From litvak.vladimir at gmail.com  Thu Mar  1 16:02:28 2012
From: litvak.vladimir at gmail.com (Vladimir Litvak)
Date: Thu, 1 Mar 2012 15:02:28 +0000
Subject: [FieldTrip] Missing triggers with Biosemi EEG data
In-Reply-To: <f0f5f26cc301f41af598ca01ebe2a853.squirrel@www.drcmr.dk>
References: <f0f5f26cc301f41af598ca01ebe2a853.squirrel@www.drcmr.dk>
Message-ID: <CACq1BhKUJwiXMGEWM-OeD2tzbKOaQo=iR15VJ6qFr4HOMMcJ_A@mail.gmail.com>

Dear Mark,

I'm not sure what the reason is for not supporting downgoing triggers
in Biosemi, but there probably is one. I'm CCing your message to
Fieldtrip mailing list where it might be better answered. Are you sure
that the missing triggers are recorded correctly? Can you see them
with any other software you have? Sometimes there is a problem with
connectors which leads to incorrect assignments of trigger codes.

Vladimir

On Thu, Mar 1, 2012 at 2:54 PM, Mark Schram Christensen <markc at drcmr.dk> wrote:
> Dear Vladimir Litvak
> I am currently analysing some EEG data with SPM8 obtained with the biosemi
> system, and I am missing quite a lot of my triggers. I get the warning
> that only upcoing flanks are supported for biosemi, and I suspect that
> that is the reason. I can see that the status channel changes when ever I
> should have had the trigger.
> I guess it is related to the field trip file ft_read_event.m, which seems
> to have this biosemi exception, that even though it should look for both
> up and down flanks it only finds up with biosemi.
> Do you know if there is a possibility of also getting downflank triggers?
> Looking forward to hear from you.
> Best wishes
> Mark Schram Christensen
>
>
> _______________________________________________
> Mark Schram Christensen, MSc, PhD
> Copenhagen Neural Control of Movement &
> Danish Research Centre for Magnetic Resonance
> Department of Exercise and Sport Sciences
> Copenhagen University Hospital Hvidovre
> Kettegård Allé 30
> DK-2650 Hvidovre
> Phone: +45 3862 3407
> E-mail: markc at drcmr.dk
> http://www.ifi.ku.dk/
> http://www.cph-ncm.ku.dk/
> http://www.drcmr.dk/markc
>
>
>
>



From ghahremani.aida at gmail.com  Fri Mar  2 00:56:57 2012
From: ghahremani.aida at gmail.com (aida ghahremani)
Date: Thu, 1 Mar 2012 18:56:57 -0500
Subject: [FieldTrip] fieldtrip Digest, Vol 16, Issue 1
In-Reply-To: <mailman.1.1330599616.2810.fieldtrip@donders.ru.nl>
References: <mailman.1.1330599616.2810.fieldtrip@donders.ru.nl>
Message-ID: <CAM50FKDcYrPq2oSYnLkFHFNrX5ALT9Q2jVc9vU9PMxUc0tEYTQ@mail.gmail.com>

Dear Fieldtrip group

I have got a problem with a very simple program to solve a forward problem.
I used the below program to compute leadfield from a source in the origin
for two electrodes in different locations. I noticed that when I change the
position of one of the electrodes, it affects on the leadfield of the
other. I know it should not be like that, since electrodes do not affect
each other. Would you please help me?


elec.pnt=[4.6*cos(pi/3) 4.6*sin(pi/3) 7.96;4.6*cos(pi/6) 4.6*sin(pi/6)
7.96];
for i=1:2
   elec.label{i} = sprintf('%03d', i);
end

% create a concentric 3-sphere volume conductor, the radius is the same as
for the electrodes
vol = [];
vol.r = [8 8.1 8.6 9.2]; % radii of spheres
vol.c = [1 1 1/80 1];       % conductivity
vol.o = [0 0 0];          % center of sphere

% compute the leadfield for a dipole at position [0 0 0]
pos = [0 0 0];
lf = ft_compute_leadfield(pos, elec, vol);

% compute the potential distribution for a dipole with z-orientation
mom = [0 0 1]';
pot = lf * mom;
end

Best
Ayda

On Thu, Mar 1, 2012 at 6:00 AM, <fieldtrip-request at donders.ru.nl> wrote:

> Send fieldtrip mailing list submissions to
>        fieldtrip at donders.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>        fieldtrip-request at donders.ru.nl
>
> You can reach the person managing the list at
>        fieldtrip-owner at donders.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>   1. question about MNI alignment (Ali Bahramisharif)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 29 Feb 2012 21:10:54 +0100
> From: "Ali Bahramisharif" <ali at cs.ru.nl>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] question about MNI alignment
> Message-ID:
>        <fac73988589583150fc4a6a7a958a215.squirrel at squirrel.science.ru.nl>
> Content-Type: text/plain;charset=iso-8859-1
>
> Dear Fieldtrip users,
>
> I want to create MNI-aligned grids in individual head-space, and I follow
> the guidelines in :
>
>
> http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s[]=template&s[]=grid
>
>
> I do not know how old this page is, but I noticed that for example in the
> current version "cfg.coordinates" should be "cfg.coordsys". I have the
> following problems:
>
> 1- When I run "ft_plot_mesh(template_grid);", I get a cubic grid which is
> apparently different from the one shown in the page.
>
> 2- When I run, ft_plot_vol(hdm), it does not seem to be aligned to
> "ft_plot_sens(ft_read_sens(dataset{i}));"
>
> I checked my segmented volumes, and they seem to be fine, and I did not
> need to run flipdim. I am wondering whether my segmented data is correct
> or it should be flipped somewhere. Please let me know if anybody knows how
> to resolve this problem.
>
> Cheers,
> Ali
>
>
>
>
> ------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> End of fieldtrip Digest, Vol 16, Issue 1
> ****************************************
>
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From r.oostenveld at donders.ru.nl  Mon Mar  5 12:27:53 2012
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Mon, 5 Mar 2012 12:27:53 +0100
Subject: [FieldTrip] FieldTrip course at the Donders in Nijmegen: 7-10 May
Message-ID: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>

Dear FieldTrip users,

The registration for our yearly toolkit course on "MEG and EEG data analysis" at the Donders Institute has opened. This year's MEG/EEG toolkit will take place from 7-10 May 2012. 

This 4-day toolkit course will teach you advanced MEG and EEG data analysis skills. Preprocessing, frequency analysis, source reconstruction and various statistical methods will be covered. The toolkit will consist of a number of lectures, followed by hands-on sessions in which you will be tutored through the complete analysis of a MEG data set using the FieldTrip toolbox. The fee for senior participants is € 400. The (PhD) student fee is € 200. Registration fee includes coffee/tea, Dutch sandwich lunches and one dinner.

Have a look at http://www.ru.nl/donders/agenda-news/courses/toolkits-2012/ for the preliminary programme and to register. Please do note that the number of seats is limited and that in the previous years the course was oversubscribed. We therefore expect to have to select participants; this is done on the basis of the information that you provide on your background, skills and research interest. Note that the registration closes 31 March. You will be informed about whether you can participate before mid-April.

Best wishes,

Robert Oostenveld & Jan-Mathijs Schoffelen

-----------------------------------------------------------
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
tel.: +31 (0)24 3619695
e-mail: r.oostenveld at donders.ru.nl
web: http://www.ru.nl/neuroimaging
skype: r.oostenveld
-----------------------------------------------------------



From ugabrewer at gmail.com  Mon Mar  5 18:58:33 2012
From: ugabrewer at gmail.com (Gene Brewer)
Date: Mon, 5 Mar 2012 10:58:33 -0700
Subject: [FieldTrip] Postdoctoral Fellowship at Arizona State University
In-Reply-To: <CADo-6W+m9eKFykATMtJhHEgEvZuA5xY09y3Y1s-bNwZgf573=Q@mail.gmail.com>
References: <CADo-6W+m9eKFykATMtJhHEgEvZuA5xY09y3Y1s-bNwZgf573=Q@mail.gmail.com>
Message-ID: <CADo-6WJRiPNv+KyL9cSAnbHonaGWX5=tV=KDMOcNmsz_njzmXg@mail.gmail.com>

List Members,

*Arizona State University Postdoctoral Fellowship in Neuropsychology of
Strategic Communication*

The Center for Strategic Communication (CSC) and the Department of
Psychology at Arizona State University are pleased to announce a new
Postdoctoral Fellowship program beginning May 2012.

*Postdoctoral Fellowship*

A postdoctoral fellowship will be awarded beginning in the May/June 2012
time frame. The appointment is for full time employment (40 hours per week)
for 18 months.  Renewal for up to two additional 18 month periods is
possible, contingent on additional funding by the sponsor and satisfactory
job performance. Salary is $60,000 and the University offers subsidized
health insurance. Support for travel to conferences will be available.
Fellows are responsible for relocation and housing expenses.  Fellows will
support a research project sponsored by the Defense Advanced Research
Projects Agency (DARPA) involving multi-modal neuroimaging (fMRI + EEG) of
narrative comprehension and persuasion.

For additional information regarding postdoctoral fellowships at ASU,
please see: http://provost.asu.edu/postdoc.

*Eligibility*

Applicants must have an earned or pending doctoral degree in Neuroscience,
Statistics, Social Psychology, Cognitive Psychology, or a related
field/discipline. The degree must have been earned no earlier than 2010.
Candidates with pending degrees who will have successfully defended their
dissertations by May 1, 2012 will also be considered. Applicants must have
no more than two years of formal postdoctoral experience.

*Required Expertise*

Applicants must have relevant expertise in fMRI data acquisition and
analysis and/or EEG data acquisition and analysis, as applied to the study
of cognitive or social psychological processes.

*Desired Expertise*

Relevant expertise or experience in multi-modal mapping (fMRI + EEG) of
cognitive and social psychological processes and/or neuropsychology of
narrative or persuasion is desirable.

*Responsibilities*

Postdoctoral scholars are expected to carry out the research plan and
fulfill the goals established with the supervising faculty members, Drs.
Gene Brewer and Leslie Baxter; to assist the supervising faculty members
and other Principal Investigators in fulfilling the requirements of the
grant in a timely manner; to communicate regularly with the supervising
faculty member and other members of the research team; and to notify the
faculty member of any change in research plans.

Beyond grant-related activities, our facilities will help create valuable
opportunities for the postdoctoral scholar to continue their fMRI and EEG
research agenda, develop new multi-modal techniques, teach, and get
training experience.

For further information about the position contact Prof. Gene Brewer,
gene.brewer at asu.edu

*Application*

Submit application materials electronically with all documents included in
a single PDF file, to include the following:

1. A cover letter stating your interest in the Postdoctoral Fellowship.
Provide details on

a. how your research and expertise relates to neuroimaging, especially with
regard to combining data from fMRI and EEG.

b. how your research and expertise relates to the project described above,
and

c. your long-term professional goals.

2. An up to date curriculum vitae.

3. Names and contact information for two references who agree to be
contacted.

4. Copies of up to three published papers/scholarly work.

5. Scanned copies of current academic transcript from all degree awarding
institutions. Official transcripts will be requested from those who
received formal offers.

The search will initially close with applications received by* April 15,
2012*.  If the position is not filled, then applications will be accepted
every subsequent Friday until search is closed.

Send materials to:

Josephine Wong, Program Manager

Center for Strategic Communication

jody at asu.edu

ASU is an equal opportunity/affirmative action employer committed to
excellence through diversity.  Women and minorities are encouraged to apply.
ASU’s complete non-discrimination statement can be found at:
http://www.asu.edu/titleIX/

-- 
Gene A. Brewer Jr.
Arizona State University
Department of Psychology
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From alotof_xd at yahoo.com  Tue Mar  6 21:52:37 2012
From: alotof_xd at yahoo.com (alotof eve)
Date: Tue, 6 Mar 2012 12:52:37 -0800 (PST)
Subject: [FieldTrip] error message in databrowser
In-Reply-To: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
References: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
Message-ID: <1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>

Hello, experts,

I am using ICA following the tutirial steps. 
I got IC dataset "comp" with the command: comp = ft_componentanalysis (cfg, data);
and ft_topoplotIC(cfg, comp) works.

However, then I used ft_databrowser(cfg, comp), I got an error message:
Operands to the || and && operators must be
convertible to logical scalar values.

Error in ft_databrowser (line 135)
if hasdata && isfield(data, 'topo') &&
strmatch (cfg.viewmode, 'component')

Can anyone know the way to settle this? 
Thanks in advance.

Eve
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From alotof_xd at yahoo.com  Wed Mar  7 09:01:59 2012
From: alotof_xd at yahoo.com (alotof eve)
Date: Wed, 7 Mar 2012 00:01:59 -0800 (PST)
Subject: [FieldTrip] error message in databrowser
In-Reply-To: <1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>
References: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
	<1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>
Message-ID: <1331107319.55433.YahooMailNeo@web125502.mail.ne1.yahoo.com>

Updated: I changed "&&" to "&", it worked but later a new error happened:

Reference to non-existent field 'hlim'.

Error in ft_databrowser>redraw_cb (line 1015)
             eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - opt.hlim(1)); 

 
Error in ft_databrowser (line 434)
redraw_cb(h);
_____
Thanks,
Eve



________________________________
 From: alotof eve <alotof_xd at yahoo.com>
To: Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
Sent: Tuesday, March 6, 2012 12:52 PM
Subject: [FieldTrip] error message in databrowser
 

Hello, experts,

I am using ICA following the tutirial steps. 
I got IC dataset "comp" with the command: comp = ft_componentanalysis (cfg, data);
and ft_topoplotIC(cfg, comp) works.

However, then I used ft_databrowser(cfg, comp), I got an error message:
Operands to the || and && operators must be
convertible to logical scalar values.

Error in ft_databrowser (line 135)
if hasdata && isfield(data, 'topo') &&
strmatch (cfg.viewmode, 'component')

Can anyone know the way to settle this? 
Thanks in advance.

Eve


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From mcoskun at mail.uh.edu  Wed Mar  7 14:26:04 2012
From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun)
Date: Wed, 07 Mar 2012 07:26:04 -0600
Subject: [FieldTrip] error message in databrowser
In-Reply-To: <1331107319.55433.YahooMailNeo@web125502.mail.ne1.yahoo.com>
References: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
	<1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>
	<1331107319.55433.YahooMailNeo@web125502.mail.ne1.yahoo.com>
Message-ID: <7050dbcfcd6be.4f570d8c@mail.uh.edu>

Hi Eve,


I have posted same error earlier but got no suggestions. In my case, the error started popping up after i tried using parallel processing, but i don't know if this has anything to do with the error. I tried many things but no result.


finally, i simply uninstalled and re-installed matlab and everything worked perfectly there after. You may want to try this as a final option if you don't hear any other solution.


Mehmet

----- Original Message -----
From: alotof eve <alotof_xd at yahoo.com>
Date: Wednesday, March 7, 2012 2:03 am
Subject: Re: [FieldTrip] error message in databrowser
To: alotof eve <alotof_xd at yahoo.com>, Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl>



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



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



> Updated: I changed "&&" to "&", it worked but later a new error happened:

> 

> Reference to non-existent field 'hlim'.
> 

> Error in ft_databrowser>redraw_cb (line 1015)
>              eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - opt.hlim(1)); 

>  
> Error in ft_databrowser (line 434)
> redraw_cb(h);
> _____
> Thanks,
> Eve

> 
>
-----------------------------------------------------------
From: alotof eve <alotof_xd at yahoo.com>
> To: Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
> Sent: Tuesday, March 6, 2012 12:52 PM
> Subject: [FieldTrip] error message in databrowser
>
> 

> Hello, experts,
> 
> I am using ICA following the tutirial steps. 
> I got IC dataset "comp" with the command: comp = ft_componentanalysis (cfg, data);
> and ft_topoplotIC(cfg, comp) works.
> 
> However, then I used ft_databrowser(cfg, comp), I got an error message:
> Operands to the || and && operators must be
> convertible to logical scalar values.
> 
> Error in ft_databrowser (line 135)
> if hasdata && isfield(data, 'topo') &&
> strmatch (cfg.viewmode, 'component')
> 
> Can anyone know the way to settle this? 
> Thanks in advance.
> 
> Eve
>

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



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From MEpstein at NKI.RFMH.ORG  Wed Mar  7 18:28:48 2012
From: MEpstein at NKI.RFMH.ORG (Epstein, Michael)
Date: Wed, 7 Mar 2012 12:28:48 -0500
Subject: [FieldTrip] Error -> ft_databrowser
Message-ID: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>

Hi - I am actually encountering the same error with databrowser, and was
wondering if you ever came up with a solution to this problem - or if
anyone else has a solution - I didn't find a response on the mailing
list.

