
> the high-gamma power for each electrode at each trial following stimulus
> presentation, normalize it against a suitable baseline (e.g. before stimulus
> presentation), and then compute a one-sample permutation test based on the
> tmax statistic. The null hypothesis assessed by this test is that there is
> no change in high-gamma power following stimulus presentation. Such an
> approach provides strong control for the family-wise type I error rate
> (otherwise, the repetition of statistical testing at each electrode and
> timeframe would give rise to an unacceptably high risk of falsely rejecting
> the null hypothesis) (Groppe et al., Psychophysiology 2011).
>
> Now, I am wondering whether something similar exists for phase
> concentration. In my experiment, there is a cue that signals imminent
> stimulus presentation (the cue is non-informative as to which condition the
> stimulus actually belongs to), and I am looking for signs that phase
> concentration (reflected by an increase in the intertrial coherence or
> phase-locking value) happened at some electrodes following the cue and
> before the actual stimulus was presented. If I have a strong prior
> hypothesis on the timing of the effect of the cue (as well as the frequency
> band that will undergo phase reset or concentration, and the electrode
> location), I can select a timepoint and electrode and use the Rayleigh test
> or the omnibus test for circular data (see e.g. Fisher, Statistical Analysis
> of Circular Data, 1993; a MATLAB toolbox implementing some of these tests
> has been developed:
> http://www.mathworks.com/matlabcentral/fileexchange/10676-circular-statistics-toolbox-directional-statistics).
> These tests assess the null hypothesis that a sample of circular data (such
> as phase angles of brain oscillations) come from a circular uniform
> distribution (the alternative hypothesis differs somewhat between these
> tests).
>
> But, what if I don't have such a strong a priori hypothesis? Is there a way
> for me to compute the intertrial coherence at each timepoint and each
> electrode (similar to the high-gamma power), and then perform some sort of
> statistical test against a null hypothesis of uniformity, all the while
> correcting for multiple comparisons?
>
> Specifically, bearing in mind the one-sample tmax statistic-based
> permutation test for changes in high-gamma power mentioned above: is there a
> way to design a permutation test for circular data that assesses the null
> hypothesis that the data do come from a circular uniform distribution?
>
> I am aware that Fieldtrip includes an option to assess differences in
> intertrial coherence across experimental conditions (a 2-sample test), but
> here I am specifically looking for a 1-sample test.
>
> Thank you for your thoughts, comments and advice!
>
> Pierre
> --
> Pierre Mégevand, MD, PhD
> Post-doctoral research fellow
> Laboratory for Multimodal Human Brain Mapping
> Feinstein Institute for Medical Research
> Manhasset, NY, USA
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From nina.merkel at brain.mpg.de  Wed Sep 25 11:14:10 2013
From: nina.merkel at brain.mpg.de (Merkel, Nina)
Date: Wed, 25 Sep 2013 09:14:10 +0000
Subject: [FieldTrip] Mapping headmodel voxels to brain regions
In-Reply-To: <CAAiwptSKQCvzPJFkZXFwEDbjgdi3p-=vqsDbW=pwiB1VoXJH_Q@mail.gmail.com>
References: <E6B37E8C99E7B14BA78AB32130F6D4D03042BF26@UM-EXCDAG-A01.um.gwdg.de>,
	<CAAiwptSKQCvzPJFkZXFwEDbjgdi3p-=vqsDbW=pwiB1VoXJH_Q@mail.gmail.com>
Message-ID: <E6B37E8C99E7B14BA78AB32130F6D4D03042BF56@UM-EXCDAG-A01.um.gwdg.de>

Dear Arjen,

thanks for the fast answer, I wonder if there is kind of a file, where I can get an overview which voxel belong to which region.
Do you know?

Best,
Nina


________________________________
Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" im Auftrag von "Arjen Stolk [a.stolk8 at gmail.com]
Gesendet: Mittwoch, 25. September 2013 09:20
An: FieldTrip discussion list
Betreff: Re: [FieldTrip] Mapping headmodel voxels to brain regions

Hi Nina,

Perhaps you might want to have a look at 'ft_volumelookup', and this page:

http://fieldtrip.fcdonders.nl/faq/how_can_i_determine_the_anatomical_label_of_a_source?

best wishes,
Arjen


2013/9/25 Merkel, Nina <nina.merkel at brain.mpg.de<mailto:nina.merkel at brain.mpg.de>>
Dear Fieltrip users,

I am looking for a nice and easy way to map the headmodel voxels to brain areas. If there are any solutions around, you could let me know?

Thank you,
Nina

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

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From jm.horschig at donders.ru.nl  Wed Sep 25 12:33:38 2013
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 25 Sep 2013 12:33:38 +0200
Subject: [FieldTrip] Mapping headmodel voxels to brain regions
In-Reply-To: <E6B37E8C99E7B14BA78AB32130F6D4D03042BF56@UM-EXCDAG-A01.um.gwdg.de>
References: <E6B37E8C99E7B14BA78AB32130F6D4D03042BF26@UM-EXCDAG-A01.um.gwdg.de>,
	<CAAiwptSKQCvzPJFkZXFwEDbjgdi3p-=vqsDbW=pwiB1VoXJH_Q@mail.gmail.com>
	<E6B37E8C99E7B14BA78AB32130F6D4D03042BF56@UM-EXCDAG-A01.um.gwdg.de>
Message-ID: <5242BC02.5070901@donders.ru.nl>

Hi Nina,

you can use an atlas, which can be found in FieldTrip/template/atlas/
See for example:
http://fieldtrip.fcdonders.nl/tutorial/beamformingextended#plotting_sources_of_oscillatory_gamma-band_activity 
(it's an excercise in there, but you can specifiy cfg.atlas=... when 
using ft_sourceplot)

Best,
Jörn

On 9/25/2013 11:14 AM, Merkel, Nina wrote:
> Dear Arjen,
>
> thanks for the fast answer, I wonder if there is kind of a file, where 
> I can get an overview which voxel belong to which region.
> Do you know?
>
> Best,
> Nina
>
>
> ------------------------------------------------------------------------
> *Von:* fieldtrip-bounces at science.ru.nl 
> [fieldtrip-bounces at science.ru.nl]" im Auftrag von "Arjen Stolk 
> [a.stolk8 at gmail.com]
> *Gesendet:* Mittwoch, 25. September 2013 09:20
> *An:* FieldTrip discussion list
> *Betreff:* Re: [FieldTrip] Mapping headmodel voxels to brain regions
>
> Hi Nina,
>
> Perhaps you might want to have a look at 'ft_volumelookup', and this page:
>
> http://fieldtrip.fcdonders.nl/faq/how_can_i_determine_the_anatomical_label_of_a_source?
>
> best wishes,
> Arjen
>
>
> 2013/9/25 Merkel, Nina <nina.merkel at brain.mpg.de 
> <mailto:nina.merkel at brain.mpg.de>>
>
>     Dear Fieltrip users,
>
>     I am looking for a nice and easy way to map the headmodel voxels
>     to brain areas. If there are any solutions around, you could let
>     me know?
>
>     Thank you,
>     Nina
>
>     _______________________________________________
>     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
Neuronal Oscillations Group
FieldTrip Development Team

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

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

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

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From lmelloni at gmail.com  Wed Sep 25 16:47:37 2013
From: lmelloni at gmail.com (Lucia Melloni)
Date: Wed, 25 Sep 2013 10:47:37 -0400
Subject: [FieldTrip] tests of uniformity for circular data (intertrial
 coherence / phase-locking value)
In-Reply-To: <CANFe_cifRD+ZbQeDcaajEUo+iPNnJzyeKAKrd-OSLMzF+3vK+Q@mail.gmail.com>
References: <CANFe_cifRD+ZbQeDcaajEUo+iPNnJzyeKAKrd-OSLMzF+3vK+Q@mail.gmail.com>
Message-ID: <151260223039439296@unknownmsgid>

Alternatively, to what elke already mentioned, you could use the circ stat
toolbox in matlab and then fdr correct.



-- Lucía


On Sep 24, 2013, at 10:38 PM, "Pierre Mégevand" <pierre.megevand at gmail.com>
wrote:

Dear Fieldtrip users,

I have a question regarding tests of uniformity for circular data.

In essence, I am looking for a one-sample permutation test of the null
hypothesis that there is no phase concentration at a given electrode and
timepoint, that controls for the repetition of testing over electrodes and
timepoints (family-wise type I error rate).

I am working with intracranial EEG data. If I want to assess which brain
regions respond to an external stimulus, a possible approach is to extract
the high-gamma power for each electrode at each trial following stimulus
presentation, normalize it against a suitable baseline (e.g. before
stimulus presentation), and then compute a one-sample permutation test
based on the tmax statistic. The null hypothesis assessed by this test is
that there is no change in high-gamma power following stimulus
presentation. Such an approach provides strong control for the family-wise
type I error rate (otherwise, the repetition of statistical testing at each
electrode and timeframe would give rise to an unacceptably high risk of
falsely rejecting the null hypothesis) (Groppe et al., Psychophysiology
2011).