 

-Michael

 

 

 

________________________________

Dear Fieldtrippers,

 

 

I am encountering a strange error while i try to use ft_databrowser. The
error code is as below. I have never seen this error earlier. I used
ft_databrowser many times and its only last 2 days that i am getting the
error. I downloaded a newer version of fieldtrip (fieldtrip-20120130)
and used the newer version but still the same error. Strangely, i dont
get this error when i tried with other computers (same matlab version
(R2010a), same operating system (windows 7) on both computers. Has
anyone got this error before? what may cause this error?

 

 

fieldtrip version 20120130, matlab version R2010a, operating system
windows 7.

 

 

Thanks in advance for any suggestions.

 

 

 

??? Error using ==> ft_fetch_data at 57

data does not contain a consistent trial definition, fetching data is
not

possible

 

 

Error in ==> ft_databrowser>redraw_cb at 1159

art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample',
endsample);

 

 

Error in ==> ft_databrowser at 535

redraw_cb(h);

 



Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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From max-philipp.stenner at med.ovgu.de  Wed Mar  7 18:46:06 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Wed, 07 Mar 2012 17:46:06 +0000
Subject: [FieldTrip] ft_sourcestatistics
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830C999B@ESEN4.imed.uni-magdeburg.de>

Dear fieldtrip users,



I am encountering a problem with ft_sourcestatistics when using output from ft_sourcegrandaverage. My parameter of interest is a logratio: log(mean(moments(time of interest))/mean(moments(baseline))) which I simply named 'pow' to be compatible with ft functions. Apart from this, nothing else deviates from how fieldtrip handles the data/nothing else was changed 'manually'.



The problem arises from the fact that the existence of 10 different subjects in the grandaverage (in the usual 1x10 struct field 'trial') isn't represented in the 'powdimord' field of the data after ft_checkdata(varargin{i}, 'datatype', {'source', 'volume'}, 'feedback', 'no', 'inside', 'index', 'sourcerepresentation', 'new'); in the new implementation of ft_sourcestatistics:



varargin{1}

ans =



(before ft_checkdata:)



        pos: [8196x3 double]
        var: [1x1 struct]
     dimord: 'voxel'
      trial: [1x10 struct]
     inside: [8196x1 double]
    outside: [0x1 double]
         df: [8196x1 double]
        cfg: [1x1 struct]



(after ft_checkdata:)



          pos: [8196x3 double]
          var: [1x1 struct]
       dimord: 'pos'
       inside: [8196x1 double]
      outside: [0x1 double]
           df: [8196x1 double]
          cfg: [1x1 struct]
          pow: [8196x10 double]
    powdimord: 'pos'



This leads to a (wrong) transpose of the design (originally row1 = uvar, row2 = ivar [with two conditions for a depsamples T test]) and ultimately to the message

'The data must contain at least two units (usually subjects).'



Any help would be much appreciated, thanks very much!

Max

(fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)


From mcoskun at mail.uh.edu  Wed Mar  7 18:55:38 2012
From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun)
Date: Wed, 07 Mar 2012 11:55:38 -0600
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
Message-ID: <7270aa3bcbfd9.4f574cba@mail.uh.edu>

Hi Michael,


I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. 


just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution.


But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution.


Mehmet





----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
Date: Wednesday, March 7, 2012 11:29 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: fieldtrip at donders.ru.nl



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



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


> Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list.
>  
> -Michael
>  
>  
>  
-----------------------------------------------------------
> Dear Fieldtrippers,
>  
>  
> I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error?
>  
>  
> fieldtrip version 20120130, matlab version R2010a, operating system windows 7.
>  
>  
> Thanks in advance for any suggestions.
>  
>  
>  
> ??? Error using ==> ft_fetch_data at 57
> data does not contain a consistent trial definition, fetching data is not
> possible
>  
>  
> Error in ==> ft_databrowser>redraw_cb at 1159
> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample);
>  
>  
> Error in ==> ft_databrowser at 535
> redraw_cb(h);
>  



-----------------------------------------------------------
> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. 

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From MEpstein at NKI.RFMH.ORG  Wed Mar  7 18:57:25 2012
From: MEpstein at NKI.RFMH.ORG (Epstein, Michael)
Date: Wed, 7 Mar 2012 12:57:25 -0500
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <7270aa3bcbfd9.4f574cba@mail.uh.edu>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
	<7270aa3bcbfd9.4f574cba@mail.uh.edu>
Message-ID: <2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>

Interesting... can I ask what version of matlab you were running? and
was it 64 bit?

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Mehmet-Akif Coskun
Sent: Wednesday, March 07, 2012 12:56 PM
To: Email discussion list for the FieldTrip project
Cc: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Michael,


I have posted the question actually but I didn't hear any suggestions
about it. The same error was posted yesterday by someone else. 


just to repeat what i have replied in the other post, i tried many
things to solve it (changed the code, run the databrowser code line by
line, updated fieldtrip version at etc.), but none of them solved the
problem. I started getting the error after I tried using parallel
processing scripts in matlab. But as i said, i have no basis to say that
this caused the problem. So basically, i do not know any scientific
solution.


But an old school method solved the problem in my case. Simply i
uninstalled and re-installed matlab. Never got the error again. You may
want to try this. I have no other solution.


Mehmet





----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
Date: Wednesday, March 7, 2012 11:29 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: fieldtrip at donders.ru.nl

> Hi - I am actually encountering the same error with databrowser, and
was wondering if you ever came up with a solution to this problem - or
if anyone else has a solution - I didn't find a response on the mailing
list.

>  

> -Michael

>  

>  

>  

________________________________

> Dear Fieldtrippers,

>  

>  

> I am encountering a strange error while i try to use ft_databrowser.
The error code is as below. I have never seen this error earlier. I used
ft_databrowser many times and its only last 2 days that i am getting the
error. I downloaded a newer version of fieldtrip (fieldtrip-20120130)
and used the newer version but still the same error. Strangely, i dont
get this error when i tried with other computers (same matlab version
(R2010a), same operating system (windows 7) on both computers. Has
anyone got this error before? what may cause this error?

>  

>  

> fieldtrip version 20120130, matlab version R2010a, operating system
windows 7.

>  

>  

> Thanks in advance for any suggestions.

>  

>  

>  

> ??? Error using ==> ft_fetch_data at 57

> data does not contain a consistent trial definition, fetching data is
not

> possible

>  

>  

> Error in ==> ft_databrowser>redraw_cb at 1159

> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample',
endsample);

>  

>  

> Error in ==> ft_databrowser at 535

> redraw_cb(h);

>  

 

________________________________

> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the
intended recipient. It may contain confidential information which is
legally privilegedor otherwise protected by law. If you received this
e-mail in error or from someone who is not authorized to send it to you,
you are strictly prohibited from reviewing, using, disseminating,
distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE
ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank
you for your cooperation. 

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



Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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From jnortonf at uci.edu  Wed Mar  7 19:05:43 2012
From: jnortonf at uci.edu (Jessamy Norton-Ford)
Date: Wed, 7 Mar 2012 10:05:43 -0800
Subject: [FieldTrip] EEG layout help
Message-ID: <CACvc6xQXFTQ+wnLafdrx7nFnjwZNF6GMOPMYOh2BvjasELDdpw@mail.gmail.com>

Hello,

I am trying to use the plotting functions with my 34-channel data (32
standard EEG channels + VEOG and HEOG).  In EEGLAB, I use the
'standard-10-5-cap385.elp' file for the locations, however I get the
following error in Fieldtrip (v. 20120220).

cfg = [];
cfg.baseline         = [-0.5 -0.1];
cfg.baselinetype     = 'absolute';
cfg.zlim             = [-3e-25 3e-25];
cfg.showlabels       = 'yes';
cfg.layout           = 'standard-10-5-cap385.elp';
figure
ft_multiplotTFR(cfg, TFRwave)
creating layout from electrode file standard-10-5-cap385.elp
??? Error using ==> ft_read_sens at 84
unknown fileformat for electrodes or gradiometers

Error in ==> ft_prepare_layout at 253
  lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
  cfg.style);

Error in ==> ft_multiplotTFR at 241
lay = ft_prepare_layout(cfg, data);

In ft_read_sens, it appears as though fieldtrip cannot yet deal with such
.elp files?  I wonder if (1) I am making an easy mistake as I am still new
to Fieldtrip, or (2) if there is perhaps an easy workaround for this .elp
incompatibility?

In case it is useful, here are the channels that I am using:

1 Fp1  2 Fpz  3 Fp2  4 F7  5 F3  6 Fz  7 F4  8 F8  9 FC5  10 FC1  11 FC2  12
FC6  13 M1  14 T7  15 C3  16 Cz  17 C4  18 T8  19 M2  20 CP5  21 CP1
22 CP2  23
CP6  24 P7  25 P3  26 Pz  27 P4  28 P8  29 POz  30 O1  31 Oz  32 O2
33 VEOG  34
HEOG

Thanks very much,

Jessamy Norton-Ford








-- 
Jessamy Norton-Ford
Doctoral Student, Department of Cognitive Sciences
University of California, Irvine
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From mcoskun at mail.uh.edu  Wed Mar  7 19:17:33 2012
From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun)
Date: Wed, 07 Mar 2012 12:17:33 -0600
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
	<7270aa3bcbfd9.4f574cba@mail.uh.edu>
	<2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
Message-ID: <72b0dfc7cc8ec.4f5751dd@mail.uh.edu>

Matlab R2010a 64-bit under windows 7. I did not update matlab version. just uninstalled and re-installed the same version. 


Mehmet

----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
Date: Wednesday, March 7, 2012 11:58 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl>



| 


> Interesting... can I ask what version of matlab you were running? and was it 64 bit?
>  
> -Michael
>  
> From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Mehmet-Akif Coskun
> Sent: Wednesday, March 07, 2012 12:56 PM
> To: Email discussion list for the FieldTrip project
> Cc: fieldtrip at donders.ru.nl
> Subject: Re: [FieldTrip] Error -> ft_databrowser
>  
> Hi Michael,
> 
> 
> I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. 
> 
> 
> just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution.
> 
> 
> But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution.
> 
> 
> Mehmet
> 
> 
> 
> 
> 
> ----- Original Message -----
> From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
> Date: Wednesday, March 7, 2012 11:29 am
> Subject: Re: [FieldTrip] Error -> ft_databrowser
> To: fieldtrip at donders.ru.nl

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

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



-----------------------------------------------------------
> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. 

|-----------------------------------------------------------


> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
-----------------------------------------------------------
|
> > Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list.
>  
> -Michael
>  
>  
>  
-----------------------------------------------------------
> > Dear Fieldtrippers,
> >  
> >  
> > I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error?
> >  
> >  
> > fieldtrip version 20120130, matlab version R2010a, operating system windows 7.
> >  
> >  
> > Thanks in advance for any suggestions.
> >  
> >  
> >  
> > ??? Error using ==> ft_fetch_data at 57
> > data does not contain a consistent trial definition, fetching data is not
> > possible
> >  
> >  
> > Error in ==> ft_databrowser>redraw_cb at 1159
> > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample);
> >  
> >  
> > Error in ==> ft_databrowser at 535
> > redraw_cb(h);
> >  
>  
-----------------------------------------------------------
> > Conserve Resources. Print only when necessary.
> > 
> > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. 
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From alotof_xd at yahoo.com  Thu Mar  8 08:04:14 2012
From: alotof_xd at yahoo.com (alotof eve)
Date: Wed, 7 Mar 2012 23:04:14 -0800 (PST)
Subject: [FieldTrip] error message in databrowser
In-Reply-To: <7050dbcfcd6be.4f570d8c@mail.uh.edu>
References: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
	<1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>
	<1331107319.55433.YahooMailNeo@web125502.mail.ne1.yahoo.com>
	<7050dbcfcd6be.4f570d8c@mail.uh.edu>
Message-ID: <1331190254.90650.YahooMailNeo@web125502.mail.ne1.yahoo.com>

Hi, Mehmet,

Thank you so much for the suggestion. I will try this and will report the result.

Thanks,
Eve



________________________________
 From: Mehmet-Akif Coskun <mcoskun at mail.uh.edu>
To: alotof eve <alotof_xd at yahoo.com>; Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
Cc: alotof eve <alotof_xd at yahoo.com>; Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
Sent: Wednesday, March 7, 2012 5:26 AM
Subject: Re: [FieldTrip] error message in databrowser
 

Hi Eve,


I have posted same error earlier but got no suggestions. In my case, the error started popping up after i tried using parallel processing, but i don't know if this has anything to do with the error. I tried many things but no result.


finally, i simply uninstalled and re-installed matlab and everything worked perfectly there after. You may want to try this as a final option if you don't hear any other solution.


Mehmet

----- Original Message -----
From: alotof eve <alotof_xd at yahoo.com>
Date: Wednesday, March 7, 2012 2:03 am
Subject: Re: [FieldTrip] error message in databrowser
To: alotof eve <alotof_xd at yahoo.com>, Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl>


> Updated: I changed "&&" to "&", it worked but later a new error happened:
> 

> Reference to non-existent field 'hlim'.
> 

> Error in ft_databrowser>redraw_cb (line 1015)
>              eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - opt.hlim(1)); 

>  
> Error in ft_databrowser (line 434)
> redraw_cb(h);
> _____
> Thanks,
> Eve

> 
>  

________________________________
 From: alotof eve <alotof_xd at yahoo.com>
>  To: Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
>  Sent: Tuesday, March 6, 2012 12:52 PM
>  Subject: [FieldTrip] error message in databrowser
>   >  



> Hello, experts,
> 
> I am using ICA following the tutirial steps. 
> I got IC dataset "comp" with the command: comp = ft_componentanalysis (cfg, data);
> and ft_topoplotIC(cfg, comp) works.
> 
> However, then I used ft_databrowser(cfg, comp), I got an error message:
> Operands to the || and && operators must be
> convertible to logical scalar values.
> 
> Error in ft_databrowser (line 135)
> if hasdata && isfield(data, 'topo') &&
> strmatch (cfg.viewmode, 'component')
> 
> Can anyone know the way to settle this? 
> Thanks in advance.
> 
> Eve
>  

>  >  > 
> _______________________________________________
> 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 h.morgan at bangor.ac.uk  Thu Mar  8 10:49:59 2012
From: h.morgan at bangor.ac.uk (Helen Morgan)
Date: Thu, 08 Mar 2012 09:49:59 +0000
Subject: [FieldTrip] Call for abstracts - HIVE workshop - Berlin,
	April 27-28th, 2012
Message-ID: <4F5880C7.7020608@bangor.ac.uk>

Call for abstracts

HIVE WORKSHOP - Berlin, April 27-28th, 2012.

Could computers someday interact directly with the human brain? The 
vision of HIVE is that in the next 50 years we will witness the coming 
of age of technologies for fluent brain-computer and computer-mediated 
brain-to-brain interaction. While recent research has delivered 
important breakthroughs in brain-to-computer transmission, little has 
been achieved in the other direction––computer-controlled brain 
stimulation. The goal of the workshop is to present research toward 
developing a new generation of powerful and controllable non-invasive 
brain stimulation technologies.

State-of-the-art presentations on current distribution models and 
multi-scale neuron current interaction modeling will be presented. 
Results from stimulation experiments using tDCS, TMS, EEG and fMRI in 
different scenarios are given in overview and original presentations. 
Discussions during the workshop will lead to the design of multisite 
transcranial current stimulation technologies using real time EEG 
monitoring and feedback.

Keynote speakers:

Dr. Michael Nitsche
Dr. Klaus-Robert Müller
Dr. Lisa Marshall
Dr. Fabio Babiloni

The HIVE project has opened this workshop to all researchers from in 
this new multi-disciplinary field, based on acceptance of an abstract. 
You can find the Call for Abstracts here.

http://hive-eu.org/hive2012/call_for_papers

Best abstracts and presentations will be selected for publication in a 
Special Issue of the journal "Physiological Measurement".

Download the flyer here 
http://hive-eu.org/sites/hive-eu.org/files/Hive%20workshop%202012_final.pdf

-- 
Dr. Helen M. Morgan
Research Officer
Wolfson Centre for Clinical and Cognitive Neuroscience
School of Psychology
Bangor University
tel: 01248 388172
email: h.morgan at bangor.ac.uk

-- 
Rhif Elusen Gofrestredig / Registered Charity No. 1141565

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From max-philipp.stenner at med.ovgu.de  Thu Mar  8 13:26:13 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Thu, 08 Mar 2012 12:26:13 +0000
Subject: [FieldTrip] monte-carlo on LCMV moments
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830C9AB1@ESEN4.imed.uni-magdeburg.de>

Dear fieldtrip users, 

in addition to the question on the new implementation of ft_sourcestatistics for sourcegrandaveraged data which I sent yesterday, I have a second question regarding sourcestatistics on grandaveraged data obtained from LCMV beamforming of ERF. 

I would like to perfrom cluster corrected monte-carlo statistics on subj_voxel_time dipole moments, comparable (in its dimensions) to the sensor-level ERF cluster permutation test on subj_channel_time data that is described in the respective tutorial and that worked well. 

However, ft_sourcegrandaverage doesn't seem to permit "averaging" (with keepindividual = yes) of parameters that have more than one value per gridpoint (i.e. other than pow, nai etc.). 

In addition, the get_source_lcmv_mom subfunction in statistics_wrapper requires 4 rather than 3 dimensions. 

Is there any way that subj_voxel_time dipole moment data can be used for monte-carlo statistics comparable to the respective sensor-level ERF test?

Thanks very much, 

best wishes
Max
(fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)






________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]&quot; im Auftrag von &quot;Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de]
Gesendet: Mittwoch, 7. März 2012 18:46
Bis: Email discussion list for the FieldTrip project
Betreff: [FieldTrip] ft_sourcestatistics

Dear fieldtrip users,



I am encountering a problem with ft_sourcestatistics when using output from ft_sourcegrandaverage. My parameter of interest is a logratio: log(mean(moments(time of interest))/mean(moments(baseline))) which I simply named 'pow' to be compatible with ft functions. Apart from this, nothing else deviates from how fieldtrip handles the data/nothing else was changed 'manually'.



The problem arises from the fact that the existence of 10 different subjects in the grandaverage (in the usual 1x10 struct field 'trial') isn't represented in the 'powdimord' field of the data after ft_checkdata(varargin{i}, 'datatype', {'source', 'volume'}, 'feedback', 'no', 'inside', 'index', 'sourcerepresentation', 'new'); in the new implementation of ft_sourcestatistics:



varargin{1}

ans =



(before ft_checkdata:)



        pos: [8196x3 double]
        var: [1x1 struct]
     dimord: 'voxel'
      trial: [1x10 struct]
     inside: [8196x1 double]
    outside: [0x1 double]
         df: [8196x1 double]
        cfg: [1x1 struct]



(after ft_checkdata:)



          pos: [8196x3 double]
          var: [1x1 struct]
       dimord: 'pos'
       inside: [8196x1 double]
      outside: [0x1 double]
           df: [8196x1 double]
          cfg: [1x1 struct]
          pow: [8196x10 double]
    powdimord: 'pos'



This leads to a (wrong) transpose of the design (originally row1 = uvar, row2 = ivar [with two conditions for a depsamples T test]) and ultimately to the message

'The data must contain at least two units (usually subjects).'



Any help would be much appreciated, thanks very much!

Max

(fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From jan.schoffelen at donders.ru.nl  Thu Mar  8 13:38:46 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 8 Mar 2012 13:38:46 +0100
Subject: [FieldTrip] ft_sourcestatistics
In-Reply-To: <FBEFFA1F493D8944969D2F5AE78E58830C999B@ESEN4.imed.uni-magdeburg.de>
References: <FBEFFA1F493D8944969D2F5AE78E58830C999B@ESEN4.imed.uni-magdeburg.de>
Message-ID: <23891D6F-057F-4DBE-8C52-C43DAB74608E@donders.ru.nl>

Hi Max,

At the moment we are designing some major code changes to deal with source level data, and we need to ask you for some patience in this regard.
For now, you could try to move the call to ft_checkdata to outside ft_sourcestatistics, and change the powdimord into 'pos_rpt'; 
Does it work if you subsequently call ft_sourcestatistics (with cfg.implementation = 'new')? This new implementation has never fully matured and may be instable. It has been found to work in certain situations, but it has never been fully tested on all possible processing histories that users may throw at it. Hence the urgent need to clean up the code. 

Best,

Jan-Mathijs



On Mar 7, 2012, at 6:46 PM, Stenner, Max-Philipp wrote:

> Dear fieldtrip users,
> 
> 
> 
> I am encountering a problem with ft_sourcestatistics when using output from ft_sourcegrandaverage. My parameter of interest is a logratio: log(mean(moments(time of interest))/mean(moments(baseline))) which I simply named 'pow' to be compatible with ft functions. Apart from this, nothing else deviates from how fieldtrip handles the data/nothing else was changed 'manually'.
> 
> 
> 
> The problem arises from the fact that the existence of 10 different subjects in the grandaverage (in the usual 1x10 struct field 'trial') isn't represented in the 'powdimord' field of the data after ft_checkdata(varargin{i}, 'datatype', {'source', 'volume'}, 'feedback', 'no', 'inside', 'index', 'sourcerepresentation', 'new'); in the new implementation of ft_sourcestatistics:
> 
> 
> 
> varargin{1}
> 
> ans =
> 
> 
> 
> (before ft_checkdata:)
> 
> 
> 
>        pos: [8196x3 double]
>        var: [1x1 struct]
>     dimord: 'voxel'
>      trial: [1x10 struct]
>     inside: [8196x1 double]
>    outside: [0x1 double]
>         df: [8196x1 double]
>        cfg: [1x1 struct]
> 
> 
> 
> (after ft_checkdata:)
> 
> 
> 
>          pos: [8196x3 double]
>          var: [1x1 struct]
>       dimord: 'pos'
>       inside: [8196x1 double]
>      outside: [0x1 double]
>           df: [8196x1 double]
>          cfg: [1x1 struct]
>          pow: [8196x10 double]
>    powdimord: 'pos'
> 
> 
> 
> This leads to a (wrong) transpose of the design (originally row1 = uvar, row2 = ivar [with two conditions for a depsamples T test]) and ultimately to the message
> 
> 'The data must contain at least two units (usually subjects).'
> 
> 
> 
> Any help would be much appreciated, thanks very much!
> 
> Max
> 
> (fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)
> _______________________________________________
> 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

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From r.vandermeij at donders.ru.nl  Thu Mar  8 13:59:07 2012
From: r.vandermeij at donders.ru.nl (Roemer van der Meij)
Date: Thu, 08 Mar 2012 13:59:07 +0100
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
	<7270aa3bcbfd9.4f574cba@mail.uh.edu>
	<2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
Message-ID: <4F58AD1B.906@donders.ru.nl>

Hi Eve, Hi Michael,

I cannot find the specific line of code in the latest version, so I 
assume you are using an old version? If you update to the latest 
version, the problem should be solved.

Just for your curiosity, the bug was most likely caused by using the 
ancient strmatch (deprecated in later version of matlab). Changing it 
strcmp would have most likely fixed the problem.

Cheers,
Roemer




On 07-03-12 18:57, Epstein, Michael wrote:
>
> Interesting... can I ask what version of matlab you were running? and 
> was it 64 bit?
>
> -Michael
>
> *From:*fieldtrip-bounces at donders.ru.nl 
> [mailto:fieldtrip-bounces at donders.ru.nl] *On Behalf Of *Mehmet-Akif Coskun
> *Sent:* Wednesday, March 07, 2012 12:56 PM
> *To:* Email discussion list for the FieldTrip project
> *Cc:* fieldtrip at donders.ru.nl
> *Subject:* Re: [FieldTrip] Error -> ft_databrowser
>
> Hi Michael,
>
>
> I have posted the question actually but I didn't hear any suggestions 
> about it. The same error was posted yesterday by someone else.
>
>
> just to repeat what i have replied in the other post, i tried many 
> things to solve it (changed the code, run the databrowser code line by 
> line, updated fieldtrip version at etc.), but none of them solved the 
> problem. I started getting the error after I tried using parallel 
> processing scripts in matlab. But as i said, i have no basis to say 
> that this caused the problem. So basically, i do not know any 
> scientific solution.
>
>
> But an old school method solved the problem in my case. Simply i 
> uninstalled and re-installed matlab. Never got the error again. You 
> may want to try this. I have no other solution.
>
>
> Mehmet
>
>
>
>
>
> ----- Original Message -----
> From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
> Date: Wednesday, March 7, 2012 11:29 am
> Subject: Re: [FieldTrip] Error -> ft_databrowser
> To: fieldtrip at donders.ru.nl
>
> > Hi - I am actually encountering the same error with databrowser, and 
> was wondering if you ever came up with a solution to this problem - or 
> if anyone else has a solution - I didn't find a response on the 
> mailing list.
>
> >
>
> > -Michael
>
> >
>
> >
>
> >
>
> ------------------------------------------------------------------------
>
> > Dear Fieldtrippers,
>
> >
>
> >
>
> > I am encountering a strange error while i try to use ft_databrowser. 
> The error code is as below. I have never seen this error earlier. I 
> used ft_databrowser many times and its only last 2 days that i am 
> getting the error. I downloaded a newer version of fieldtrip 
> (fieldtrip-20120130) and used the newer version but still the same 
> error. Strangely, i dont get this error when i tried with other 
> computers (same matlab version (R2010a), same operating system 
> (windows 7) on both computers. Has anyone got this error before? what 
> may cause this error?
>
> >
>
> >
>
> > fieldtrip version 20120130, matlab version R2010a, operating system 
> windows 7.
>
> >
>
> >
>
> > Thanks in advance for any suggestions.
>
> >
>
> >
>
> >
>
> > ??? Error using ==> ft_fetch_data at 57
>
> > data does not contain a consistent trial definition, fetching data is not
>
> > possible
>
> >
>
> >
>
> > Error in ==> ft_databrowser>redraw_cb at 1159
>
> > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', 
> endsample);
>
> >
>
> >
>
> > Error in ==> ft_databrowser at 535
>
> > redraw_cb(h);
>
> >
>
> ------------------------------------------------------------------------
>
> > Conserve Resources. Print only when necessary.
> >
> > IMPORTANT NOTICE: This e-mail is meant only for the use of the 
> intended recipient. It may contain confidential information which is 
> legally privilegedor otherwise protected by law. If you received this 
> e-mail in error or from someone who is not authorized to send it to 
> you, you are strictly prohibited from reviewing, using, disseminating, 
> distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF 
> THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. 
> Thank you for your cooperation.
>
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> ------------------------------------------------------------------------
> Conserve Resources. Print only when necessary.
>
> IMPORTANT NOTICE: This e-mail is meant only for the use of the 
> intended recipient. It may contain confidential information which is 
> legally privilegedor otherwise protected by law. If you received this 
> e-mail in error or from someone who is not authorized to send it to 
> you, you are strictly prohibited from reviewing, using, disseminating, 
> distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF 
> THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. 
> Thank you for your cooperation.
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

-- 
Roemer van der Meij M.Sc.
PhD student
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 max-philipp.stenner at med.ovgu.de  Thu Mar  8 14:36:16 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Thu, 08 Mar 2012 13:36:16 +0000
Subject: [FieldTrip] ft_sourcestatistics
In-Reply-To: <23891D6F-057F-4DBE-8C52-C43DAB74608E@donders.ru.nl>
References: <FBEFFA1F493D8944969D2F5AE78E58830C999B@ESEN4.imed.uni-magdeburg.de>
	<23891D6F-057F-4DBE-8C52-C43DAB74608E@donders.ru.nl>
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830C9AD3@ESEN4.imed.uni-magdeburg.de>

Hi Jan-Mathijs,



thank you for your response, since it worked for cfg.implementation = 'old' I haven't tried your suggestion of calling ft_checkdata outside of ft_sourcestatistics so far but will later during the day,



thanks again,

best

Max



________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von "jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl]
Gesendet: Donnerstag, 8. März 2012 13:38
Bis: Email discussion list for the FieldTrip project
Betreff: Re: [FieldTrip] ft_sourcestatistics

Hi Max,

At the moment we are designing some major code changes to deal with source level data, and we need to ask you for some patience in this regard.
For now, you could try to move the call to ft_checkdata to outside ft_sourcestatistics, and change the powdimord into 'pos_rpt';
Does it work if you subsequently call ft_sourcestatistics (with cfg.implementation = 'new')? This new implementation has never fully matured and may be instable. It has been found to work in certain situations, but it has never been fully tested on all possible processing histories that users may throw at it. Hence the urgent need to clean up the code.

Best,

Jan-Mathijs



On Mar 7, 2012, at 6:46 PM, Stenner, Max-Philipp wrote:

Dear fieldtrip users,



I am encountering a problem with ft_sourcestatistics when using output from ft_sourcegrandaverage. My parameter of interest is a logratio: log(mean(moments(time of interest))/mean(moments(baseline))) which I simply named 'pow' to be compatible with ft functions. Apart from this, nothing else deviates from how fieldtrip handles the data/nothing else was changed 'manually'.



The problem arises from the fact that the existence of 10 different subjects in the grandaverage (in the usual 1x10 struct field 'trial') isn't represented in the 'powdimord' field of the data after ft_checkdata(varargin{i}, 'datatype', {'source', 'volume'}, 'feedback', 'no', 'inside', 'index', 'sourcerepresentation', 'new'); in the new implementation of ft_sourcestatistics:



varargin{1}

ans =



(before ft_checkdata:)



       pos: [8196x3 double]
       var: [1x1 struct]
    dimord: 'voxel'
     trial: [1x10 struct]
    inside: [8196x1 double]
   outside: [0x1 double]
        df: [8196x1 double]
       cfg: [1x1 struct]



(after ft_checkdata:)



         pos: [8196x3 double]
         var: [1x1 struct]
      dimord: 'pos'
      inside: [8196x1 double]
     outside: [0x1 double]
          df: [8196x1 double]
         cfg: [1x1 struct]
         pow: [8196x10 double]
   powdimord: 'pos'



This leads to a (wrong) transpose of the design (originally row1 = uvar, row2 = ivar [with two conditions for a depsamples T test]) and ultimately to the message

'The data must contain at least two units (usually subjects).'



Any help would be much appreciated, thanks very much!

Max

(fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto: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<mailto:J.Schoffelen at donders.ru.nl>
Telephone: +31-24-3614793




From MEpstein at NKI.RFMH.ORG  Thu Mar  8 16:17:56 2012
From: MEpstein at NKI.RFMH.ORG (Epstein, Michael)
Date: Thu, 8 Mar 2012 10:17:56 -0500
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <4F58AD1B.906@donders.ru.nl>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org><7270aa3bcbfd9.4f574cba@mail.uh.edu><2586A1048152BE4D
	861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
	<4F58AD1B.906@donders.ru.nl>
Message-ID: <2586A1048152BE4D861E64A98700AD420A999DCD@nki-mail.NKI.rfmh.org>

Interesting... I'll look into that if I ever have the issue again.
However following Mehmet's advice and simply reinstalling the same
version of MATLAB seems to have fixed the problem anyway - not exactly
sure how that happened, but at least it worked. 