Now, I am wondering whether something similar exists for phase
concentration. In my experiment, there is a cue that signals imminent
stimulus presentation (the cue is non-informative as to which condition the
stimulus actually belongs to), and I am looking for signs that phase
concentration (reflected by an increase in the intertrial coherence or
phase-locking value) happened at some electrodes following the cue and
before the actual stimulus was presented. If I have a strong prior
hypothesis on the timing of the effect of the cue (as well as the frequency
band that will undergo phase reset or concentration, and the electrode
location), I can select a timepoint and electrode and use the Rayleigh test
or the omnibus test for circular data (see e.g. Fisher, Statistical
Analysis of Circular Data, 1993; a MATLAB toolbox implementing some of
these tests has been developed:
http://www.mathworks.com/matlabcentral/fileexchange/10676-circular-statistics-toolbox-directional-statistics).
These tests assess the null hypothesis that a sample of circular data (such
as phase angles of brain oscillations) come from a circular uniform
distribution (the alternative hypothesis differs somewhat between these
tests).

But, what if I don't have such a strong a priori hypothesis? Is there a way
for me to compute the intertrial coherence at each timepoint and each
electrode (similar to the high-gamma power), and then perform some sort of
statistical test against a null hypothesis of uniformity, all the while
correcting for multiple comparisons?

Specifically, bearing in mind the one-sample tmax statistic-based
permutation test for changes in high-gamma power mentioned above: is there
a way to design a permutation test for circular data that assesses the null
hypothesis that the data do come from a circular uniform distribution?

I am aware that Fieldtrip includes an option to assess differences in
intertrial coherence across experimental conditions (a 2-sample test), but
here I am specifically looking for a 1-sample test.

Thank you for your thoughts, comments and advice!

Pierre
--
Pierre Mégevand, MD, PhD
Post-doctoral research fellow
Laboratory for Multimodal Human Brain Mapping
Feinstein Institute for Medical Research
Manhasset, NY, USA

_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From Keith.McConnell at cchmc.org  Wed Sep 25 20:07:24 2013
From: Keith.McConnell at cchmc.org (McConnell, Keith)
Date: Wed, 25 Sep 2013 18:07:24 +0000
Subject: [FieldTrip] simple question
Message-ID: <F8170A13692BD94597081861B03931C627620801@MCEXMB1.chmccorp.cchmc.org>

Neophyte question:

I am working through the planar gradient tutorial with data that I have collected.

I don't know what 'fully incongruent', 'initially incongruent' or 'fully congruent' mean in the context of my data.

Can you help?

Keith McConnell, M.S.

513.636.0739 (desk)
513.504.9907 (cell)

Division of Pulmonary Medicine
Cincinnati Children's Hospital Medical Center
Cincinnati, OH  45229

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From a.stolk at fcdonders.ru.nl  Wed Sep 25 20:26:07 2013
From: a.stolk at fcdonders.ru.nl (Stolk, A.)
Date: Wed, 25 Sep 2013 20:26:07 +0200 (CEST)
Subject: [FieldTrip] simple question
In-Reply-To: <F8170A13692BD94597081861B03931C627620801@MCEXMB1.chmccorp.cchmc.org>
Message-ID: <583737048.2963451.1380133567204.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Keith, These labels refers to the different conditions of the experimental manipulation. If I remember correctly; whether the meaning of an utterance, or parts of an sentence, is (semantically) congruent/incongruent with world knowledge. These labels are not crucial for the analysis described in the tutorial, and you might want to change them according to your own experimental manipulation. Best, Arjen ----- Oorspronkelijk bericht -----
> Van: "Keith McConnell" <Keith.McConnell at cchmc.org>
> Aan: fieldtrip at science.ru.nl
> Verzonden: Woensdag 25 september 2013 20:07:24
> Onderwerp: [FieldTrip] simple question
> Neophyte question:
> I am working through the planar gradient tutorial with data that I
> have collected.
> I don't know what 'fully incongruent', 'initially incongruent' or
> 'fully congruent' mean in the context of my data.
> Can you help?
> Keith McConnell, M.S.
> 513.636.0739 (desk)
> 513.504.9907 (cell)
> Division of Pulmonary Medicine
> Cincinnati Children's Hospital Medical Center
> Cincinnati, OH 45229
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From j.herring at fcdonders.ru.nl  Thu Sep 26 09:21:14 2013
From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim))
Date: Thu, 26 Sep 2013 09:21:14 +0200 (CEST)
Subject: [FieldTrip] simple question
In-Reply-To: <F8170A13692BD94597081861B03931C627620801@MCEXMB1.chmccorp.cchmc.org>
References: <F8170A13692BD94597081861B03931C627620801@MCEXMB1.chmccorp.cchmc.org>
Message-ID: <00a501ceba88$fc68d390$f53a7ab0$@herring@fcdonders.ru.nl>

Hi Keith,

 

Here is some more information on the dataset including the meaning of the
labels: http://fieldtrip.fcdonders.nl/tutorial/shared/dataset

 

Best,

 

Jim

 

From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of McConnell, Keith
Sent: woensdag 25 september 2013 20:07
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] simple question

 

Neophyte question:

 

I am working through the planar gradient tutorial with data that I have
collected.

 

I don't know what 'fully incongruent', 'initially incongruent' or 'fully
congruent' mean in the context of my data.

 

Can you help?

 

Keith McConnell, M.S.

 

513.636.0739 (desk)

513.504.9907 (cell)

 

Division of Pulmonary Medicine

Cincinnati Children's Hospital Medical Center

Cincinnati, OH  45229

 

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From deleted  Thu Sep 26 12:43:12 2013
From: deleted (deleted)
Date: Thu, 26 Sep 2013 12:43:12 +0200
Subject: [FieldTrip] ft_singleplotTFR seems broken
In-Reply-To: <CABPNLUo5=dHpPA8JER_7yLg5YPM1qCcjkCXm11imJ-rGvEt_ew@mail.gmail.com>
References: <CAJ7RtRGw_o4pO5tR8RFWJad4K32pArxMXRJcXnOp5irtEcOxOA@mail.gmail.com>
	<CABPNLUo5=dHpPA8JER_7yLg5YPM1qCcjkCXm11imJ-rGvEt_ew@mail.gmail.com>
Message-ID: <CAJ7RtRFQ_49yRWP0TnTgkRwwG5BnfwMJa9EMv_x+6JFmnuHjgA@mail.gmail.com>

Dear Eelke,

I've put up an exerpt of my code, with the data from a single subject
(no.10, 9MB) in a separate folder
here<https://www.dropbox.com/sh/nr4s0yu4voh5w3l/6XvAvmaMdk>
.
It also includes a screenshot of what I see with when I run the code with
this exact dataset, and a small program 'filehandler', which I've been to
lazy to replace.

Note that this specific subject only has about 60 seconds of data (and I'm
still waiting for the student to tell me why).

I'm hoping you'll get the same result as the screenshot, and you'll be able
to tell me why...

Best regards,

Casper


On Wed, Sep 18, 2013 at 1:25 PM, Eelke Spaak <eelke.spaak at donders.ru.nl>wrote:

> Dear Casper,
>
> Could you maybe post a snippet online somewhere (e.g. dropbox) of data
> corresponding to this plot (i.e. the output of ft_freqanalysis that
> you input to ft_singleplotTFR, assuming that it's averaged over trials
> and therefore small)? Then we can see whether this is reproducable on
> our systems.
>
> Best,
> Eelke
>
> On 16 September 2013 17:12, deleted <deleted>
> wrote:
> > Dear Fieldtrippers,
> >
> > I've been doing some exploratory plotting of a dataset where several
> > subjects were exposed to a continuous stimulus (CPM) over the course of
> > three minutes. One of the things that was asked was a time-frequency
> plot,
> > over those three minutes. While I'm not quite sure a TFR can be used on
> that
> > scale without problems, I went ahead with it just to see what Fieldtrip
> > would do. What I got, was this:
> > http://tinypic.com/r/zx2tqs/5|
> > And I have no idea what went wrong (note that this specific subject only
> got
> > a 60s stimulus). Quality of the picture and the validity of the analysis
> > aside, I have a severe problem with the axes, which seem to be all over
> the
> > place.
> >
> > I simply read the data using ft_preprocessing (no filters or anything,
> since
> > the student in charge already used a 10Hz high-pass and a 150Hz low-pass
> > filter).
> > The only field in 'cfg' is 'headerfile'.
> >
> > Next, I call ft_freqanalysis with:
> >     cfg.output = 'pow';
> >     cfg.method = 'wavelet'; % default; Morlet wavelet
> >     cfg.taper = 'hanning';
> >     cfg.tapsmofrq = 4;
> >     cfg.channel = 'Cz';
> >     cfg.foi = [20:0.5:30];
> >     cfg.t_ftimwin = ones(length(cfg.foi),1).*0.25;
> >     cfg.toi = 0:0.5:60;
> >
> > And finally, I end up with the monstrocity shown earlier. This problem
> only
> > presents itself with Fieldtrip-related functions, the normal Matlab-plots
> > work as well as they've ever done, so I'm thinking it's something in
> > Fieldtrip that's causing this.
> >
> > My hope is that someone has encountered this problem before, and knows
> how
> > to solve it...
> >
> > Sincerely,
> >
> > Casper
> >
> >
> > _______________________________________________
> > 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 alik.widge at gmail.com  Fri Sep 27 21:57:17 2013
From: alik.widge at gmail.com (Alik Widge)
Date: Fri, 27 Sep 2013 15:57:17 -0400
Subject: [FieldTrip] cfg.plotlabels and ft_databrowser
Message-ID: <CAGZVU0_-MNYggLww+O0PbU7S36T5gcwwdnQS+F8H40vpEhpT_A@mail.gmail.com>

I have pounded on this one from a few different angles and even gone and
looked at the source, and still can't quite figure out what I'm doing wrong.