 

Thanks for the advice anyway though,

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Roemer van der
Meij
Sent: Thursday, March 08, 2012 7:59 AM
To: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Eve, Hi Michael,

I cannot find the specific line of code in the latest version, so I
assume you are using an old version? If you update to the latest
version, the problem should be solved.

Just for your curiosity, the bug was most likely caused by using the
ancient strmatch (deprecated in later version of matlab). Changing it
strcmp would have most likely fixed the problem.

Cheers,
Roemer




On 07-03-12 18:57, Epstein, Michael wrote: 

Interesting... can I ask what version of matlab you were running? and
was it 64 bit?

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Mehmet-Akif Coskun
Sent: Wednesday, March 07, 2012 12:56 PM
To: Email discussion list for the FieldTrip project
Cc: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Michael,


I have posted the question actually but I didn't hear any suggestions
about it. The same error was posted yesterday by someone else. 


just to repeat what i have replied in the other post, i tried many
things to solve it (changed the code, run the databrowser code line by
line, updated fieldtrip version at etc.), but none of them solved the
problem. I started getting the error after I tried using parallel
processing scripts in matlab. But as i said, i have no basis to say that
this caused the problem. So basically, i do not know any scientific
solution.


But an old school method solved the problem in my case. Simply i
uninstalled and re-installed matlab. Never got the error again. You may
want to try this. I have no other solution.


Mehmet





----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
<mailto:MEpstein at NKI.RFMH.ORG> 
Date: Wednesday, March 7, 2012 11:29 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: fieldtrip at donders.ru.nl

> Hi - I am actually encountering the same error with databrowser, and
was wondering if you ever came up with a solution to this problem - or
if anyone else has a solution - I didn't find a response on the mailing
list.

>  

> -Michael

>  

>  

>  

________________________________

> Dear Fieldtrippers,

>  

>  

> I am encountering a strange error while i try to use ft_databrowser.
The error code is as below. I have never seen this error earlier. I used
ft_databrowser many times and its only last 2 days that i am getting the
error. I downloaded a newer version of fieldtrip (fieldtrip-20120130)
and used the newer version but still the same error. Strangely, i dont
get this error when i tried with other computers (same matlab version
(R2010a), same operating system (windows 7) on both computers. Has
anyone got this error before? what may cause this error?

>  

>  

> fieldtrip version 20120130, matlab version R2010a, operating system
windows 7.

>  

>  

> Thanks in advance for any suggestions.

>  

>  

>  

> ??? Error using ==> ft_fetch_data at 57

> data does not contain a consistent trial definition, fetching data is
not

> possible

>  

>  

> Error in ==> ft_databrowser>redraw_cb at 1159

> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample',
endsample);

>  

>  

> Error in ==> ft_databrowser at 535

> redraw_cb(h);

>  

 

________________________________

> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the
intended recipient. It may contain confidential information which is
legally privilegedor otherwise protected by law. If you received this
e-mail in error or from someone who is not authorized to send it to you,
you are strictly prohibited from reviewing, using, disseminating,
distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE
ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank
you for your cooperation. 

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

________________________________

Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally
privilegedor otherwise protected by law. If you received this e-mail in
error or from someone who is not authorized to send it to you, you are
strictly prohibited from reviewing, using, disseminating, distributing
or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY
RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for
your cooperation. 






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

 

-- 
Roemer van der Meij M.Sc.
PhD student
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



Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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From MEpstein at NKI.RFMH.ORG  Thu Mar  8 16:27:03 2012
From: MEpstein at NKI.RFMH.ORG (Epstein, Michael)
Date: Thu, 8 Mar 2012 10:27:03 -0500
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <2586A1048152BE4D861E64A98700AD420A999DCD@nki-mail.NKI.rfmh.org>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org><7270aa3bcbfd9.4f574cba@mail.uh.edu><2586A1048152BE4D
	861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org><4F58AD1B.906@donders.ru.nl>
	<2586A1048152BE4D861E64A98700AD420A999DCD@nki-mail.NKI.rfmh.org>
Message-ID: <2586A1048152BE4D861E64A98700AD420A999DE5@nki-mail.NKI.rfmh.org>

Stephan said David is a 'guru' so that sounds good. He actually said
that he uses EEGLAB for ICA too, so I guess that really is the way to
go.

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Epstein, Michael
Sent: Thursday, March 08, 2012 10:18 AM
To: r.vandermeij at donders.ru.nl; Email discussion list for the FieldTrip
project
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Interesting... I'll look into that if I ever have the issue again.
However following Mehmet's advice and simply reinstalling the same
version of MATLAB seems to have fixed the problem anyway - not exactly
sure how that happened, but at least it worked. 

 

Thanks for the advice anyway though,

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Roemer van der
Meij
Sent: Thursday, March 08, 2012 7:59 AM
To: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Eve, Hi Michael,

I cannot find the specific line of code in the latest version, so I
assume you are using an old version? If you update to the latest
version, the problem should be solved.

Just for your curiosity, the bug was most likely caused by using the
ancient strmatch (deprecated in later version of matlab). Changing it
strcmp would have most likely fixed the problem.

Cheers,
Roemer




On 07-03-12 18:57, Epstein, Michael wrote: 

Interesting... can I ask what version of matlab you were running? and
was it 64 bit?

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Mehmet-Akif Coskun
Sent: Wednesday, March 07, 2012 12:56 PM
To: Email discussion list for the FieldTrip project
Cc: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Michael,


I have posted the question actually but I didn't hear any suggestions
about it. The same error was posted yesterday by someone else. 


just to repeat what i have replied in the other post, i tried many
things to solve it (changed the code, run the databrowser code line by
line, updated fieldtrip version at etc.), but none of them solved the
problem. I started getting the error after I tried using parallel
processing scripts in matlab. But as i said, i have no basis to say that
this caused the problem. So basically, i do not know any scientific
solution.


But an old school method solved the problem in my case. Simply i
uninstalled and re-installed matlab. Never got the error again. You may
want to try this. I have no other solution.


Mehmet





----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
<mailto:MEpstein at NKI.RFMH.ORG> 
Date: Wednesday, March 7, 2012 11:29 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: fieldtrip at donders.ru.nl

> Hi - I am actually encountering the same error with databrowser, and
was wondering if you ever came up with a solution to this problem - or
if anyone else has a solution - I didn't find a response on the mailing
list.

>  

> -Michael

>  

>  

>  

________________________________

> Dear Fieldtrippers,

>  

>  

> I am encountering a strange error while i try to use ft_databrowser.
The error code is as below. I have never seen this error earlier. I used
ft_databrowser many times and its only last 2 days that i am getting the
error. I downloaded a newer version of fieldtrip (fieldtrip-20120130)
and used the newer version but still the same error. Strangely, i dont
get this error when i tried with other computers (same matlab version
(R2010a), same operating system (windows 7) on both computers. Has
anyone got this error before? what may cause this error?

>  

>  

> fieldtrip version 20120130, matlab version R2010a, operating system
windows 7.

>  

>  

> Thanks in advance for any suggestions.

>  

>  

>  

> ??? Error using ==> ft_fetch_data at 57

> data does not contain a consistent trial definition, fetching data is
not

> possible

>  

>  

> Error in ==> ft_databrowser>redraw_cb at 1159

> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample',
endsample);

>  

>  

> Error in ==> ft_databrowser at 535

> redraw_cb(h);

>  

 

________________________________

> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the
intended recipient. It may contain confidential information which is
legally privilegedor otherwise protected by law. If you received this
e-mail in error or from someone who is not authorized to send it to you,
you are strictly prohibited from reviewing, using, disseminating,
distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE
ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank
you for your cooperation. 

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

________________________________

Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally
privilegedor otherwise protected by law. If you received this e-mail in
error or from someone who is not authorized to send it to you, you are
strictly prohibited from reviewing, using, disseminating, distributing
or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY
RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for
your cooperation. 





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

 

-- 
Roemer van der Meij M.Sc.
PhD student
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

________________________________

Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally
privilegedor otherwise protected by law. If you received this e-mail in
error or from someone who is not authorized to send it to you, you are
strictly prohibited from reviewing, using, disseminating, distributing
or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY
RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for
your cooperation. 



Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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From frerap at gist.ac.kr  Fri Mar  9 12:56:13 2012
From: frerap at gist.ac.kr (MinKyu Ahn)
Date: Fri, 9 Mar 2012 20:56:13 +0900 (KST)
Subject: [FieldTrip] question for ft_freqanalysis()
Message-ID: <1182294678.1331294173648.JavaMail.root@eunhasu>

I am new fieldtrip and wavelet analysis.



Fortunately, fieldtrip webpage has some examples for that.



While I follow it, I found that the scale between the resuts of fixed hann method and wavelet method in http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis.



When it plots results, the zlimt is used  as cfg.zlim         = [-3e-27 3e-27] while  it is used as [-3e-25 3e-25]    for wavelet.



The scale difference is about 10^2, why this happen?





Please let me know about it.







Thank you.






============================================================ MinKyu Ahn, Ph.D. Student, Member of BioComputing Lab. School of Information and Communications Gwangju Institute of Science and Technology (GIST)  261 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, Korea  Tel : +82-62-715-3126/2266  Cell : +82-10-7360-8232  E-mail : frerap at gist.ac.kr  URL : http://biocomput.gist.ac.kr ============================================================

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From matt.mollison at gmail.com  Fri Mar  9 20:16:42 2012
From: matt.mollison at gmail.com (Matt Mollison)
Date: Fri, 9 Mar 2012 12:16:42 -0700
Subject: [FieldTrip] Oscillatory power normalization
Message-ID: <CAJB8axm9J3=ktKM16bVhjFiToBOcD1RrVbn+1xxD4HiiqP1_WA@mail.gmail.com>

My questions essentially boil down to: what do people do for power
normalization when assessing statistical differences?

It gets more detailed below regarding examining event-related power changes
relative to a baseline (within-subjects, comparing two conditions, stimulus
onset = 0 ms). I didn't find much discussion of this on the list or the
wiki. Any references for these issues would also be appreciated.

(1) Does power data need to be baseline normalized for statistical tests
comparing conditions? Normalization would put power on equal footing across
all subjects, conditions, sensors, times, frequencies, etc., but it will
surely affect power during the stimulus period in a particular way. If so,
do the two (or more) conditions need to use the same baseline condition, or
can each trial be normalized to its own pre-stim baseline period (a la
ft_freqbaseline)? For either, it seems like you'd always need
keeptrials='yes' in ft_freqanalysis. However, it does not seem to get
normalized in the cluster_permutation_freq tutorial (within-subjects)---am
I missing something?

If we should normalize:
(2) I've read a number of papers that Z-transform stimulus period power
relative to pre-stim activity (subtract mean, divide by std) before doing
statistics. I've also read a lot that don't mention baselines, or e.g. do a
decibel [dB] transform. ft_freqbaseline does not have a Z-transform option.
There is ft_preproc_standardize, but this seems to operate at a lower level
than is usually recommended. Z-transforming seems like a good option, but
how can I use it in the FT pipeline for within-subjects analyses
(especially with keeptrials='no')? Alternatively, when should one use
'absolute', 'relative', or 'relchange'?

Regarding choosing the baseline period:
(3) It seems that the baseline period needs to precede stimulus onset by a
sufficient amount of time so that the stimulus period doesn't bleed into
the baseline; this time would be specific to both the frequency and either
wavelet width or taper window length. For example, at 4 Hz with wavelet
width=6 or a taper with 6 cycles per time window (t_ftimwin) the
wavelet/window would be 1500 ms long, and the end of the baseline must
precede stimulus onset by at least half this to keep them separate. At
lower frequencies this could get quite unruly (e.g., 1 Hz would require
ending 3000 ms before stimulus). Is this correct? Maybe that's why it's
better to have a single separate baseline condition. Anyway, the
timefrequencyanalysis tutorial seems to disregard this separation of
baseline and stimulus activity (as have many papers I've read), so maybe
I'm wrong about this being necessary.

Thanks for your time,
Matt Mollison

--
Univ. of Colorado at Boulder
Dept. of Psychology and Neuroscience
matthew.mollison at colorado.edu
http://psych.colorado.edu/~mollison/
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From cas243 at georgetown.edu  Sun Mar 11 22:52:15 2012
From: cas243 at georgetown.edu (Clara A. Scholl)
Date: Sun, 11 Mar 2012 17:52:15 -0400
Subject: [FieldTrip] clustering, spatial neighbors and minnbchan
In-Reply-To: <CAAHOyr7pc8qkmeJ4X9NOsGQAmEUsg3viPPYo5v+4d5rE3bQ-Mw@mail.gmail.com>
References: <CAAHOyr7pc8qkmeJ4X9NOsGQAmEUsg3viPPYo5v+4d5rE3bQ-Mw@mail.gmail.com>
Message-ID: <CAAHOyr6APDwrRwfONA0xuYXNJbhYKtNrpd0QuVxcKcAXTUL5Yg@mail.gmail.com>

Hi,

I have a question about how to identify appropriate parameters for
neighbor distance in ft_neighbourselection and how to set minnbchan
for space-time cluster analysis.

I identified a neighbor distance based on our sensor layout, so that
spatially adjacent channels were defined as neighbors, and spatially
non-adjacent channels were not defined as neighbors.  I then ran
space-time cluster analysis and identified a cluster with a large
spatial and temporal extent which appears to be the continuation of
several effects lumped together.  I subsequently increased minnbchan,
so that this cluster gets separated into separate clusters following
the logic in this discussion thread:
http://mailman.science.ru.nl/pipermail/fieldtrip/2011-February/003501.html

However now a new problem appears: it seems that channels near the
periphery of the sensor layout, which have few adjacent spatial
neighbors, are not included in the clusters when minnbchan has a value
greater than the number of neighbors the channels have according to
the neighbor distance used in ft_neighbourselection.  Is this correct?
 Put differently, increasing minnbchan appears to bias clusters toward
including only channels at the center of the sensor layout, with many
adjacent other channels (and channels at the periphery of the layout,
which have fewer spatial neighbors, are excluded from the identified
clusters).

Obviously I want a principled, data-independent selection of cluster
identification parameters so I want to ask what the "correct" way to
identify these parameters (neighbor distance, and minnbchan) is.
Should minnbchan be used differently for channel-time cluster analysis
(what I'm doing) compared to channel-time-frequency cluster analysis?

Thanks,
Clara



From jm.horschig at donders.ru.nl  Mon Mar 12 09:48:53 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 12 Mar 2012 09:48:53 +0100
Subject: [FieldTrip] clustering, spatial neighbors and minnbchan
In-Reply-To: <CAAHOyr6APDwrRwfONA0xuYXNJbhYKtNrpd0QuVxcKcAXTUL5Yg@mail.gmail.com>
References: <CAAHOyr7pc8qkmeJ4X9NOsGQAmEUsg3viPPYo5v+4d5rE3bQ-Mw@mail.gmail.com>
	<CAAHOyr6APDwrRwfONA0xuYXNJbhYKtNrpd0QuVxcKcAXTUL5Yg@mail.gmail.com>
Message-ID: <4F5DB875.9080501@donders.ru.nl>

Dear Clara,

First of all, defining neighbours based on a sensor layout may not be 
the best approach. If you have 3D positions of your sensors available, I 
would suggest that you use these for neighbour selection (note that for 
EEG sensors, this is much less an issue than for MEG sensors, but you 
didn't mention what system you are using)

Second, for minnbchan, I think you are right. Of course sensors at the 
outer rim have, by definition, less neighbouring sensors than other 
sensors. As far as I know, minnbchan is defined as the number of 
neighbouring significant sensors. So, if you specify it to be e.g. 10, 
than of course all sensors with less than 10 neighbours can never be 
part of a cluster. Those with more than 10 need to have also at least 10 
neighbouring sensors that are significant as well. Of course, sensors in 
the center have more neighbouring sensors, thus higher minnbchan will 
have a less tremendous effect there. So as far as I can see, there are 
four ways out for you:

1) If you didn't do so already, you can choose a finer time-scale, 
hoping that this will separate the different neural effects (if they are 
different)

2) Do the same on source level - maybe this will reduce spatial leakage.