I have a datafile from an eXimia TMS-EEG system. Right now, all I'm trying
to do is load it up and inspect the data a bit to get a sense of how badly
artifacted it is. So:

%%%%%%

cfg = [];
cfg.blocksize = 30;         % num of seconds to display at once
cfg.continuous = 'yes';     % not yet cut into trials
cfg.plotlabels = 'some';
cfg.viewmode = 'vertical';
cfg.colorgroups = 'chantype';

cfg.dataset = [DataDir filesep EEGFile];
cfg.channel = {'EEG'};

ft_databrowser(cfg)


%%%%%%

This does 90% of what it ought to do -- it shows me the EEG channels (no
triggers or EOG), 30 second segments at a time. What it does *not* do is
label the channels along the y-axis so that I can readily tell which one is
Pz, F3, O1, etc., etc. I am pretty sure that's what cfg.plotlabels is
supposed to do, and yet, it does not. I've also tried doing this as
ft_databrowser(cfg,data), where I explicitly make sure that data.label
contains the correct channel names, and that *still* doesn't work.

I'm aware that this was marked as a bug before, but bugzilla shows it
closed long ago, before r7276 that I'm using I believe.

MATLAB r2013a on OS X, if it matters.

Am I simply misunderstanding what this cfg argument does or how to use it?


Alik Widge, MD, PhD
alik.widge at gmail.com
(206) 866-5435
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From Keith.McConnell at cchmc.org  Fri Sep 27 22:08:50 2013
From: Keith.McConnell at cchmc.org (McConnell, Keith)
Date: Fri, 27 Sep 2013 20:08:50 +0000
Subject: [FieldTrip] Beamformer question
Message-ID: <F8170A13692BD94597081861B03931C627620F3A@MCEXMB1.chmccorp.cchmc.org>

Hello,

working through the beamformer tutorial with my own data.

I am getting an error at ft_sourceinterpolate step:

Reference to non-existent field 'ave'.

My code is:

cfg = [];
cfg.downsample = 2;
cfg.parameter = 'avg.pow';
sourcePostInt_nocon = ft_sourceinterpolate(cfg, sourcePost_nocon, mri);

Any ideas?

Keith McConnell, M.S.

513.636.0739 (desk)
513.504.9907 (cell)

Division of Pulmonary Medicine
Cincinnati Children's Hospital Medical Center
Cincinnati, OH  45229

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From pierre.megevand at gmail.com  Fri Sep 27 22:11:07 2013
From: pierre.megevand at gmail.com (=?ISO-8859-1?Q?Pierre_M=E9gevand?=)
Date: Fri, 27 Sep 2013 16:11:07 -0400
Subject: [FieldTrip] tests of uniformity for circular data (intertrial
 coherence / phase-locking value)
Message-ID: <CANFe_chdC6_u+XAjQhDHR3Q7ZyhP+33oqbxbcMY_YqYn_ZtUKg@mail.gmail.com>

Thanks Eelke and Lucia for your great suggestions.

I've implemented something along the lines of Eelke's proposal number 2. In
keeping with the spirit of tmax-stat-based one-sample permutation tests for
amplitude data, for each iteration of the randomization loop, I am randomly
shifting the "zero time" of the dataset for each individual trial, across
all electrodes, thus keeping any existing relationship between datapoints
at neighboring electrodes and timeframes (except around the "wraparound" or
"rollover" time obviously).

As Eelke said, getting this to work with a cluster-based permutation test
would require some more work. But if anyone is interested in trying this
ITC_max permutation one-sample test as it is now, just send me a message
and I'll be happy to discuss the matter in more detail and share the code.

Pierre
--
Pierre Mégevand, MD, PhD
Post-doctoral research fellow
Laboratory for Multimodal Human Brain Mapping
Feinstein Institute for Medical Research
Manhasset, NY, USA
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From zizlsperger at gmail.com  Sat Sep 28 15:25:32 2013
From: zizlsperger at gmail.com (Zizlsperger Leopold)
Date: Sat, 28 Sep 2013 15:25:32 +0200
Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the volume
	conductor misaligned
Message-ID: <06D14B0C-655A-4EF2-A69A-B735DBDBC504@gmail.com>

Hi all,
I am following the instructions in the "Source reconstruction of event-related fields using minimum-norm estimate" tutorial closely to do a source-analysis of EEG data using the example MRI. As I am following the tutorial almost unchanged I am not including the script here.

When I re-align the volume conduction model to the sourcespace they are not aligned very well, see screenshot attached. I remember a similar question in the mailing list a while ago but cannot find it...

Is there a way to interactively realign volume conduction model and sourcespace? Re-doing the fiducials did not change the aligment considerably. Also, my volume conduction model looks weird...
I used ft_determine_coordsys on both the vol and the sourcespace, see screenshots attached, too.
Would be nice if you could point me in the right direction.
Thanks in advance.
Leo

----




Dr. med. Leopold Zizlsperger
Klinik für Neurologie
Uniklinik RWTH Aachen
Pauwelsstrasse 30
52074 Aachen
Tel: +49 241 80 35465
lzizlsperger at ukaachen.de

Leopold Zizlsperger, MD
Department of Neurology
RWTH Aachen University
Pauwelsstrasse 30
52074 Aachen, Germany
Tel: +49 241 80 35465
lzizlsperger at ukaachen.de

 
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From politzerahless at gmail.com  Sat Sep 28 20:53:53 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sat, 28 Sep 2013 22:53:53 +0400
Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the volume
	conductor misaligned
Message-ID: <CAJT2k_8NixEr4orEK4JCnqORjYPW_QXCn5y79dHchNCCtusqKA@mail.gmail.com>

Hello Leo,

This looks like the same problem I was having a few months ago, and there
should be some messages on the list about it. I am not able to look at my
data and scripts right now, but if I remember correctly (you can check the
lists for more) the problem had to do with the transformation matrix, and
ft_convert_units. In my case, during the "volume conduction model" step of
the tutorial (the last step before you can plot the vol and sourcespace
together), I had to add an extra

vol = ft_convert_units(vol, 'cm')

before ft_transform_geometry. I don't remember if this alone will solve the
problem (unfortunately the the situation is kind of complicated right now,
there is also a different version of the minimum norms tutorial that is
still in development--see the previous messages for links--and I think my
processing pipeline ended up being a mixture of the two to get things
working. Which means that it's hard to track where exactly I solved the
problem.)

Best,
Steve


>
> Message: 1
> Date: Sat, 28 Sep 2013 15:25:32 +0200
> From: Zizlsperger Leopold <zizlsperger at gmail.com>
> To: <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the
>         volume  conductor misaligned
> Message-ID: <06D14B0C-655A-4EF2-A69A-B735DBDBC504 at gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi all,
> I am following the instructions in the "Source reconstruction of
> event-related fields using minimum-norm estimate" tutorial closely to do a
> source-analysis of EEG data using the example MRI. As I am following the
> tutorial almost unchanged I am not including the script here.
>
> When I re-align the volume conduction model to the sourcespace they are
> not aligned very well, see screenshot attached. I remember a similar
> question in the mailing list a while ago but cannot find it...
>
> Is there a way to interactively realign volume conduction model and
> sourcespace? Re-doing the fiducials did not change the aligment
> considerably. Also, my volume conduction model looks weird...
> I used ft_determine_coordsys on both the vol and the sourcespace, see
> screenshots attached, too.
> Would be nice if you could point me in the right direction.
> Thanks in advance.
> Leo
>
> ----
>
>
>
>
> Dr. med. Leopold Zizlsperger
> Klinik f?r Neurologie
> Uniklinik RWTH Aachen
> Pauwelsstrasse 30
> 52074 Aachen
> Tel: +49 241 80 35465
> lzizlsperger at ukaachen.de
>
> Leopold Zizlsperger, MD
> Department of Neurology
> RWTH Aachen University
> Pauwelsstrasse 30
> 52074 Aachen, Germany
> Tel: +49 241 80 35465
> lzizlsperger at ukaachen.de
>
>
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>
> ------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> End of fieldtrip Digest, Vol 34, Issue 28
> *****************************************
>
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From Lilla.Magyari at mpi.nl  Mon Sep 30 09:53:31 2013
From: Lilla.Magyari at mpi.nl (Lilla.Magyari at mpi.nl)
Date: Mon, 30 Sep 2013 09:53:31 +0200 (CEST)
Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the
 volume conductor misaligned
In-Reply-To: <CAJT2k_8NixEr4orEK4JCnqORjYPW_QXCn5y79dHchNCCtusqKA@mail.gmail.com>
References: <CAJT2k_8NixEr4orEK4JCnqORjYPW_QXCn5y79dHchNCCtusqKA@mail.gmail.com>
Message-ID: <2249.87.78.44.33.1380527611.squirrel@87.78.44.33>

Hello Leo and Stephen,

yes, it is unfortunate, that there is still a problem with the MNE
tutorial. I think the main problem is the integration of the pipeline with
Freesurfer which requires a more careful look on the script.
I could not find the attached image from Leo. If the sourcespace and the
volume conduction models are not well-aligned because one of them is too
small compared to the other, then it will probably help if you convert the
units.
In Fieldtrip, the handling of the units of the volume conduction model has
changed, which means that they are not automatically converted to 'cm'
anymore.
Lilla


> Hello Leo,
>
> This looks like the same problem I was having a few months ago, and there
> should be some messages on the list about it. I am not able to look at my
> data and scripts right now, but if I remember correctly (you can check the
> lists for more) the problem had to do with the transformation matrix, and
> ft_convert_units. In my case, during the "volume conduction model" step of
> the tutorial (the last step before you can plot the vol and sourcespace
> together), I had to add an extra
>
> vol = ft_convert_units(vol, 'cm')
>
> before ft_transform_geometry. I don't remember if this alone will solve
> the
> problem (unfortunately the the situation is kind of complicated right now,
> there is also a different version of the minimum norms tutorial that is
> still in development--see the previous messages for links--and I think my
> processing pipeline ended up being a mixture of the two to get things
> working. Which means that it's hard to track where exactly I solved the
> problem.)
>
> Best,
> Steve
>
>
>>
>> Message: 1
>> Date: Sat, 28 Sep 2013 15:25:32 +0200
>> From: Zizlsperger Leopold <zizlsperger at gmail.com>
>> To: <fieldtrip at science.ru.nl>
>> Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the
>>         volume  conductor misaligned
>> Message-ID: <06D14B0C-655A-4EF2-A69A-B735DBDBC504 at gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi all,
>> I am following the instructions in the "Source reconstruction of
>> event-related fields using minimum-norm estimate" tutorial closely to do
>> a
>> source-analysis of EEG data using the example MRI. As I am following the
>> tutorial almost unchanged I am not including the script here.
>>
>> When I re-align the volume conduction model to the sourcespace they are
>> not aligned very well, see screenshot attached. I remember a similar
>> question in the mailing list a while ago but cannot find it...
>>
>> Is there a way to interactively realign volume conduction model and
>> sourcespace? Re-doing the fiducials did not change the aligment
>> considerably. Also, my volume conduction model looks weird...
>> I used ft_determine_coordsys on both the vol and the sourcespace, see
>> screenshots attached, too.
>> Would be nice if you could point me in the right direction.
>> Thanks in advance.
>> Leo
>>
>> ----
>>
>>
>>
>>
>> Dr. med. Leopold Zizlsperger
>> Klinik f?r Neurologie
>> Uniklinik RWTH Aachen
>> Pauwelsstrasse 30
>> 52074 Aachen
>> Tel: +49 241 80 35465
>> lzizlsperger at ukaachen.de
>>
>> Leopold Zizlsperger, MD
>> Department of Neurology
>> RWTH Aachen University
>> Pauwelsstrasse 30
>> 52074 Aachen, Germany
>> Tel: +49 241 80 35465
>> lzizlsperger at ukaachen.de
>>
>>
>> -------------- next part --------------
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>> >
>>
>> ------------------------------
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> End of fieldtrip Digest, Vol 34, Issue 28
>> *****************************************
>>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip




From jan.schoffelen at donders.ru.nl  Mon Sep 30 10:29:53 2013
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Mon, 30 Sep 2013 10:29:53 +0200
Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the
	volume conductor misaligned
In-Reply-To: <2249.87.78.44.33.1380527611.squirrel@87.78.44.33>
References: <CAJT2k_8NixEr4orEK4JCnqORjYPW_QXCn5y79dHchNCCtusqKA@mail.gmail.com>
	<2249.87.78.44.33.1380527611.squirrel@87.78.44.33>
Message-ID: <F62A987C-853C-4CB0-942F-B4947345D29D@donders.ru.nl>

Hi Leo,

May I add to Lilla's comments that the reconstructed headmodel looks quite bad to me. This suggests that the automatic anatomical segmentation did not work well. The most likely cause is that the coordinate system which you specified for the anatomical image in the input was incorrect (e.g. specifying 'spm', while it should have been 'ctf' or so), or that the transformation matrix mapping from voxels to head coordinates was not correct.

Best,
Jan-Mathijs


On Sep 30, 2013, at 9:53 AM, lilla.magyari at mpi.nl wrote:

> Hello Leo and Stephen,
> 
> yes, it is unfortunate, that there is still a problem with the MNE
> tutorial. I think the main problem is the integration of the pipeline with
> Freesurfer which requires a more careful look on the script.
> I could not find the attached image from Leo. If the sourcespace and the
> volume conduction models are not well-aligned because one of them is too
> small compared to the other, then it will probably help if you convert the
> units.
> In Fieldtrip, the handling of the units of the volume conduction model has
> changed, which means that they are not automatically converted to 'cm'
> anymore.
> Lilla
> 
> 
>> Hello Leo,
>> 
>> This looks like the same problem I was having a few months ago, and there
>> should be some messages on the list about it. I am not able to look at my
>> data and scripts right now, but if I remember correctly (you can check the
>> lists for more) the problem had to do with the transformation matrix, and
>> ft_convert_units. In my case, during the "volume conduction model" step of
>> the tutorial (the last step before you can plot the vol and sourcespace
>> together), I had to add an extra
>> 
>> vol = ft_convert_units(vol, 'cm')
>> 
>> before ft_transform_geometry. I don't remember if this alone will solve
>> the
>> problem (unfortunately the the situation is kind of complicated right now,
>> there is also a different version of the minimum norms tutorial that is
>> still in development--see the previous messages for links--and I think my
>> processing pipeline ended up being a mixture of the two to get things
>> working. Which means that it's hard to track where exactly I solved the
>> problem.)
>> 
>> Best,
>> Steve
>> 
>> 
>>> 
>>> Message: 1
>>> Date: Sat, 28 Sep 2013 15:25:32 +0200
>>> From: Zizlsperger Leopold <zizlsperger at gmail.com>
>>> To: <fieldtrip at science.ru.nl>
>>> Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the
>>>        volume  conductor misaligned
>>> Message-ID: <06D14B0C-655A-4EF2-A69A-B735DBDBC504 at gmail.com>
>>> Content-Type: text/plain; charset="iso-8859-1"
>>> 
>>> Hi all,
>>> I am following the instructions in the "Source reconstruction of
>>> event-related fields using minimum-norm estimate" tutorial closely to do
>>> a
>>> source-analysis of EEG data using the example MRI. As I am following the
>>> tutorial almost unchanged I am not including the script here.
>>> 
>>> When I re-align the volume conduction model to the sourcespace they are
>>> not aligned very well, see screenshot attached. I remember a similar
>>> question in the mailing list a while ago but cannot find it...
>>> 
>>> Is there a way to interactively realign volume conduction model and
>>> sourcespace? Re-doing the fiducials did not change the aligment
>>> considerably. Also, my volume conduction model looks weird...
>>> I used ft_determine_coordsys on both the vol and the sourcespace, see
>>> screenshots attached, too.
>>> Would be nice if you could point me in the right direction.
>>> Thanks in advance.
>>> Leo
>>> 
>>> ----
>>> 
>>> 
>>> 
>>> 
>>> Dr. med. Leopold Zizlsperger
>>> Klinik f?r Neurologie
>>> Uniklinik RWTH Aachen
>>> Pauwelsstrasse 30
>>> 52074 Aachen
>>> Tel: +49 241 80 35465
>>> lzizlsperger at ukaachen.de
>>> 
>>> Leopold Zizlsperger, MD
>>> Department of Neurology
>>> RWTH Aachen University
>>> Pauwelsstrasse 30
>>> 52074 Aachen, Germany
>>> Tel: +49 241 80 35465
>>> lzizlsperger at ukaachen.de
>>> 
>>> 
>>> -------------- next part --------------
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>>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130928/aff715c6/attachment.html
>>>> 
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>>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130928/aff715c6/attachment.png
>>>> 
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>>>> 
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>>>> 
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>>> URL: <
>>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130928/aff715c6/attachment-0003.png
>>>> 
>>> 
>>> ------------------------------
>>> 
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> 
>>> End of fieldtrip Digest, Vol 34, Issue 28
>>> *****************************************
>>> 
>> _______________________________________________
>> 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