3) Define a wider range of neighbours for sensors at the outer rim, 
thereby forcing a minimum number of neighbouring sensors. Instead (or 
additionally), you could try to use cfg.method = 'triangulation' or 
'template' for neighbour selection. For more information, see here: 
http://fieldtrip.fcdonders.nl/faq/how_does_ft_prepare_neighbours_work
I would suggest that you use cfg.feedback = 'yes' and choose the 
method/parameters that seem most optimal to you (there is not *the* best 
way, unfortunately)

4) Live with it, as there are technical limitations with our recording 
equipment, and of course physiological limitations. As Eric pointed out 
in the old mails you referred to:
"

In fact, it is looking for isolated blobs that one would like to interpret as separate physiological entities.
This contrast with the nature of the EEG/MEG data, which has poor spatial resolution (due to volume conduction and common pick-up),
often poor spectral resolution (due to the short time windows of our time-resolved spectral analysis), and often poor time resolution
(due to latency jitter over trials).
"



Hope this helps.
Best,
Jörn



On 3/11/2012 10:52 PM, Clara A. Scholl wrote:
> Hi,
>
> I have a question about how to identify appropriate parameters for
> neighbor distance in ft_neighbourselection and how to set minnbchan
> for space-time cluster analysis.
>
> I identified a neighbor distance based on our sensor layout, so that
> spatially adjacent channels were defined as neighbors, and spatially
> non-adjacent channels were not defined as neighbors.  I then ran
> space-time cluster analysis and identified a cluster with a large
> spatial and temporal extent which appears to be the continuation of
> several effects lumped together.  I subsequently increased minnbchan,
> so that this cluster gets separated into separate clusters following
> the logic in this discussion thread:
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-February/003501.html
>
> However now a new problem appears: it seems that channels near the
> periphery of the sensor layout, which have few adjacent spatial
> neighbors, are not included in the clusters when minnbchan has a value
> greater than the number of neighbors the channels have according to
> the neighbor distance used in ft_neighbourselection.  Is this correct?
>   Put differently, increasing minnbchan appears to bias clusters toward
> including only channels at the center of the sensor layout, with many
> adjacent other channels (and channels at the periphery of the layout,
> which have fewer spatial neighbors, are excluded from the identified
> clusters).
>
> Obviously I want a principled, data-independent selection of cluster
> identification parameters so I want to ask what the "correct" way to
> identify these parameters (neighbor distance, and minnbchan) is.
> Should minnbchan be used differently for channel-time cluster analysis
> (what I'm doing) compared to channel-time-frequency cluster analysis?
>
> Thanks,
> Clara
>
> _______________________________________________
> 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

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 vitoria.piai at gmail.com  Mon Mar 12 11:06:19 2012
From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=)
Date: Mon, 12 Mar 2012 11:06:19 +0100
Subject: [FieldTrip] bug in new ft_checkdata?
Message-ID: <4F5DCA9B.5030208@gmail.com>

Hi everyone,

I've just got an error when running ft_megplanar and ft_multiplotER that 
I had never had before when running the exact same scripts on exact same 
data:

"Undefined function or method 'fixname' for input arguments of type 'char'.
The chain of errors makes reference to warning_once at 66, fixsampleinfo 
at 66/68, and ft_checkdata at 604.

I'm using the most up-to-date fieldtrip version since I'm working within 
the Donders.
Is this a bug or should I re-structure my data?

Thanks a lot, Vitória

-- 
** Please consider the environment - do you really need to print? **	



From ali at cs.ru.nl  Mon Mar 12 11:32:53 2012
From: ali at cs.ru.nl (Ali Bahramisharif)
Date: Mon, 12 Mar 2012 11:32:53 +0100
Subject: [FieldTrip] bug in new ft_checkdata?
In-Reply-To: <4F5DCA9B.5030208@gmail.com>
References: <4F5DCA9B.5030208@gmail.com>
Message-ID: <8590fee73375ab9349c94481d6a98ebf.squirrel@squirrel.science.ru.nl>

Hi Vitória,

Just be sure that you have removed SPM from your path. SPM has an old
version of fieldtrip and if you have it in your path, it causes a lot of
troubles.

Cheers,
Ali

> Hi everyone,
>
> I've just got an error when running ft_megplanar and ft_multiplotER that
> I had never had before when running the exact same scripts on exact same
> data:
>
> "Undefined function or method 'fixname' for input arguments of type
> 'char'.
> The chain of errors makes reference to warning_once at 66, fixsampleinfo
> at 66/68, and ft_checkdata at 604.
>
> I'm using the most up-to-date fieldtrip version since I'm working within
> the Donders.
> Is this a bug or should I re-structure my data?
>
> Thanks a lot, Vitória
>
> --
> ** Please consider the environment - do you really need to print? **
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>


-- 
Address:
        HG02.517
        Intelligent Systems
        Radboud University Nijmegen
        Heyendaalseweg 135
        6525 AJ Nijmegen
        The Netherlands

http://www.cs.ru.nl/~ali
Tel.:   +31 (0)24 36 52634



From bibi.raquel at gmail.com  Mon Mar 12 13:03:33 2012
From: bibi.raquel at gmail.com (Raquel Bibi)
Date: Mon, 12 Mar 2012 08:03:33 -0400
Subject: [FieldTrip] bug in new ft_checkdata?
In-Reply-To: <4F5DCA9B.5030208@gmail.com>
References: <4F5DCA9B.5030208@gmail.com>
Message-ID: <D550BDC5-8AED-45A9-A8F9-DBEDB52BDB82@gmail.com>

I had the had same error running ft_redefinetrial. As a quick fix I put fixname.m (in private folder) into fieldtrip folder. 

Best,

Raquel

Sent from my iPhone

On Mar 12, 2012, at 6:06 AM, Vitória Magalhães Piai <vitoria.piai at gmail.com> wrote:

> Hi everyone,
> 
> I've just got an error when running ft_megplanar and ft_multiplotER that I had never had before when running the exact same scripts on exact same data:
> 
> "Undefined function or method 'fixname' for input arguments of type 'char'.
> The chain of errors makes reference to warning_once at 66, fixsampleinfo at 66/68, and ft_checkdata at 604.
> 
> I'm using the most up-to-date fieldtrip version since I'm working within the Donders.
> Is this a bug or should I re-structure my data?
> 
> Thanks a lot, Vitória
> 
> -- 
> ** Please consider the environment - do you really need to print? **    
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From g.piantoni at nin.knaw.nl  Mon Mar 12 14:22:39 2012
From: g.piantoni at nin.knaw.nl (Gio Piantoni)
Date: Mon, 12 Mar 2012 14:22:39 +0100
Subject: [FieldTrip] bug in new ft_checkdata?
In-Reply-To: <D550BDC5-8AED-45A9-A8F9-DBEDB52BDB82@gmail.com>
References: <4F5DCA9B.5030208@gmail.com>
	<D550BDC5-8AED-45A9-A8F9-DBEDB52BDB82@gmail.com>
Message-ID: <CAHeOcrtUjpEaVA_bnkWFCHUe3H5P1a6oDJ-fB9HwdRk2VuU2ag@mail.gmail.com>

Hi all,

Raquel is correct. fixname.m was missing from utilities/private

I added it to the dev version, should be fixed now and available on FTP tonight.

Gio

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

+31 20 5665492
gio at gpiantoni.com
www.gpiantoni.com

On Mon, Mar 12, 2012 at 13:03, Raquel Bibi <bibi.raquel at gmail.com> wrote:
> I had the had same error running ft_redefinetrial. As a quick fix I put fixname.m (in private folder) into fieldtrip folder.
>
> Best,
>
> Raquel
>
> Sent from my iPhone
>
> On Mar 12, 2012, at 6:06 AM, Vitória Magalhães Piai <vitoria.piai at gmail.com> wrote:
>
>> Hi everyone,
>>
>> I've just got an error when running ft_megplanar and ft_multiplotER that I had never had before when running the exact same scripts on exact same data:
>>
>> "Undefined function or method 'fixname' for input arguments of type 'char'.
>> The chain of errors makes reference to warning_once at 66, fixsampleinfo at 66/68, and ft_checkdata at 604.
>>
>> I'm using the most up-to-date fieldtrip version since I'm working within the Donders.
>> Is this a bug or should I re-structure my data?
>>
>> Thanks a lot, Vitória
>>
>> --
>> ** Please consider the environment - do you really need to print? **
>>
>> _______________________________________________
>> 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 fredericroux at hotmail.de  Mon Mar 12 15:11:07 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Mon, 12 Mar 2012 15:11:07 +0100
Subject: [FieldTrip] read_fcdc_mri error
Message-ID: <DUB113-W99483229B6AF1ABB816C85B75B0@phx.gbl>


Dear all,

I am getting an error when trying to read CTF-V2 formatted
MRI data using the read_fcdc_mri function.

??? Error using ==> reshape
To RESHAPE the number of elements must not change.

Error in ==> fieldtrip-20081208/private/read_ctf_mri at 113
mri = reshape(mri, [256 256 256]);

Error in ==> read_fcdc_mri at 95
 [img,hdr] = read_ctf_mri(filename);

Error in ==> warpMRI_DEV at 18
 mri = read_fcdc_mri([path2files,mrifiles(sujIt).name]);

The error results because at line 105 of the read_fcfc_mri.m function

mri = unint16(fread(fid,256*256*256,'uint16'));

returns a vector of  length = 16777215 when in fact it should be of
lentgh = 16777216. This means that 1 single value is missing.

The ackward thing is that I can open the MR-file without problem
in the MRIViewer and that there it appears to have 256 values
in the x,y and z dimension. Also this error appears only in 
a subset of files. 

I suspect that there is an error somewhere maybe in the data
acquisition or conversion pipeline.
Any suggestions or help would be highly appreciated.

Have a nice day!

Fred


-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From fredericroux at hotmail.de  Mon Mar 12 17:15:58 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Mon, 12 Mar 2012 17:15:58 +0100
Subject: [FieldTrip] how to set lambda for resting state lcmv-beamformer
Message-ID: <DUB113-W27C7B2A586CF97AE4D0EC8B75B0@phx.gbl>


Dear fieldtrip users,

I am trying to compute a spatial filter
to localize alpha-band activity in an
eyes closed resting state meg recording
using the LCMV-method.

The condition of my covariance matrix is > 1*10e6
so I set lambda = 0.01. When I then plot the NAI
I find two clusters of activity: 
one in the center of the head,
one in the occipital cortex.

In Exercise 5 of the tutorial, it is 
mentioned to set lambda to 1e-29 in order 
to suppresses the center of head artifact.

I wanted to ask if anybody could tell me what the
rationale was to set lambda = 1e-29? 
Is there a standardized way to compute lambda?

Best regards,

Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225

 		 	   		  
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From ali at cs.ru.nl  Mon Mar 12 18:30:52 2012
From: ali at cs.ru.nl (Ali Bahramisharif)
Date: Mon, 12 Mar 2012 18:30:52 +0100
Subject: [FieldTrip] how to set lambda for resting state lcmv-beamformer
In-Reply-To: <DUB113-W27C7B2A586CF97AE4D0EC8B75B0@phx.gbl>
References: <DUB113-W27C7B2A586CF97AE4D0EC8B75B0@phx.gbl>
Message-ID: <b81684b6e207fbd7cbfccb066a4fa413.squirrel@squirrel.science.ru.nl>

Hi Fred,

As far as I remember, lambda is used to regularize the covariance matrix.
I mean: regularized_covariance= XX'+lambda*Identity. To set it properly,
you need to look at the eigen-values of XX'. Normally you want to get rid
of the small eigen values. One way is to choose lambda to be 1/1000 of the
largest eigen-value.

Hope this helps.
Ali

>
> Dear fieldtrip users,
>
> I am trying to compute a spatial filter
> to localize alpha-band activity in an
> eyes closed resting state meg recording
> using the LCMV-method.
>
> The condition of my covariance matrix is > 1*10e6
> so I set lambda = 0.01. When I then plot the NAI
> I find two clusters of activity:
> one in the center of the head,
> one in the occipital cortex.
>
> In Exercise 5 of the tutorial, it is
> mentioned to set lambda to 1e-29 in order
> to suppresses the center of head artifact.
>
> I wanted to ask if anybody could tell me what the
> rationale was to set lambda = 1e-29?
> Is there a standardized way to compute lambda?
>
> Best regards,
>
> Fred
>
> --
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
>
>  		 	   		  _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Address:
        HG02.517
        Intelligent Systems
        Radboud University Nijmegen
        Heyendaalseweg 135
        6525 AJ Nijmegen
        The Netherlands

http://www.cs.ru.nl/~ali
Tel.:   +31 (0)24 36 52634



From nathanweisz at mac.com  Mon Mar 12 20:59:42 2012
From: nathanweisz at mac.com (Nathan Weisz)
Date: Mon, 12 Mar 2012 20:59:42 +0100
Subject: [FieldTrip] Master Cognitive Science Trento
Message-ID: <5BE61BE0-E292-4EF6-B6DD-82814DD0F62A@mac.com>

Dear all,

sorry for (mis-)using this mailing list as advertisement platform. 
http://international.unitn.it/sites/international.unitn.it/files/439_11_MCS_Cop_web.pdf


best,
n

International Masters in Cognitive Science, University of Trento, Italy:

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Cognitive neuroscience is the study of the mind and brain, investigating how and why people think and act the way they do. The knowledge and skills gained in the Master’s course will provide a foundation for advanced scientific research, with professional applications in the fields of education, consumer and economic decision making, psychology and clinical research.
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In order to be considered for admission, a Bachelor’s degree and a certified English knowledge (e.g. TOEFL, IELTS, CPE) is required.
In the absence of a document certifying the level of English language, the candidate is encouraged to submit alternative proof of English proficiency (i.e. an official letter from the University stating that the candidate completed university courses taught entirely in English). The evaluation of this alternative document will be entirely at discretion of the admission committee.

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All courses are taught in English. For students wishing to familiarize with the Italian culture, Italian language courses will be offered by the Faculty of Cognitive Science.

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The program is intended for a small number of top level students. In the academic year 2009-2010, the program will admit at most 40 students.

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After successful completion of the curriculum and fulfilment of the Master’s requirements, students will be awarded a Master of Science degree (laurea magistrale) in Cognitive Science.
Please note that, thanks to an agreement with the University of Osnabrück, students will be awarded a double Master’s degree (Italian and German), valid in both countries.

Deadline
The deadline to complete the on-line application is 31st July, 2009. Please note that this call is for EU citizens only, or non-EU applicants who already have a valid visa to study in the EU.
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University of Trento
Corso Bettini, 84 - 38068 Rovereto (TN), Italy
fax + 39 0464 808415
www.cogsci.unitn.it
mcs at unitn.it
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From cas243 at georgetown.edu  Tue Mar 13 02:29:39 2012
From: cas243 at georgetown.edu (Clara A. Scholl)
Date: Mon, 12 Mar 2012 21:29:39 -0400
Subject: [FieldTrip] clustering, spatial neighbors and minnbchan
In-Reply-To: <4F5DB875.9080501@donders.ru.nl>
References: <CAAHOyr7pc8qkmeJ4X9NOsGQAmEUsg3viPPYo5v+4d5rE3bQ-Mw@mail.gmail.com>
	<CAAHOyr6APDwrRwfONA0xuYXNJbhYKtNrpd0QuVxcKcAXTUL5Yg@mail.gmail.com>
	<4F5DB875.9080501@donders.ru.nl>
Message-ID: <CAAHOyr5S+U6ZRtBZ77hjQx9EPe0qcq3O8tL++mAkNeZ5aj2HtQ@mail.gmail.com>

Dear Jörn,

Thank you for directing me to ft_prepare_neighbours instead of
ft_neighbourselection, the triangulation method is excellent and I'll
be sure to stick to the most recent version of fieldtrip from now on.

I really like the spirit of the minnbchan parameter for tightening
cluster extent, but as long as different channels have different
numbers of neighbors (which seems both inevitable and sensible), I
find it problematic that for example, for minnbchan=2, a channel with
5 neighbors will be rejected at a given timepoint if fewer than 40% of
its neighbors belong to a cluster, while a channel with 10 neighbors
will be rejected only when fewer than 20% of its neighbors belong to
the cluster (if I understand what's going on correctly -- and I use 5
and 10 as examples because this is the range of neighbors I get using
triangulation for an EGI 128 channel EEG sensor layout).  I have two
questions about a possible modification to this parameter that I've
implemented:

1) Instead of setting minnbchan to a fixed number of channels, would
it make sense to use a percentage of neighbors so that, for the
example above, instead of using minnbchan=2, use
minnbchan=0.4*numneighbours (at each channel), so that a channel with
5 neighbors would need 2 neighboring channels in the cluster to
remain, while a channel with 10 neighbors would need 4 neighboring
channels in the cluster to remain?  Would this introduce problems I'm
not considering?

2) I implemented it by modifying beginning at line 83 of
findcluster.m, so that instead of looking for
remove=(onoff.*nsigneighb)<minnbchan;

I'm now adding an additional line for the number of neighbors at each
channel (in addition to nsigneighb, the number of significant
neighbors), followed by remove:

nneighb=reshape(selectmat*reshape(single(ones(size(onoff))),[spatdimlength
(nfreq*ntime)]),[spatdimlength nfreq ntime]);
remove=(onoff.*nsigneighb)<(nneighb.*minnbchan);

Where now the minnbchan input must be between 0 and 1 so that the
channels removed at each timepoint are some fraction of each channels
number of neighbors.  It seems to work but I want to run it by users
who are more familiar with the parameters & code than I am, because
it's very possible that (1) the concept is esoteric and problematic
and (2) my implementation is faulty.

Thanks enormously for any & all feedback,
Clara


On Mon, Mar 12, 2012 at 4:48 AM, "Jörn M. Horschig"
<jm.horschig at donders.ru.nl> wrote:
> Dear Clara,
>
> First of all, defining neighbours based on a sensor layout may not be the
> best approach. If you have 3D positions of your sensors available, I would
> suggest that you use these for neighbour selection (note that for EEG
> sensors, this is much less an issue than for MEG sensors, but you didn't
> mention what system you are using)
>
> Second, for minnbchan, I think you are right. Of course sensors at the outer
> rim have, by definition, less neighbouring sensors than other sensors. As
> far as I know, minnbchan is defined as the number of neighbouring
> significant sensors. So, if you specify it to be e.g. 10, than of course all
> sensors with less than 10 neighbours can never be part of a cluster. Those
> with more than 10 need to have also at least 10 neighbouring sensors that
> are significant as well. Of course, sensors in the center have more
> neighbouring sensors, thus higher minnbchan will have a less tremendous
> effect there. So as far as I can see, there are four ways out for you:
>
> 1) If you didn't do so already, you can choose a finer time-scale, hoping
> that this will separate the different neural effects (if they are different)
>
> 2) Do the same on source level - maybe this will reduce spatial leakage.
>
> 3) Define a wider range of neighbours for sensors at the outer rim, thereby
> forcing a minimum number of neighbouring sensors. Instead (or additionally),
> you could try to use cfg.method = 'triangulation' or 'template' for
> neighbour selection. For more information, see here:
> http://fieldtrip.fcdonders.nl/faq/how_does_ft_prepare_neighbours_work
> I would suggest that you use cfg.feedback = 'yes' and choose the
> method/parameters that seem most optimal to you (there is not *the* best
> way, unfortunately)
>
> 4) Live with it, as there are technical limitations with our recording
> equipment, and of course physiological limitations. As Eric pointed out in
> the old mails you referred to:
> "
>
> In fact, it is looking for isolated blobs that one would like to interpret
> as separate physiological entities.
> This contrast with the nature of the EEG/MEG data, which has poor spatial
> resolution (due to volume conduction and common pick-up),
> often poor spectral resolution (due to the short time windows of our
> time-resolved spectral analysis), and often poor time resolution
> (due to latency jitter over trials).
> "
>
>
>
> Hope this helps.
> Best,
> Jörn
>
>
>
>
> On 3/11/2012 10:52 PM, Clara A. Scholl wrote:
>>
>> Hi,
>>
>> I have a question about how to identify appropriate parameters for
>> neighbor distance in ft_neighbourselection and how to set minnbchan
>> for space-time cluster analysis.
>>
>> I identified a neighbor distance based on our sensor layout, so that
>> spatially adjacent channels were defined as neighbors, and spatially
>> non-adjacent channels were not defined as neighbors.  I then ran
>> space-time cluster analysis and identified a cluster with a large
>> spatial and temporal extent which appears to be the continuation of
>> several effects lumped together.  I subsequently increased minnbchan,
>> so that this cluster gets separated into separate clusters following
>> the logic in this discussion thread:
>> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-February/003501.html
>>
>> However now a new problem appears: it seems that channels near the
>> periphery of the sensor layout, which have few adjacent spatial
>> neighbors, are not included in the clusters when minnbchan has a value
>> greater than the number of neighbors the channels have according to
>> the neighbor distance used in ft_neighbourselection.  Is this correct?
>>  Put differently, increasing minnbchan appears to bias clusters toward
>> including only channels at the center of the sensor layout, with many
>> adjacent other channels (and channels at the periphery of the layout,
>> which have fewer spatial neighbors, are excluded from the identified
>> clusters).
>>
>> Obviously I want a principled, data-independent selection of cluster
>> identification parameters so I want to ask what the "correct" way to
>> identify these parameters (neighbor distance, and minnbchan) is.
>> Should minnbchan be used differently for channel-time cluster analysis
>> (what I'm doing) compared to channel-time-frequency cluster analysis?
>>
>> Thanks,
>> Clara
>>
>> _______________________________________________
>> 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
>
> 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



From olivia.mariani at epfl.ch  Tue Mar 13 11:44:53 2012
From: olivia.mariani at epfl.ch (Mariani Olivia)
Date: Tue, 13 Mar 2012 10:44:53 +0000
Subject: [FieldTrip] Mesh intersecting BEM headmodel
Message-ID: <BD7CF73B66D0674980FC749AE22A9BFD2B83B0A0@rexma.intranet.epfl.ch>

Hello,

I am using the "create a BEM headmodel" script but I am getting spikes and unwanted holes in the brain compartment when using the triplot function and don't know how to get rid of it.

I get the following warnings on matlab (R2011a):

%%%%%%%%%%%%%%%%%%%%%
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!! WARNING !!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Mesh is self intersecting !
Mesh Info :
    # points : 1000
    # triangles : 1996
    Euler characteristic : 2
    Min Area : 14
    Max Area : 152.381
Self intersection for mesh number 2
%%%%%%%%%%%%%%%%%%%%%%

I get this self intersecting warning for my three meshes and additional warnings that two meshes are intersecting.
My problem may come from ill-defined boundaries. Would you know how to better define the boundaries between the meshes?

And then I get the following error:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
| ------ om_minverser
| ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin
| ./tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin
| -----------------------
Exception: Unable to open the file ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin for reading Doing my best....
Warning: an error ocurred while running OpenMEEG
> In openmeeg at 127
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Error using ==> fread
Invalid file identifier.  Use fopen to generate a valid file identifier.
Warning: File 'tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin' not found.
> In openmeeg>cleaner at 142
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Warning: File 'tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin' not found.
> In openmeeg>cleaner at 143
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The file om_minverser from openmeeg closes and the figures open.

Thank you,

Olivia


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From lihqih at gmail.com  Tue Mar 13 18:10:16 2012
From: lihqih at gmail.com (qi li)
Date: Tue, 13 Mar 2012 13:10:16 -0400
Subject: [FieldTrip] ICA problem
Message-ID: <CAMWMXsDEoFUpC5JhfLBZgcN7PDEJHtJvA3zgrmYH=a36uV3z=A@mail.gmail.com>

Hi there,

I am having trouble to prepare neighbors of the channels after I do
the ICA with the following commands,

cfg            = [];
cfg.method = 'runica';
cfg.runica.pca=64;
comp           = ft_componentanalysis(cfg, datas)

Then I remove the bad components by

cfg=[];
cfg.component=[2 5];
data_c=ft_rejectcomponent(cfg,comp_o);

now I want to prepare the neighbors
cfg=[];
cfg.neighbours = ft_prepare_neighbours(cfg, data_c);

I have the following error message,

'undoing the invcomp balancing
Index exceeds matrix dimensions.

Error in undobalancing (line 25)
      tra3(iy,iy) = (eye(numel(ix))+tmp(ix,ix))*tra1(iy,iy);

Error in channelposition (line 39)
sens = undobalancing(sens);

Error in ft_datatype_sens (line 95)
        [chanpos, chanori, chanlab] = channelposition(sens, 'channel', 'all');

Error in ft_datatype_raw (line 95)
      data.grad = ft_datatype_sens(data.grad);

Error in ft_checkdata (line 177)
  data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo);

Error in ft_prepare_neighbours (line 84)
if hasdata, data = ft_checkdata(data); end'.


From k.muesch at uke.uni-hamburg.de  Tue Mar 13 19:13:31 2012
From: k.muesch at uke.uni-hamburg.de (=?iso-8859-1?Q?Kathrin_M=FCsch?=)
Date: Tue, 13 Mar 2012 19:13:31 +0100
Subject: [FieldTrip] ICA problem
In-Reply-To: <CAMWMXsDEoFUpC5JhfLBZgcN7PDEJHtJvA3zgrmYH=a36uV3z=A@mail.gmail.com>
References: <CAMWMXsDEoFUpC5JhfLBZgcN7PDEJHtJvA3zgrmYH=a36uV3z=A@mail.gmail.com>
Message-ID: <A1BDA1C1-3106-44E3-A0EA-45D9A92B0524@uke.uni-hamburg.de>

Hi Qi,

This error message pops up recently with many ft_functions after ICA and is due to some updates. I don't know with which FieldTrip version it started. After ICA component rejection, the number of gradiometers seems to change and this error message pops up. As a workaround, you can either remove the grad field if you don't need it for your analysis at hand or you can load the grad structure from a processing step before the ICA.

Hope that helps,
Kathrin

Am 13.03.2012 um 18:10 schrieb qi li:

> Hi there,
> 
> I am having trouble to prepare neighbors of the channels after I do
> the ICA with the following commands,
> 
> cfg            = [];
> cfg.method = 'runica';
> cfg.runica.pca=64;
> comp           = ft_componentanalysis(cfg, datas)
> 
> Then I remove the bad components by
> 
> cfg=[];
> cfg.component=[2 5];
> data_c=ft_rejectcomponent(cfg,comp_o);
> 
> now I want to prepare the neighbors
> cfg=[];
> cfg.neighbours = ft_prepare_neighbours(cfg, data_c);
> 
> I have the following error message,
> 
> 'undoing the invcomp balancing
> Index exceeds matrix dimensions.
> 
> Error in undobalancing (line 25)
>      tra3(iy,iy) = (eye(numel(ix))+tmp(ix,ix))*tra1(iy,iy);
> 
> Error in channelposition (line 39)
> sens = undobalancing(sens);
> 
> Error in ft_datatype_sens (line 95)
>        [chanpos, chanori, chanlab] = channelposition(sens, 'channel', 'all');
> 
> Error in ft_datatype_raw (line 95)
>      data.grad = ft_datatype_sens(data.grad);
> 
> Error in ft_checkdata (line 177)
>  data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo);
> 
> Error in ft_prepare_neighbours (line 84)
> if hasdata, data = ft_checkdata(data); end'.
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg

Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus 

From chan at med.uni-frankfurt.de  Wed Mar 14 17:28:49 2012
From: chan at med.uni-frankfurt.de (Jason Chan)
Date: Wed, 14 Mar 2012 17:28:49 +0100
Subject: [FieldTrip] missing pos in beamforming
Message-ID: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>

Greetings,

I am adapting the beamformer tutorial to my data.  When I sourceinterpolate
the subtracted sourceA from sourceB data, the 'pos'  disappears.  This seems
to be important for the volume normalization and Grand Average.  I am
running Fieldtrip version: 20110917.  I have placed the code below.

 

Many thanks in advance.

Jason

 

 

Young_CombineFilter_sourceDiff_16_3={};

for i=1:length(Young_CombineFilter_beamform_16_3);

    cfg=[];

    Young_CombineFilter_sourceDiff_16_3{i}
=Young_CombineFilter_beamform_16_3{i}.sourceA;

    Young_CombineFilter_sourceDiff_16_3{i}.avg.pow
=(Young_CombineFilter_beamform_16_3{i}.sourceA.avg.pow -
Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow)./Young_CombineFilter_b
eamform_16_3{i}.sourceB.avg.pow;

    

    cfg            = [];

    cfg.downsample = 2;

    cfg.parameter  = 'avg.pow';

    cfg.anatomy    = mri{i};

    cfg.keepfilter='yes';

    cfg.interpmethod='linear';

 
Young_CombineFilter_sourceDiffInt_16_3{i}=ft_sourceinterpolate(cfg,Young_Com
bineFilter_sourceDiff_16_3{i}, mri_young{i});

end;

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From michael.wibral at web.de  Wed Mar 14 20:28:31 2012
From: michael.wibral at web.de (Michael Wibral)
Date: Wed, 14 Mar 2012 20:28:31 +0100 (CET)
Subject: [FieldTrip] missing pos in beamforming
In-Reply-To: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
References: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
Message-ID: <trinity-f95591b5-c49e-407e-9e7e-edbf090da54e-1331753310885@3capp-webde-bs48.dlan.cinetic.de>

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From nathanweisz at mac.com  Wed Mar 14 20:29:56 2012
From: nathanweisz at mac.com (Nathan Weisz)
Date: Wed, 14 Mar 2012 20:29:56 +0100
Subject: [FieldTrip] missing pos in beamforming
In-Reply-To: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
References: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
Message-ID: <5AC98AFE-D119-411D-81A9-FE44B021847D@mac.com>

Hi,

don't have any data at hand right now. but i can't recall that a pos-field should be there after ft_sourceinterpolate (you get your data in 3D corresponding to the dimensions of your MRI). did you actually try ft_volumenormalise? did you run into problems and if yes what does the error look like?

totally unrelated to your problem (if there is any problem), I do not think that cfg.keepfilter is a meaningful input to this function.

best,
n

On 14.03.2012, at 17:28, Jason Chan wrote:

> Greetings,
> I am adapting the beamformer tutorial to my data.  When I sourceinterpolate the subtracted sourceA from sourceB data, the ‘pos’  disappears.  This seems to be important for the volume normalization and Grand Average.  I am running Fieldtrip version: 20110917.  I have placed the code below.
>  
> Many thanks in advance.
> Jason
>  
>  
> Young_CombineFilter_sourceDiff_16_3={};
> for i=1:length(Young_CombineFilter_beamform_16_3);
>     cfg=[];
>     Young_CombineFilter_sourceDiff_16_3{i} =Young_CombineFilter_beamform_16_3{i}.sourceA;
>     Young_CombineFilter_sourceDiff_16_3{i}.avg.pow =(Young_CombineFilter_beamform_16_3{i}.sourceA.avg.pow - Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow)./Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow;
>    
>     cfg            = [];
>     cfg.downsample = 2;
>     cfg.parameter  = 'avg.pow';
>     cfg.anatomy    = mri{i};
>     cfg.keepfilter='yes';
>     cfg.interpmethod='linear';
>     Young_CombineFilter_sourceDiffInt_16_3{i}=ft_sourceinterpolate(cfg,Young_CombineFilter_sourceDiff_16_3{i}, mri_young{i});
> end;
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From jeremiemattout at yahoo.fr  Wed Mar 14 21:22:55 2012
From: jeremiemattout at yahoo.fr (Jeremie MATTOUT)
Date: Wed, 14 Mar 2012 20:22:55 +0000 (GMT)
Subject: [FieldTrip] Post-doctoral Position
Message-ID: <1331756575.90158.YahooMailNeo@web29504.mail.ird.yahoo.com>



Two years Post-doctoral position available
 
Lyon Neuroscience Research Center, Brain Dynamics and Cognition Team, Lyon,
France 
 
----------------------------------------------------------------------------------------------------------------------------------------

Applications are invited for a Post-doctoral position at the Brain Dynamics and
Cognition Team, in the Lyon Neuroscience Research Center, in France. The focus
of the position is on the investigation of the electrophysiological markers of attention,
vigilance and conscious perception, in healthy subjects and non-communicating
and non-responsive patients.
 