Jan-Mathijs Schoffelen, MD PhD 

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

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

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

http://www.hettaligebrein.nl

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From zizlsperger at gmail.com  Mon Sep 30 12:53:06 2013
From: zizlsperger at gmail.com (Leopold Zizlsperger)
Date: Mon, 30 Sep 2013 12:53:06 +0200
Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the
 volume conductor misaligned
In-Reply-To: <CAAk5s=V3zug3HfMxSxnu8NXW-=iq5rqADitBJWKMM0Eb4Abk5w@mail.gmail.com>
References: <CAJT2k_8NixEr4orEK4JCnqORjYPW_QXCn5y79dHchNCCtusqKA@mail.gmail.com>
	<2249.87.78.44.33.1380527611.squirrel@87.78.44.33>
	<F62A987C-853C-4CB0-942F-B4947345D29D@donders.ru.nl>
	<CAAk5s=V3zug3HfMxSxnu8NXW-=iq5rqADitBJWKMM0Eb4Abk5w@mail.gmail.com>
Message-ID: <CAAk5s=WTe+T1PZO0jMb6KUvpHFyi-c0tFuG8Mc0m9um6vVdacA@mail.gmail.com>

Hello
thanks for your answers, in combination with the tutorial they were a big
help.
I think I got closer but have a last issue:
@ Jan-Mathijs: I redid the headmodel and it looks better now as shown on
the screenshots attached, thanks
@ Lilla and Stephen: the scaling in general should not be the problem I
think, the sizes seem to match, thank you
While both the volume conduction and the headmodel are expressed in CTF
coordinates, see second screenshot vol vs sourcespace, they don't align
very well > first screenshot
Is there a way to align them manually? Or would it be legitimate to "cheat"
with the fiducials of the sourcemodel ? By changing the preauricular points
I think I could align them, but I am not sure if that would cuase problems
later on...
Thanks in advance
Leo


On Mon, Sep 30, 2013 at 12:43 PM, Leopold Zizlsperger <zizlsperger at gmail.com
> wrote:

> Hello
> thanks for your answers, in combination with the tutorial they were a big
> help.
> I think I got closer but have a last issue:
> @ Jan-Mathijs: I redid the headmodel and it looks better now as shown on
> the screenshots attached, thanks
> @ Lilla and Stephen: the scaling in general should not be the problem I
> think, the sizes seem to match, thank you
> While both the volume conduction and the headmodel are expressed in CTF
> coordinates, see third screenshot vol vs sourcespace, they don't align very
> well > first two screenshots
> Is there a way to align them manually? Or would it be legitimate to
> "cheat" with the fiducials of the sourcemodel ? By changing the
> preauricular points I think I could align them, but I am not sure if that
> would cuase problems later on...
> Thanks in advance
> Leo
>
>
>
> On Mon, Sep 30, 2013 at 10:29 AM, jan-mathijs schoffelen <
> jan.schoffelen at donders.ru.nl> wrote:
>
>> Hi Leo,
>>
>> May I add to Lilla's comments that the reconstructed headmodel looks
>> quite bad to me. This suggests that the automatic anatomical segmentation
>> did not work well. The most likely cause is that the coordinate system
>> which you specified for the anatomical image in the input was incorrect
>> (e.g. specifying 'spm', while it should have been 'ctf' or so), or that the
>> transformation matrix mapping from voxels to head coordinates was not
>> correct.
>>
>> Best,
>> Jan-Mathijs
>>
>>
>> On Sep 30, 2013, at 9:53 AM, lilla.magyari at mpi.nl wrote:
>>
>> Hello Leo and Stephen,
>>
>> yes, it is unfortunate, that there is still a problem with the MNE
>> tutorial. I think the main problem is the integration of the pipeline with
>> Freesurfer which requires a more careful look on the script.
>> I could not find the attached image from Leo. If the sourcespace and the
>> volume conduction models are not well-aligned because one of them is too
>> small compared to the other, then it will probably help if you convert the
>> units.
>> In Fieldtrip, the handling of the units of the volume conduction model has
>> changed, which means that they are not automatically converted to 'cm'
>> anymore.
>> Lilla
>>
>>
>> Hello Leo,
>>
>>
>> This looks like the same problem I was having a few months ago, and there
>>
>> should be some messages on the list about it. I am not able to look at my
>>
>> data and scripts right now, but if I remember correctly (you can check the
>>
>> lists for more) the problem had to do with the transformation matrix, and
>>
>> ft_convert_units. In my case, during the "volume conduction model" step of
>>
>> the tutorial (the last step before you can plot the vol and sourcespace
>>
>> together), I had to add an extra
>>
>>
>> vol = ft_convert_units(vol, 'cm')
>>
>>
>> before ft_transform_geometry. I don't remember if this alone will solve
>>
>> the
>>
>> problem (unfortunately the the situation is kind of complicated right now,
>>
>> there is also a different version of the minimum norms tutorial that is
>>
>> still in development--see the previous messages for links--and I think my
>>
>> processing pipeline ended up being a mixture of the two to get things
>>
>> working. Which means that it's hard to track where exactly I solved the
>>
>> problem.)
>>
>>
>> Best,
>>
>> Steve
>>
>>
>>
>>
>> Message: 1
>>
>>  Date: Sat, 28 Sep 2013 15:25:32 +0200
>>
>> From: Zizlsperger Leopold <zizlsperger at gmail.com>
>>
>> To: <fieldtrip at science.ru.nl>
>>
>> Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the
>>
>>        volume  conductor misaligned
>>
>> Message-ID: <06D14B0C-655A-4EF2-A69A-B735DBDBC504 at gmail.com>
>>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>
>> Hi all,
>>
>> I am following the instructions in the "Source reconstruction of
>>
>> event-related fields using minimum-norm estimate" tutorial closely to do
>>
>> a
>>
>> source-analysis of EEG data using the example MRI. As I am following the
>>
>> tutorial almost unchanged I am not including the script here.
>>
>>
>> When I re-align the volume conduction model to the sourcespace they are
>>
>> not aligned very well, see screenshot attached. I remember a similar
>>
>> question in the mailing list a while ago but cannot find it...
>>
>>
>> Is there a way to interactively realign volume conduction model and
>>
>> sourcespace? Re-doing the fiducials did not change the aligment
>>
>> considerably. Also, my volume conduction model looks weird...
>>
>> I used ft_determine_coordsys on both the vol and the sourcespace, see
>>
>> screenshots attached, too.
>>
>> Would be nice if you could point me in the right direction.
>>
>> Thanks in advance.
>>
>> Leo
>>
>>
>> ----
>>
>>
>>
>>
>>
>> Dr. med. Leopold Zizlsperger
>>
>> Klinik f?r Neurologie
>>
>> Uniklinik RWTH Aachen
>>
>> Pauwelsstrasse 30
>>
>> 52074 Aachen
>>
>> Tel: +49 241 80 35465
>>
>> lzizlsperger at ukaachen.de
>>
>>
>> Leopold Zizlsperger, MD
>>
>> Department of Neurology
>>
>> RWTH Aachen University
>>
>> Pauwelsstrasse 30
>>
>> 52074 Aachen, Germany
>>
>> Tel: +49 241 80 35465
>>
>> lzizlsperger at ukaachen.de
>>
>>
>>
>> -------------- next part --------------
>>
>> An HTML attachment was scrubbed...
>>
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>>
>>
>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130928/aff715c6/attachment.html
>>
>>
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>> URL: <
>>
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>>
>>
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>> URL: <
>>
>>
>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130928/aff715c6/attachment-0003.png
>>
>>
>>
>> ------------------------------
>>
>>
>> _______________________________________________
>>
>> fieldtrip mailing list
>>
>> fieldtrip at donders.ru.nl
>>
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>> End of fieldtrip Digest, Vol 34, Issue 28
>>
>> *****************************************
>>
>>
>> _______________________________________________
>>
>> 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
>>
>>
>>     Jan-Mathijs Schoffelen, MD PhD
>>
>> Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>>
>> Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>>
>> J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>>
>> http://www.hettaligebrein.nl
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
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From politzerahless at gmail.com  Mon Sep 30 13:12:39 2013
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Mon, 30 Sep 2013 15:12:39 +0400
Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the
	volume conductor misaligned
Message-ID: <CAJT2k__V-aPQdXEPZydquGCxxvDv82w7aXfZDugBs-6ZSAmU+Q@mail.gmail.com>

Hi Leo,

If I am remembering correctly, I think the problem could still be related
to ft_convert_units even if the volume conductor and head model look like
they're similar in size. For example, in the images I sent out when I was
having this problem earlier, the volume conductor and hte sourcespace are
the same size but one is tilted more, and the solution was nevertheless
related to ft_convert_units (I think). In my case, this was because the
conversion had to happen at a different time than it does in the tutorial.
(I had to insert ft_convert_units somewhere earlier in the pipeline than
where it was happening in the tutorial.) I'm sorry I can't be more
specific, but if it will help I could try to look through my old code and
re-figure out what I changed at the time.