The post-doctoral fellow will be part of a three years multi-partner
project. Within the laboratory, she/he will be incorporated in a team of
researchers, engineers, post-doctoral and doctoral fellows who work on various research
and clinical applications of human electrophysiology. Techniques range from
EEG, MEG to SEEG (in collaboration with the Neurological Hospital on site).
In interaction with the team members, the post-doctoral fellow will be in
charge of designing and performing new experiments to test hypothesis about the
functional role of electrophysiological markers.
 
The candidates should have a PhD in Neuroimaging, Human electrophysiology,
Cognitive neuroscience, Biomedical Engineering or a related area. Experience
with high density EEG or MEG in humans is highly desirable (acquisition,
processing, statistics) as well as programming skills (Matlab).  Application from candidates with previous
experience or special interest in related fields such as research in attention,
coma or vegetative state patients, real-time electrophysiology and
brain-computer interfaces are welcome.
 
The Lyon Neuroscience Research Center integrates the multidisciplinary
expertise of 14 teams (about 350 researchers), including university-researchers,
clinician-researchers, technicians and engineers, doctoral and post-doctoral
fellows, making possible a synergistic approach on integrative and cognitive
neurophysiology and its related brain disorders. The neural and molecular
substrates of brain functions, from sensory and motor processes to cognition
and mind, are investigated along two entwined strategic directions: from gene
to behavior, and from bench to patient. Our aim is to bridge the gaps between
the different levels of investigation, and to reinforce a translational
research with reciprocal exchanges between basic conceptual advances and
clinical challenges. The Neuroimaging facilities include an EEG, MEG, TMS, MR and
PET scans as well as access to SEEG recordings in epileptic patients.

Please address questions or send CV, letter of application with research
interests, and two references to Jérémie Mattout (jeremie.mattout at inserm.fr). Applications will be considered until position is
filled. Starting date is negotiable.
 
Jérémie Mattout,
PhD   and   Dominique Morlet, PhD
Lyon Neuroscience
Research Center
Brain Dynamics and
Cognition Team
CHS
Le Vinatier
95
Boulevard Pinel
69500
Bron
France
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From c.micheli at fcdonders.ru.nl  Wed Mar 14 21:48:42 2012
From: c.micheli at fcdonders.ru.nl (Micheli, C.)
Date: Wed, 14 Mar 2012 21:48:42 +0100 (CET)
Subject: [FieldTrip] Mesh intersecting BEM headmodel
In-Reply-To: <BD7CF73B66D0674980FC749AE22A9BFD2B83B0A0@rexma.intranet.epfl.ch>
Message-ID: <767172752.17756.1331758122289.JavaMail.root@draco.zimbra.ru.nl>

Dear Olivia, The documentation you are referring to is not up-to-date and I would not recommend to rely on it. Notwithstanding the old documentation, the problem that you encounter is a known issue with the automatic generation of triangulated surfaces. In fact, the surfaces created from any volumetric data (anatomical MRI or segmentations) should be topologically correct for the BEM to work correctly and at the moment FieldTrip does not check for this (we are working currently on this topic). If you plan to use a head model with 3 compartments I would recommend to start with the function ft_prepare_headmodel, and work with concentric spheres.You can call it like this: cfg=[]; cfg.method = 'concentricspheres'; bnd = ft_prepare_headmodel(cfg,seg) The variable seg is the output of ft_volume_segment containing the skin, skull, brain compartments as and you can refer to the standard documentation for this function: http://fieldtrip.fcdonders.nl/tutorial/headmodel This should automatically solve in most of the cases the problem of intersecting or self-intersecting surfaces. If you want to use the openmeeg toolbox with realistic head models the analysis is complicated by the non-correctness of the surfaces topologies, due probably to the outcome of the segmentation and the successive triangulation step (which happens within the ft_prepare_bemmodel function, now obsolete). The generation of the meshes might work straight away also with the realistic segmented compartments, but it would be difficult to visually check for surface correctness (for example by using the ft_plot_mesh function). When you have the three surfaces you can eventually attach them to your next mail, so that I can verify things with the prototype surface management functions, that we are developing/integrating (see http://code.google.com/p/fieldtrip/source). Let me know if this helps Cristiano ----- Oorspronkelijk bericht -----
> Van: "Mariani Olivia" <olivia.mariani at epfl.ch>
> Aan: fieldtrip at donders.ru.nl
> Verzonden: Dinsdag 13 maart 2012 11:44:53
> Onderwerp: [FieldTrip] Mesh intersecting BEM headmodel
> Hello,
> I am using the "create a BEM headmodel" script but I am getting spikes
> and unwanted holes in the brain compartment when using the triplot
> function and don't know how to get rid of it.
> I get the following warnings on matlab (R2011a):
> %%%%%%%%%%%%%%%%%%%%%
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!! WARNING !!!!!!!!!!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> Mesh is self intersecting !
> Mesh Info :
> # points : 1000
> # triangles : 1996
> Euler characteristic : 2
> Min Area : 14
> Max Area : 152.381
> Self intersection for mesh number 2
> %%%%%%%%%%%%%%%%%%%%%%
> I get this self intersecting warning for my three meshes and
> additional warnings that two meshes are intersecting.
> My problem may come from ill-defined boundaries. Would you know how to
> better define the boundaries between the meshes?
> And then I get the following error:
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> | ------ om_minverser
> | ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin
> | ./tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin
> | -----------------------
> Exception: Unable to open the file
> ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin for reading Doing my
> best....
> Warning: an error ocurred while running OpenMEEG
> > In openmeeg at 127
> In ft_prepare_bemmodel at 232
> In projet_mineur at 106
> Error using ==> fread
> Invalid file identifier. Use fopen to generate a valid file
> identifier.
> Warning: File 'tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin' not found.
> > In openmeeg>cleaner at 142
> In openmeeg at 129
> In ft_prepare_bemmodel at 232
> In projet_mineur at 106
> Warning: File 'tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin' not found.
> > In openmeeg>cleaner at 143
> In openmeeg at 129
> In ft_prepare_bemmodel at 232
> In projet_mineur at 106
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> The file om_minverser from openmeeg closes and the figures open.
> Thank you,
> Olivia
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From olivia.mariani at epfl.ch  Fri Mar 16 09:13:29 2012
From: olivia.mariani at epfl.ch (Mariani Olivia)
Date: Fri, 16 Mar 2012 08:13:29 +0000
Subject: [FieldTrip] RE :  Mesh intersecting BEM headmodel
In-Reply-To: <767172752.17756.1331758122289.JavaMail.root@draco.zimbra.ru.nl>
References: <BD7CF73B66D0674980FC749AE22A9BFD2B83B0A0@rexma.intranet.epfl.ch>,
	<767172752.17756.1331758122289.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <BD7CF73B66D0674980FC749AE22A9BFD2B83B1C3@rexma.intranet.epfl.ch>

Hello Cristiano,

yes it was useful thank you very much, I will use for now the concentric sphere model and will try with the ft_plot_mesh.

I forgot to mention that I am actually using the avg152T1 head model. Does an other method exist to extract the skin from an average? I was thinking of defining the skin and skull as outer and inner skull. Do you think it might solve the triangulation problem?

Thank you very much,

Olivia
________________________________
De : fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] de la part de Micheli, C. [c.micheli at fcdonders.ru.nl]
Date d'envoi : mercredi 14 mars 2012 21:48
À : Email discussion list for the FieldTrip project
Objet : Re: [FieldTrip] Mesh intersecting BEM headmodel

Dear Olivia,
The documentation you are referring to is not up-to-date and I would not recommend to rely on it.
Notwithstanding the old documentation, the problem that you encounter is a known issue with the automatic generation of triangulated surfaces. In fact, the surfaces created from any volumetric data (anatomical MRI or segmentations) should be topologically correct for the BEM to work correctly and at the moment FieldTrip does not check for this (we are working currently on this topic).
If you plan to use a head model with 3 compartments I would recommend to start with the function ft_prepare_headmodel, and work with concentric spheres.You can call it like this:

cfg=[];
cfg.method = 'concentricspheres';
bnd = ft_prepare_headmodel(cfg,seg)

The variable seg is the output of ft_volume_segment containing the skin, skull, brain compartments as
and you can refer to the standard documentation for this function:

http://fieldtrip.fcdonders.nl/tutorial/headmodel

This should automatically solve in most of the cases the problem of intersecting or self-intersecting surfaces.
If you want to use the openmeeg toolbox with realistic head models the analysis is complicated by the non-correctness of the surfaces topologies, due probably to the outcome of the segmentation and the successive triangulation step (which happens within the ft_prepare_bemmodel function, now obsolete).
The generation of the meshes might work straight away also with the realistic segmented compartments, but it would be difficult to visually check for surface correctness (for example by using the ft_plot_mesh function).
When you have the three surfaces you can eventually attach them to your next mail, so that I can verify things with the prototype surface management functions, that we are developing/integrating (see http://code.google.com/p/fieldtrip/source).

Let me know if this helps
Cristiano


________________________________
Van: "Mariani Olivia" <olivia.mariani at epfl.ch>
Aan: fieldtrip at donders.ru.nl
Verzonden: Dinsdag 13 maart 2012 11:44:53
Onderwerp: [FieldTrip] Mesh intersecting BEM headmodel

Hello,

I am using the "create a BEM headmodel" script but I am getting spikes and unwanted holes in the brain compartment when using the triplot function and don't know how to get rid of it.

I get the following warnings on matlab (R2011a):

%%%%%%%%%%%%%%%%%%%%%
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!! WARNING !!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Mesh is self intersecting !
Mesh Info :
    # points : 1000
    # triangles : 1996
    Euler characteristic : 2
    Min Area : 14
    Max Area : 152.381
Self intersection for mesh number 2
%%%%%%%%%%%%%%%%%%%%%%

I get this self intersecting warning for my three meshes and additional warnings that two meshes are intersecting.
My problem may come from ill-defined boundaries. Would you know how to better define the boundaries between the meshes?

And then I get the following error:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
| ------ om_minverser
| ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin
| ./tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin
| -----------------------
Exception: Unable to open the file ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin for reading Doing my best....
Warning: an error ocurred while running OpenMEEG
> In openmeeg at 127
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Error using ==> fread
Invalid file identifier.  Use fopen to generate a valid file identifier.
Warning: File 'tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin' not found.
> In openmeeg>cleaner at 142
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Warning: File 'tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin' not found.
> In openmeeg>cleaner at 143
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The file om_minverser from openmeeg closes and the figures open.

Thank you,

Olivia



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

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From ivano_triggiani at yahoo.it  Fri Mar 16 09:42:10 2012
From: ivano_triggiani at yahoo.it (Ivano Triggiani)
Date: Fri, 16 Mar 2012 08:42:10 +0000 (GMT)
Subject: [FieldTrip] channel type (EEG, EMG,etc.) and when to filter data
Message-ID: <1331887330.12945.YahooMailNeo@web132104.mail.ird.yahoo.com>

Hi everybody,


I'm back to use fieldtrip after a long period, and now everything seems to work (I used .edf file and I had problem with trigger).

Now I have some questions, if someone would be so kind to help me:

1. I'd like to label my channel to select among EEG type, EMG type etc. because my acquire system labeled them all as EEG. When is it specified in cfg ? I can't find it! And if I can't, how can I exclude EMG,TRIGGER and EOG channels from ICA computation? 


2. I have a lot of channel, but ICA gave me back just 33 of them. How can I proceed to obtain a correct ICA from my 56 channels?

3. is it wrong if I filter my data before ICA?


4. If I use ICA probably I can't use other source separation method (like BSS) to analyze my data, am I wrong?


Sorry
 if I post so much questions, but I'm back with fieldtrip and I want to improve my techniques.

Ivano 
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From nathanweisz at mac.com  Fri Mar 16 09:53:20 2012
From: nathanweisz at mac.com (Nathan Weisz)
Date: Fri, 16 Mar 2012 09:53:20 +0100
Subject: [FieldTrip] channel type (EEG, EMG,
	etc.) and when to filter data
In-Reply-To: <1331887330.12945.YahooMailNeo@web132104.mail.ird.yahoo.com>
References: <1331887330.12945.YahooMailNeo@web132104.mail.ird.yahoo.com>
Message-ID: <83DC888D-74CA-467E-90BE-8615B181E8AB@mac.com>

hi,

> I'm back to use fieldtrip after a long period, and now everything seems to work (I used .edf file and I had problem with trigger).

congratulations.

> 1. I'd like to label my channel to select among EEG type, EMG type etc. because my acquire system labeled them all as EEG. When is it specified in cfg ? I can't find it! And if I can't, how can I exclude EMG,TRIGGER and EOG channels from ICA computation? 

you must have had a consitent way of plugging in the channels into your amplifier, haven't you? if yes, then you should find out which channel corresponds to which row in your EEG data and you can relabel them within Matlab.

Your EMG, TRIGGER and EOG channels should also be easy to detect when looking at your data. but you should get back to your recording configurations (also data acquisition software) if you are interested in the positions / labels of the other EEG electrodes. You may want to keep your EOG channels if they have a common reference like the EEG channels.

> 2. I have a lot of channel, but ICA gave me back just 33 of them. How can I proceed to obtain a correct ICA from my 56 channels?

you mean components? 

> 3. is it wrong if I filter my data before ICA?

no.

> 4. If I use ICA probably I can't use other source separation method (like BSS) to analyze my data, am I wrong?

dunno.

good luck,
n

> 
> Sorry if I post so much questions, but I'm back with fieldtrip and I want to improve my techniques.
> 
> Ivano 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From olivia.mariani at epfl.ch  Fri Mar 16 11:16:39 2012
From: olivia.mariani at epfl.ch (Mariani Olivia)
Date: Fri, 16 Mar 2012 10:16:39 +0000
Subject: [FieldTrip] Concentricspheres method
Message-ID: <BD7CF73B66D0674980FC749AE22A9BFD2B83B1EF@rexma.intranet.epfl.ch>

Hello Cristiano,

I am using the concentricsphere but get the following errors:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

??? Error using ==> ft_prepare_headmodel at 233
no input available

Error in ==> Olivia at 29
vol = ft_prepare_headmodel(cfg, seg);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

My code is as follows:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%adds the path toward fieldtrip
addpath_projet;

%récupère les données du fichier mri
mri = ft_read_mri('avg152T1.nii');

%segmentation du volume
cfg = [];
cfg.coordinates = 'spm';

seg = ft_volumesegment(cfg, mri);

seg.anatomy = mri.anatomy;

cfg                = [];
cfg.tissue         = [1 2 3]; % value of each tissue type in the segmentation
cfg.numvertices    = [1000 2000 3000];
cfg.conductivity   = [1 1/80 1];
cfg.isolatedsource = true;
cfg.method         = 'concentricspheres';
cfg.smooth = 'no';

cfg.sourceunits = 'mm';
cfg.mriunits = 'mm';

vol = ft_prepare_headmodel(cfg, seg);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

It seems that I never have the good conditions to put some values in "geometry" but I can't find what I am missing.