Best,
Steve



Stephen Politzer-Ahles
New York University, Abu Dhabi
Neuroscience of Language Lab
http://www.nyu.edu/projects/politzer-ahles/



>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 30 Sep 2013 12:53:06 +0200
> From: Leopold Zizlsperger <zizlsperger at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] EEG Source reconstruction: sourcespace and
>         the volume conductor misaligned
> Message-ID:
>         <CAAk5s=
> WTe+T1PZO0jMb6KUvpHFyi-c0tFuG8Mc0m9um6vVdacA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello
> thanks for your answers, in combination with the tutorial they were a big
> help.
> I think I got closer but have a last issue:
> @ Jan-Mathijs: I redid the headmodel and it looks better now as shown on
> the screenshots attached, thanks
> @ Lilla and Stephen: the scaling in general should not be the problem I
> think, the sizes seem to match, thank you
> While both the volume conduction and the headmodel are expressed in CTF
> coordinates, see second screenshot vol vs sourcespace, they don't align
> very well > first screenshot
> Is there a way to align them manually? Or would it be legitimate to "cheat"
> with the fiducials of the sourcemodel ? By changing the preauricular points
> I think I could align them, but I am not sure if that would cuase problems
> later on...
> Thanks in advance
> Leo
>
>
> On Mon, Sep 30, 2013 at 12:43 PM, Leopold Zizlsperger <
> zizlsperger at gmail.com
> > wrote:
>
> > Hello
> > thanks for your answers, in combination with the tutorial they were a big
> > help.
> > I think I got closer but have a last issue:
> > @ Jan-Mathijs: I redid the headmodel and it looks better now as shown on
> > the screenshots attached, thanks
> > @ Lilla and Stephen: the scaling in general should not be the problem I
> > think, the sizes seem to match, thank you
> > While both the volume conduction and the headmodel are expressed in CTF
> > coordinates, see third screenshot vol vs sourcespace, they don't align
> very
> > well > first two screenshots
> > Is there a way to align them manually? Or would it be legitimate to
> > "cheat" with the fiducials of the sourcemodel ? By changing the
> > preauricular points I think I could align them, but I am not sure if that
> > would cuase problems later on...
> > Thanks in advance
> > Leo
> >
> >
> >
> > On Mon, Sep 30, 2013 at 10:29 AM, jan-mathijs schoffelen <
> > jan.schoffelen at donders.ru.nl> wrote:
> >
> >> Hi Leo,
> >>
> >> May I add to Lilla's comments that the reconstructed headmodel looks
> >> quite bad to me. This suggests that the automatic anatomical
> segmentation
> >> did not work well. The most likely cause is that the coordinate system
> >> which you specified for the anatomical image in the input was incorrect
> >> (e.g. specifying 'spm', while it should have been 'ctf' or so), or that
> the
> >> transformation matrix mapping from voxels to head coordinates was not
> >> correct.
> >>
> >> Best,
> >> Jan-Mathijs
> >>
> >>
> >> On Sep 30, 2013, at 9:53 AM, lilla.magyari at mpi.nl wrote:
> >>
> >> Hello Leo and Stephen,
> >>
> >> yes, it is unfortunate, that there is still a problem with the MNE
> >> tutorial. I think the main problem is the integration of the pipeline
> with
> >> Freesurfer which requires a more careful look on the script.
> >> I could not find the attached image from Leo. If the sourcespace and the
> >> volume conduction models are not well-aligned because one of them is too
> >> small compared to the other, then it will probably help if you convert
> the
> >> units.
> >> In Fieldtrip, the handling of the units of the volume conduction model
> has
> >> changed, which means that they are not automatically converted to 'cm'
> >> anymore.
> >> Lilla
> >>
> >>
> >> Hello Leo,
> >>
> >>
> >> This looks like the same problem I was having a few months ago, and
> there
> >>
> >> should be some messages on the list about it. I am not able to look at
> my
> >>
> >> data and scripts right now, but if I remember correctly (you can check
> the
> >>
> >> lists for more) the problem had to do with the transformation matrix,
> and
> >>
> >> ft_convert_units. In my case, during the "volume conduction model" step
> of
> >>
> >> the tutorial (the last step before you can plot the vol and sourcespace
> >>
> >> together), I had to add an extra
> >>
> >>
> >> vol = ft_convert_units(vol, 'cm')
> >>
> >>
> >> before ft_transform_geometry. I don't remember if this alone will solve
> >>
> >> the
> >>
> >> problem (unfortunately the the situation is kind of complicated right
> now,
> >>
> >> there is also a different version of the minimum norms tutorial that is
> >>
> >> still in development--see the previous messages for links--and I think
> my
> >>
> >> processing pipeline ended up being a mixture of the two to get things
> >>
> >> working. Which means that it's hard to track where exactly I solved the
> >>
> >> problem.)
> >>
> >>
> >> Best,
> >>
> >> Steve
> >>
> >>
> >>
> >>
> >> Message: 1
> >>
> >>  Date: Sat, 28 Sep 2013 15:25:32 +0200
> >>
> >> From: Zizlsperger Leopold <zizlsperger at gmail.com>
> >>
> >> To: <fieldtrip at science.ru.nl>
> >>
> >> Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the
> >>
> >>        volume  conductor misaligned
> >>
> >> Message-ID: <06D14B0C-655A-4EF2-A69A-B735DBDBC504 at gmail.com>
> >>
> >> Content-Type: text/plain; charset="iso-8859-1"
> >>
> >>
> >> Hi all,
> >>
> >> I am following the instructions in the "Source reconstruction of
> >>
> >> event-related fields using minimum-norm estimate" tutorial closely to do
> >>
> >> a
> >>
> >> source-analysis of EEG data using the example MRI. As I am following the
> >>
> >> tutorial almost unchanged I am not including the script here.
> >>
> >>
> >> When I re-align the volume conduction model to the sourcespace they are
> >>
> >> not aligned very well, see screenshot attached. I remember a similar
> >>
> >> question in the mailing list a while ago but cannot find it...
> >>
> >>
> >> Is there a way to interactively realign volume conduction model and
> >>
> >> sourcespace? Re-doing the fiducials did not change the aligment
> >>
> >> considerably. Also, my volume conduction model looks weird...
> >>
> >> I used ft_determine_coordsys on both the vol and the sourcespace, see
> >>
> >> screenshots attached, too.
> >>
> >> Would be nice if you could point me in the right direction.
> >>
> >> Thanks in advance.
> >>
> >> Leo
> >>
> >>
> >> ----
> >>
> >>
> >>
> >>
> >>
> >> Dr. med. Leopold Zizlsperger
> >>
> >> Klinik f?r Neurologie
> >>
> >> Uniklinik RWTH Aachen
> >>
> >> Pauwelsstrasse 30
> >>
> >> 52074 Aachen
> >>
> >> Tel: +49 241 80 35465
> >>
> >> lzizlsperger at ukaachen.de
> >>
> >>
> >> Leopold Zizlsperger, MD
> >>
> >> Department of Neurology
> >>
> >> RWTH Aachen University
> >>
> >> Pauwelsstrasse 30
> >>
> >> 52074 Aachen, Germany
> >>
> >> Tel: +49 241 80 35465
> >>
> >> lzizlsperger at ukaachen.de
> >>
> >>
> >>
> >> -------------- next part --------------
> >>
> >> An HTML attachment was scrubbed...
> >>
> >> URL: <
> >>
> >>
> >>
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> >>
> >>
> >> -------------- next part --------------
> >>
> >> A non-text attachment was scrubbed...
> >>
> >> Name: align 2.png
> >>
> >> Type: image/png
> >>
> >> Size: 200601 bytes
> >>
> >> Desc: not available
> >>
> >> URL: <
> >>
> >>
> >>
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> >>
> >>
> >> -------------- next part --------------
> >>
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> >>
> >>
> >>
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> >>
> >>
> >> -------------- next part --------------
> >>
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> >>
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> >>
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> >>
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> >>
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> >>
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> >>
> >>
> >>
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> >>
> >>
> >> -------------- next part --------------
> >>
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> >>
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> >>
> >>
> >>
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130928/aff715c6/attachment-0003.png
> >>
> >>
> >>
> >> ------------------------------
> >>
> >>
> >> _______________________________________________
> >>
> >> fieldtrip mailing list
> >>
> >> fieldtrip at donders.ru.nl
> >>
> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >>
> >>
> >> End of fieldtrip Digest, Vol 34, Issue 28
> >>
> >> *****************************************
> >>
> >>
> >> _______________________________________________
> >>
> >> 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
> >>
> >>
> >>     Jan-Mathijs Schoffelen, MD PhD
> >>
> >> Donders Institute for Brain, Cognition and Behaviour,
> >> Centre for Cognitive Neuroimaging,
> >> Radboud University Nijmegen, The Netherlands
> >>
> >> Max Planck Institute for Psycholinguistics,
> >> Nijmegen, The Netherlands
> >>
> >> J.Schoffelen at donders.ru.nl
> >> Telephone: +31-24-3614793
> >>
> >> http://www.hettaligebrein.nl
> >>
> >>
> >> _______________________________________________
> >> fieldtrip mailing list
> >> fieldtrip at donders.ru.nl
> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >>
> >
> >
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> >
>
> ------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> End of fieldtrip Digest, Vol 34, Issue 31
> *****************************************
>
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From cmuehl at gmail.com  Mon Sep 30 14:54:13 2013
From: cmuehl at gmail.com (Christian Muehl)
Date: Mon, 30 Sep 2013 14:54:13 +0200
Subject: [FieldTrip] Call for Papers for BCI journal special issue on
 affective brain-computer interfaces
Message-ID: <CAG6OC8sumSVz9Yk6=HFnn41gus9cttyVZ1Q31BmW8miJVy981Q@mail.gmail.com>

--------------------------------------
Call for Papers - Special Issue on Affective Brain-Computer Interfaces (aBCI)
Brain-Computer Interfaces Journal
--------------------------------------

You are cordially invited to make a contribution to a special issue of
Brain-Computer Interfaces (http://tinyurl.com/BCIjournal), entitled
“Affective Brain-Computer Interfaces”. The special issue is a
follow-up to the successful 3rd aBCI workshop held at the ACII
conference in Geneva, in September 2013
(http://hmi.ewi.utwente.nl/abci2013). But, this Call is open for every
researcher working in the field of affective brain-computer
interfacing and interested to contribute.

Affective BCI aims at the detection of affective states, such as
emotions or moods, from neuro-physiological signals. Such systems,
allowing users to control computer games by their emotions, support
relaxation training, or trigger your alarm clock during a shallow
sleep stage have been proposed, implemented, and sold. Moreover, the
affordable hardware and software tools also encouraged artists to play
with the idea of a direct access to people's most private information:
their affective and cognitive states. From these explorations followed
a number of interesting installations, suggesting novel ways of
human-computer as well as human-human interaction: encouraging
affective self-reflection, the synchronization and empathizing between
or the competition of different minds, and the collaborative creation
and manipulation of digital multimodal content.

This special issue on aBCI explores the current possibilities and
limitations of using neuro-physiological signals as a modality for the
recognition of affective/cognitive states, and looks at visions for
the use of this information about the user state in applications for
domains like health, arts, and entertainment. We are seeking
theoretical, methodological, and empirical papers dealing with
different topics that include, but are not limited to:
- novel methods and protocols for affective/cognitive state induction
and data collection for aBCI, addressing challenges such as
generalization/specificity of mental state classification;
- the detection of affective/cognitive states via neurophysiological activity;
- the incorporation of additional modalities, such as physiological
sensors, video, or audio, to support the aBCI calibration and
validation;
- innovative concepts for communication or adaptive interfaces using aBCI.

SCHEDULE FOR SUBMISSION
- Deadline for Full Paper Submission: November 22, 2013
- Notification of 1st review outcome: December 15, 2013
- First Revision Due: January 15, 2014
- Notification of 2nd review outcome:  February 01, 2014
- Camera-ready Papers due: February 15, 2014
- Expected publication: June 2014

Manuscripts should be submitted to abci at ewi.utwente.nl
Manuscripts should follow the journal’s guidelines:
http://www.tandfonline.com/action/authorSubmission?journalCode=tbci

SPECIAL ISSUE GUEST EDITORS
Authors are requested to inform the Special Issue Guest Editors about
their intention to submit. Please direct any inquiries, including
those about the suitability of your possible paper, to the
Special-Issue Guest Editors via abci at ewi.utwente.nl :
- Brendan Allison, University of California San Diego, USA
- Guillaume Chanel, Swiss Center for Affective Sciences, Geneva, Switzerland
- Christian Mühl, INRIA Bordeaux - Sud-Ouest, France
- Anton Nijholt, University of Twente, The Netherlands



-- 
Christian Muehl
Postdoctoral Research Associate

INRIA Bordeaux - Sud-Ouest Research Centre
200 avenue de la Vieille Tour
33405 Talence Cedex

http://www.inria.fr/en/
Tel: +33(0)535002644
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From zizlsperger at gmail.com  Mon Sep 30 16:01:04 2013
From: zizlsperger at gmail.com (Leopold Zizlsperger)
Date: Mon, 30 Sep 2013 16:01:04 +0200
Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the
 volume conductor misaligned
In-Reply-To: <CAJT2k__V-aPQdXEPZydquGCxxvDv82w7aXfZDugBs-6ZSAmU+Q@mail.gmail.com>
References: <CAJT2k__V-aPQdXEPZydquGCxxvDv82w7aXfZDugBs-6ZSAmU+Q@mail.gmail.com>
Message-ID: <CAAk5s=WxknkT+7euQhEuSmFfrU04M2BPg30enkna2=fKfu545Q@mail.gmail.com>

Hey Steve,
thanks, you are great, I tried that again and it basically fixed my problem
(see picture).
For documentation and maybe others to profit from:
Going through the
http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
tutorial I had problems building the volume conduction model which I solved
by going through the additional tutorial
http://fieldtrip.fcdonders.nl/tutorial/headmodel_eeg

But after the combination of the matrices and aligning them I got a
considerable sizing problem, see 2nd picture
[[[ mri_nom_ctf = ft_convert_units(mri_nom_ctf, 'cm');


T   = mri_nom_ctf.transform*inv(mri_nom_ctf.transformorig);
% go to the Subject01/bem directory
bnd  = ft_read_headshape('Subject01-oct-6-src.fif', 'format', 'mne_source');
sourcespace = ft_convert_units(bnd, 'cm');
sourcespace = ft_transform_geometry(T, sourcespace);
save sourcespace sourcespace;
save T T; %we will need the transformation matrix in the next step


...

figure;hold on;
ft_plot_vol(vol, 'facecolor', 'none');alpha 0.5;
ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight]]]

So I included Steve's suggestion

vol = ft_convert_units(vol, 'cm')

and specified the location of the fiducials again

[[[ cfg = [];


cfg.method = 'interactive';
mri_nom_ctf = ft_volumerealign(cfg, mri_nom);


with the preauricular points this time in front of the auditory canals
and it worked out well.


Thanks all


Leo






On Mon, Sep 30, 2013 at 1:12 PM, Stephen Politzer-Ahles <
politzerahless at gmail.com> wrote:

> Hi Leo,
>
> If I am remembering correctly, I think the problem could still be related
> to ft_convert_units even if the volume conductor and head model look like
> they're similar in size. For example, in the images I sent out when I was
> having this problem earlier, the volume conductor and hte sourcespace are
> the same size but one is tilted more, and the solution was nevertheless
> related to ft_convert_units (I think). In my case, this was because the
> conversion had to happen at a different time than it does in the tutorial.
> (I had to insert ft_convert_units somewhere earlier in the pipeline than
> where it was happening in the tutorial.) I'm sorry I can't be more
> specific, but if it will help I could try to look through my old code and
> re-figure out what I changed at the time.
>
> Best,
> Steve
>
>
>
> Stephen Politzer-Ahles
> New York University, Abu Dhabi
> Neuroscience of Language Lab
> http://www.nyu.edu/projects/politzer-ahles/
>
>
>
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 30 Sep 2013 12:53:06 +0200
>> From: Leopold Zizlsperger <zizlsperger at gmail.com>
>> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
>> Subject: Re: [FieldTrip] EEG Source reconstruction: sourcespace and
>>
>>         the volume conductor misaligned
>> Message-ID:
>>         <CAAk5s=
>> WTe+T1PZO0jMb6KUvpHFyi-c0tFuG8Mc0m9um6vVdacA at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>
>> Hello
>> thanks for your answers, in combination with the tutorial they were a big
>> help.
>> I think I got closer but have a last issue:
>> @ Jan-Mathijs: I redid the headmodel and it looks better now as shown on
>> the screenshots attached, thanks
>> @ Lilla and Stephen: the scaling in general should not be the problem I
>> think, the sizes seem to match, thank you
>> While both the volume conduction and the headmodel are expressed in CTF
>> coordinates, see second screenshot vol vs sourcespace, they don't align
>> very well > first screenshot
>> Is there a way to align them manually? Or would it be legitimate to
>> "cheat"
>> with the fiducials of the sourcemodel ? By changing the preauricular
>> points
>> I think I could align them, but I am not sure if that would cuase problems
>> later on...
>> Thanks in advance
>> Leo
>>
>>
>> On Mon, Sep 30, 2013 at 12:43 PM, Leopold Zizlsperger <
>> zizlsperger at gmail.com
>> > wrote:
>>
>> > Hello
>> > thanks for your answers, in combination with the tutorial they were a
>> big
>> > help.
>> > I think I got closer but have a last issue:
>> > @ Jan-Mathijs: I redid the headmodel and it looks better now as shown on
>> > the screenshots attached, thanks
>> > @ Lilla and Stephen: the scaling in general should not be the problem I
>> > think, the sizes seem to match, thank you
>> > While both the volume conduction and the headmodel are expressed in CTF
>> > coordinates, see third screenshot vol vs sourcespace, they don't align
>> very
>> > well > first two screenshots
>> > Is there a way to align them manually? Or would it be legitimate to
>> > "cheat" with the fiducials of the sourcemodel ? By changing the
>> > preauricular points I think I could align them, but I am not sure if
>> that
>> > would cuase problems later on...
>> > Thanks in advance
>> > Leo
>> >
>> >
>> >
>> > On Mon, Sep 30, 2013 at 10:29 AM, jan-mathijs schoffelen <
>> > jan.schoffelen at donders.ru.nl> wrote:
>> >
>> >> Hi Leo,
>> >>
>> >> May I add to Lilla's comments that the reconstructed headmodel looks
>> >> quite bad to me. This suggests that the automatic anatomical
>> segmentation
>> >> did not work well. The most likely cause is that the coordinate system
>> >> which you specified for the anatomical image in the input was incorrect
>> >> (e.g. specifying 'spm', while it should have been 'ctf' or so), or
>> that the
>> >> transformation matrix mapping from voxels to head coordinates was not
>> >> correct.
>> >>
>> >> Best,
>> >> Jan-Mathijs
>> >>
>> >>
>> >> On Sep 30, 2013, at 9:53 AM, lilla.magyari at mpi.nl wrote:
>> >>
>> >> Hello Leo and Stephen,
>> >>
>> >> yes, it is unfortunate, that there is still a problem with the MNE
>> >> tutorial. I think the main problem is the integration of the pipeline
>> with
>> >> Freesurfer which requires a more careful look on the script.
>> >> I could not find the attached image from Leo. If the sourcespace and
>> the
>> >> volume conduction models are not well-aligned because one of them is
>> too
>> >> small compared to the other, then it will probably help if you convert
>> the
>> >> units.
>> >> In Fieldtrip, the handling of the units of the volume conduction model
>> has
>> >> changed, which means that they are not automatically converted to 'cm'
>> >> anymore.
>> >> Lilla
>> >>
>> >>
>> >> Hello Leo,
>> >>
>> >>
>> >> This looks like the same problem I was having a few months ago, and
>> there
>> >>
>> >> should be some messages on the list about it. I am not able to look at
>> my
>> >>
>> >> data and scripts right now, but if I remember correctly (you can check
>> the
>> >>
>> >> lists for more) the problem had to do with the transformation matrix,
>> and
>> >>
>> >> ft_convert_units. In my case, during the "volume conduction model"
>> step of
>> >>
>> >> the tutorial (the last step before you can plot the vol and sourcespace
>> >>
>> >> together), I had to add an extra
>> >>
>> >>
>> >> vol = ft_convert_units(vol, 'cm')
>> >>
>> >>
>> >> before ft_transform_geometry. I don't remember if this alone will solve
>> >>
>> >> the
>> >>
>> >> problem (unfortunately the the situation is kind of complicated right
>> now,
>> >>
>> >> there is also a different version of the minimum norms tutorial that is
>> >>
>> >> still in development--see the previous messages for links--and I think
>> my
>> >>
>> >> processing pipeline ended up being a mixture of the two to get things
>> >>
>> >> working. Which means that it's hard to track where exactly I solved the
>> >>
>> >> problem.)
>> >>
>> >>
>> >> Best,
>> >>
>> >> Steve
>> >>
>> >>
>> >>
>> >>
>> >> Message: 1
>> >>
>> >>  Date: Sat, 28 Sep 2013 15:25:32 +0200
>> >>
>> >> From: Zizlsperger Leopold <zizlsperger at gmail.com>
>> >>
>> >> To: <fieldtrip at science.ru.nl>
>> >>
>> >> Subject: [FieldTrip] EEG Source reconstruction: sourcespace and the
>> >>
>> >>        volume  conductor misaligned
>> >>
>> >> Message-ID: <06D14B0C-655A-4EF2-A69A-B735DBDBC504 at gmail.com>
>> >>
>> >> Content-Type: text/plain; charset="iso-8859-1"
>> >>
>> >>
>> >> Hi all,
>> >>
>> >> I am following the instructions in the "Source reconstruction of
>> >>
>> >> event-related fields using minimum-norm estimate" tutorial closely to
>> do
>> >>
>> >> a
>> >>
>> >> source-analysis of EEG data using the example MRI. As I am following
>> the
>> >>
>> >> tutorial almost unchanged I am not including the script here.
>> >>
>> >>
>> >> When I re-align the volume conduction model to the sourcespace they are
>> >>
>> >> not aligned very well, see screenshot attached. I remember a similar
>> >>
>> >> question in the mailing list a while ago but cannot find it...
>> >>
>> >>
>> >> Is there a way to interactively realign volume conduction model and
>> >>
>> >> sourcespace? Re-doing the fiducials did not change the aligment
>> >>
>> >> considerably. Also, my volume conduction model looks weird...
>> >>
>> >> I used ft_determine_coordsys on both the vol and the sourcespace, see
>> >>
>> >> screenshots attached, too.
>> >>
>> >> Would be nice if you could point me in the right direction.
>> >>
>> >> Thanks in advance.
>> >>
>> >> Leo
>> >>
>> >>
>> >> ----
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> Dr. med. Leopold Zizlsperger
>> >>
>> >> Klinik f?r Neurologie
>> >>
>> >> Uniklinik RWTH Aachen
>> >>
>> >> Pauwelsstrasse 30
>> >>
>> >> 52074 Aachen
>> >>
>> >> Tel: +49 241 80 35465
>> >>
>> >> lzizlsperger at ukaachen.de
>> >>
>> >>
>> >> Leopold Zizlsperger, MD
>> >>
>> >> Department of Neurology
>> >>
>> >> RWTH Aachen University
>> >>
>> >> Pauwelsstrasse 30
>> >>
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From r.vandermeij at donders.ru.nl  Mon Sep 30 16:15:39 2013
From: r.vandermeij at donders.ru.nl (Roemer van der Meij)
Date: Mon, 30 Sep 2013 16:15:39 +0200
Subject: [FieldTrip] cfg.plotlabels and ft_databrowser
In-Reply-To: <CAGZVU0_-MNYggLww+O0PbU7S36T5gcwwdnQS+F8H40vpEhpT_A@mail.gmail.com>
References: <CAGZVU0_-MNYggLww+O0PbU7S36T5gcwwdnQS+F8H40vpEhpT_A@mail.gmail.com>
Message-ID: <CA+WpQ35GC9MRP42A4e2G1_pxqUoxdf_nNnDXTT_ecUOegC4S_w@mail.gmail.com>

Hi Alik,

Using cfg.plotlabels = 'some', only plots several of the channel labels.
Leaving it empty, or setting it to 'yes', will show all labels, is that
what you intended?

Additionally, right now we cannot guarantee compatibility with matlab
R2012b onwards due to low level changes in several MathWorks functions.
Please use a version older dan R2013a.

Cheers,
Roemer


On Fri, Sep 27, 2013 at 9:57 PM, Alik Widge <alik.widge at gmail.com> wrote:

> I have pounded on this one from a few different angles and even gone and
> looked at the source, and still can't quite figure out what I'm doing wrong.
>
> I have a datafile from an eXimia TMS-EEG system. Right now, all I'm trying
> to do is load it up and inspect the data a bit to get a sense of how badly
> artifacted it is. So:
>
> %%%%%%
>
> cfg = [];
> cfg.blocksize = 30;         % num of seconds to display at once
> cfg.continuous = 'yes';     % not yet cut into trials
> cfg.plotlabels = 'some';
> cfg.viewmode = 'vertical';
> cfg.colorgroups = 'chantype';
>
> cfg.dataset = [DataDir filesep EEGFile];
> cfg.channel = {'EEG'};
>
> ft_databrowser(cfg)
>
>
> %%%%%%
>
> This does 90% of what it ought to do -- it shows me the EEG channels (no
> triggers or EOG), 30 second segments at a time. What it does *not* do is
> label the channels along the y-axis so that I can readily tell which one is
> Pz, F3, O1, etc., etc. I am pretty sure that's what cfg.plotlabels is
> supposed to do, and yet, it does not. I've also tried doing this as
> ft_databrowser(cfg,data), where I explicitly make sure that data.label
> contains the correct channel names, and that *still* doesn't work.
>
> I'm aware that this was marked as a bug before, but bugzilla shows it
> closed long ago, before r7276 that I'm using I believe.
>
> MATLAB r2013a on OS X, if it matters.
>
> Am I simply misunderstanding what this cfg argument does or how to use it?
>
>
> Alik Widge, MD, PhD
> alik.widge at gmail.com
> (206) 866-5435
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 
Roemer van der Meij M.Sc.
PhD Candidate
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognition
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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