Thank you very much,

Olivia
________________________________
De : fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] de la part de Micheli, C. [c.micheli at fcdonders.ru.nl]
Date d'envoi : mercredi 14 mars 2012 21:48
À : Email discussion list for the FieldTrip project
Objet : Re: [FieldTrip] Mesh intersecting BEM headmodel

Dear Olivia,
The documentation you are referring to is not up-to-date and I would not recommend to rely on it.
Notwithstanding the old documentation, the problem that you encounter is a known issue with the automatic generation of triangulated surfaces. In fact, the surfaces created from any volumetric data (anatomical MRI or segmentations) should be topologically correct for the BEM to work correctly and at the moment FieldTrip does not check for this (we are working currently on this topic).
If you plan to use a head model with 3 compartments I would recommend to start with the function ft_prepare_headmodel, and work with concentric spheres.You can call it like this:

cfg=[];
cfg.method = 'concentricspheres';
bnd = ft_prepare_headmodel(cfg,seg)

The variable seg is the output of ft_volume_segment containing the skin, skull, brain compartments as
and you can refer to the standard documentation for this function:

http://fieldtrip.fcdonders.nl/tutorial/headmodel

This should automatically solve in most of the cases the problem of intersecting or self-intersecting surfaces.
If you want to use the openmeeg toolbox with realistic head models the analysis is complicated by the non-correctness of the surfaces topologies, due probably to the outcome of the segmentation and the successive triangulation step (which happens within the ft_prepare_bemmodel function, now obsolete).
The generation of the meshes might work straight away also with the realistic segmented compartments, but it would be difficult to visually check for surface correctness (for example by using the ft_plot_mesh function).
When you have the three surfaces you can eventually attach them to your next mail, so that I can verify things with the prototype surface management functions, that we are developing/integrating (see http://code.google.com/p/fieldtrip/source).

Let me know if this helps
Cristiano


________________________________
Van: "Mariani Olivia" <olivia.mariani at epfl.ch>
Aan: fieldtrip at donders.ru.nl
Verzonden: Dinsdag 13 maart 2012 11:44:53
Onderwerp: [FieldTrip] Mesh intersecting BEM headmodel

Hello,

I am using the "create a BEM headmodel" script but I am getting spikes and unwanted holes in the brain compartment when using the triplot function and don't know how to get rid of it.

I get the following warnings on matlab (R2011a):

%%%%%%%%%%%%%%%%%%%%%
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!! WARNING !!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Mesh is self intersecting !
Mesh Info :
    # points : 1000
    # triangles : 1996
    Euler characteristic : 2
    Min Area : 14
    Max Area : 152.381
Self intersection for mesh number 2
%%%%%%%%%%%%%%%%%%%%%%

I get this self intersecting warning for my three meshes and additional warnings that two meshes are intersecting.
My problem may come from ill-defined boundaries. Would you know how to better define the boundaries between the meshes?

And then I get the following error:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
| ------ om_minverser
| ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin
| ./tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin
| -----------------------
Exception: Unable to open the file ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin for reading Doing my best....
Warning: an error ocurred while running OpenMEEG
> In openmeeg at 127
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Error using ==> fread
Invalid file identifier.  Use fopen to generate a valid file identifier.
Warning: File 'tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin' not found.
> In openmeeg>cleaner at 142
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Warning: File 'tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin' not found.
> In openmeeg>cleaner at 143
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The file om_minverser from openmeeg closes and the figures open.

Thank you,

Olivia



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

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From michael.wibral at web.de  Fri Mar 16 14:32:21 2012
From: michael.wibral at web.de (Michael Wibral)
Date: Fri, 16 Mar 2012 14:32:21 +0100 (CET)
Subject: [FieldTrip] Workshop on Non-linear and model-free Interdependence
 Measures in Neuroscience and TRENTOOL course
Message-ID: <trinity-c81db96e-2921-4177-8653-0919d68bd344-1331904741681@3capp-webde-bs47.dlan.cinetic.de>

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From chan at med.uni-frankfurt.de  Fri Mar 16 15:17:09 2012
From: chan at med.uni-frankfurt.de (Jason Chan)
Date: Fri, 16 Mar 2012 15:17:09 +0100
Subject: [FieldTrip] missing pos in beamforming
In-Reply-To: <trinity-f95591b5-c49e-407e-9e7e-edbf090da54e-1331753310885@3capp-webde-bs48.dlan.cinetic.de>
References: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
	<trinity-f95591b5-c49e-407e-9e7e-edbf090da54e-1331753310885@3capp-webde-bs48.dlan.cinetic.de>
Message-ID: <002601cd037f$793ca580$6bb5f080$@med.uni-frankfurt.de>

Hi Michael,

 

Many thanks for your informative reply.  I was able to use the reverse normalization technique and eliminated the ft_sourceinterpolate and ft_volumenormalise commands.

However, after I subtract ‘sourceA’ from ‘sourceB’ I now get the error “different grid locations in source reconstructions” when I try to do a ft_sourcegrandaverage.  Any suggestions would be very welcome.

 

Thanks in advance.

Jason

 

From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Michael Wibral
Sent: Mittwoch, 14. März 2012 20:29
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] missing pos in beamforming

 

Dear Jason,

the pos indicates where the original sources were (i.e. on a regular grid with a certain spacing or self-defined). After interpolation this information does not reflect the data anymore. I would suggest to use Ingrid nieuwenhuis famous reverse normalization technique to create individual subject grids taht all match in MNI space - the script is found on the ft website. Sourceinterpoltae should really only be used for plotting IMHO.

Michael

Gesendet: Mittwoch, 14. März 2012 um 17:28 Uhr
Von: "Jason Chan" <chan at med.uni-frankfurt.de>
An: fieldtrip at donders.ru.nl
Betreff: [FieldTrip] missing pos in beamforming 

Greetings,

I am adapting the beamformer tutorial to my data.  When I sourceinterpolate the subtracted sourceA from sourceB data, the ‘pos’  disappears.  This seems to be important for the volume normalization and Grand Average.  I am running Fieldtrip version: 20110917.  I have placed the code below.

 

Many thanks in advance.

Jason

 

 

Young_CombineFilter_sourceDiff_16_3={};

for i=1:length(Young_CombineFilter_beamform_16_3);

    cfg=[];

    Young_CombineFilter_sourceDiff_16_3{i} =Young_CombineFilter_beamform_16_3{i}.sourceA;

    Young_CombineFilter_sourceDiff_16_3{i}.avg.pow =(Young_CombineFilter_beamform_16_3{i}.sourceA.avg.pow - Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow)./Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow;

    

    cfg            = [];

    cfg.downsample = 2;

    cfg.parameter  = 'avg.pow';

    cfg.anatomy    = mri{i};

    cfg.keepfilter='yes';

    cfg.interpmethod='linear';

    Young_CombineFilter_sourceDiffInt_16_3{i}=ft_sourceinterpolate(cfg,Young_CombineFilter_sourceDiff_16_3{i}, mri_young{i});

end;

 

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From michael.wibral at web.de  Fri Mar 16 16:21:46 2012
From: michael.wibral at web.de (Michael Wibral)
Date: Fri, 16 Mar 2012 16:21:46 +0100 (CET)
Subject: [FieldTrip] missing pos in beamforming
In-Reply-To: <002601cd037f$793ca580$6bb5f080$@med.uni-frankfurt.de>
References: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
	<trinity-f95591b5-c49e-407e-9e7e-edbf090da54e-1331753310885@3capp-webde-bs48.dlan.cinetic.de>,
	<002601cd037f$793ca580$6bb5f080$@med.uni-frankfurt.de>
Message-ID: <trinity-d7e7ebe6-1de2-434c-a5e2-1f12f9f5681b-1331911306816@3capp-webde-bs47.dlan.cinetic.de>

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From mark.noordenbos at gmail.com  Fri Mar 16 18:05:39 2012
From: mark.noordenbos at gmail.com (Mark Noordenbos)
Date: Fri, 16 Mar 2012 18:05:39 +0100
Subject: [FieldTrip] Combine Grand Average
Message-ID: <CAJSb8nPaJcyFsKU7+nMzPd9r9trs70t=iRWvCgGSxw-k_QFZ0Q@mail.gmail.com>

Hi,

I'm looking for a function that combines two timelocked Grand Averages
(keeping the 'subj_chan_time' dimord).
I have for several conditions seperate Grand Averages, but now I need to
combine some of them into a new Grand Average while keeping the individual
data.

Does Fieldtrip has a buit-in function to do this?

When just calculating the mean, one dimension ('subj' or 'chan' or 'time')
is always lost.

Thanks,
Mark


-- 
Mark Noordenbos, MSc

Radboud University Nijmegen
Behavioural Science Institute

P.O. Box 9104, Room A05.36
6500 HE Nijmegen
The Netherlands

Email: m.noordenbos at bsi.ru.nl
Telephone: +31 24 3612070
Fax:          +31 24 3616211

http://www.ru.nl
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From michael.wibral at web.de  Fri Mar 16 21:51:42 2012
From: michael.wibral at web.de (Michael Wibral)
Date: Fri, 16 Mar 2012 21:51:42 +0100 (CET)
Subject: [FieldTrip] Post-doctoral position available at the Group of
 Michael Wibral, Brain Imaging Center, Frankurt Germany
Message-ID: <trinity-d1f8194a-a8c2-4ba5-b861-c808251892a8-1331931102882@3capp-webde-bs47.dlan.cinetic.de>

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From batrod at gmail.com  Fri Mar 16 18:49:09 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Fri, 16 Mar 2012 12:49:09 -0500
Subject: [FieldTrip] channel type (EEG, EMG,
	etc.) and when to filter data
In-Reply-To: <83DC888D-74CA-467E-90BE-8615B181E8AB@mac.com>
References: <1331887330.12945.YahooMailNeo@web132104.mail.ird.yahoo.com>
	<83DC888D-74CA-467E-90BE-8615B181E8AB@mac.com>
Message-ID: <CAPy7a9B2nCTYXDvr4o86wtxN1na1yAUnystjaMDRTXeWYaxQhA@mail.gmail.com>

Let me add my 2 cents :

I'm back to use fieldtrip after a long period, and now everything seems to
> work (I used .edf file and I had problem with trigger).
>
>
> congratulations.
>

Rodolphe: Congratulations too

>
> 1. I'd like to label my channel to select among EEG type, EMG type etc.
> because my acquire system labeled them all as EEG. When is it specified in
> cfg ? I can't find it! And if I can't, how can I exclude EMG,TRIGGER and
> EOG channels from ICA computation?
>
>
> you must have had a consitent way of plugging in the channels into your
> amplifier, haven't you? if yes, then you should find out which channel
> corresponds to which row in your EEG data and you can relabel them within
> Matlab.
>
> Your EMG, TRIGGER and EOG channels should also be easy to detect when
> looking at your data. but you should get back to your recording
> configurations (also data acquisition software) if you are interested in
> the positions / labels of the other EEG electrodes. You may want to keep
> your EOG channels if they have a common reference like the EEG channels.
>

Rodolphe: Same answer

>
> 2. I have a lot of channel, but ICA gave me back just 33 of them. How can
> I proceed to obtain a correct ICA from my 56 channels?
>
>
> you mean components?
>

Rodolphe: Did you use a PCA to reduce your components first?

>
> 3. is it wrong if I filter my data before ICA?
>
>
> no.
>

Rodolphe: I would tend to say yes. ICA needs a maximum of information to
separate the components,
See for example Snyder and Foxe (2010) where they used ICA to get
components with a dominant of alpha oscillations. They argued that
filtering before is making ICA analysis worse

>
> 4. If I use ICA probably I can't use other source separation method (like
> BSS) to analyze my data, am I wrong?
>
>
> dunno.
>
Rodolphe : as ICA is a BSS, what other method did you have in mind?

>
> good luck,
> n
>
>
> Rodolphe Nenert, PhD.
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From fredericroux at hotmail.de  Sun Mar 18 15:51:21 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Sun, 18 Mar 2012 15:51:21 +0100
Subject: [FieldTrip] indepsamplesF with sourcestatistics
Message-ID: <DUB113-W53D91DAF011D28E811FBE7B75D0@phx.gbl>


Dear all,

I noticed that the result of sourcestatistics can be quite different when using cfg.statistic = 'indepsamplesF'
or also cfg.statistic ='indepsamplesregrT', depending on whether you specify a unit of observations (UO's)
variable in the design matrix or not.

For example when running the code without the UOs-variable as following

cfg.design(1,:) = [ones(1,length(indx1)) 2*ones(1,length(indx1)) 3*ones(1,length(indx1)) 4*ones(1,length(indx1))];
cfg.ivar = 1;

I get a different result than if I run:

cfg.design(1,:) = [ones(1,length(indx1)) 2*ones(1,length(indx2)) 3*ones(1,length(indx3)) 4*ones(1,length(indx4))];
cfg.design(2,:) = [indx1' indx2' indx3' indx4'];
cfg.ivar = 1;

cfg.uvar = 2;

Note that in the second case the indexes in the UOs variable are not sorted.

I guess that you are not supposed to run the code as in the second case,
but I would still like to know why I get different results. Shouldn't it be the same anyways?

It would be great to get an explanation for the discrepancy between both codes.

Best,
Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From eelke.spaak at donders.ru.nl  Mon Mar 19 11:37:47 2012
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Mon, 19 Mar 2012 11:37:47 +0100
Subject: [FieldTrip] Combine Grand Average
In-Reply-To: <CAJSb8nPaJcyFsKU7+nMzPd9r9trs70t=iRWvCgGSxw-k_QFZ0Q@mail.gmail.com>
References: <CAJSb8nPaJcyFsKU7+nMzPd9r9trs70t=iRWvCgGSxw-k_QFZ0Q@mail.gmail.com>
Message-ID: <CABPNLUoTApRzDeyZGvWFfwJjxQcE_QgTwf+pRJcy-jjh+_E7iA@mail.gmail.com>

Hi Mark,

I am not entirely sure, but I think ft_appendtimelock might be what
you are looking for. If not, you could probably also just append the
timelocked information 'by hand':

tl_combined = tl1;
tl_combined.individual = [tl1.individual; tl2.individual];

But be aware that this could get messy, and you then need to make sure
the .avg and other fields are still consistent. So, if at all
possible, stick to ft_appendtimelock :)

Best,
Eelke

On 16 March 2012 18:05, Mark Noordenbos <mark.noordenbos at gmail.com> wrote:
> Hi,
>
> I'm looking for a function that combines two timelocked Grand Averages
> (keeping the 'subj_chan_time' dimord).
> I have for several conditions seperate Grand Averages, but now I need to
> combine some of them into a new Grand Average while keeping the individual
> data.
>
> Does Fieldtrip has a buit-in function to do this?
>
> When just calculating the mean, one dimension ('subj' or 'chan' or 'time')
> is always lost.
>
> Thanks,
> Mark
>
>
> --
> Mark Noordenbos, MSc
>
> Radboud University Nijmegen
> Behavioural Science Institute
>
> P.O. Box 9104, Room A05.36
> 6500 HE Nijmegen
> The Netherlands
>
> Email: m.noordenbos at bsi.ru.nl
> Telephone: +31 24 3612070
> Fax:          +31 24 3616211
>
> http://www.ru.nl
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From politzerahless at gmail.com  Mon Mar 19 12:08:49 2012
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Mon, 19 Mar 2012 06:08:49 -0500
Subject: [FieldTrip] Combine Grand Average
Message-ID: <CAJT2k_80VhT3oBTNCLipJz5J9PDg2y-DjuRecYWdP9ZaP1ZThQ@mail.gmail.com>

Hi Mark,

Do you mean to combine multiple conditions into a single condition? For
that I'm not sure of a built-in function that can do this using grand
averages; you might need to re-do ft_timelockanalysis for the new condition
and then make new grand averages. Since it's possible that a given subject
has more trials contributing to her average for condition A than for
condition B, simply averaging the two condition averages together might not
be accurate.

Best,
Steve Politzer-Ahles

Message: 2
> Date: Mon, 19 Mar 2012 11:37:47 +0100
> From: Eelke Spaak <eelke.spaak at donders.ru.nl>
> To: Email discussion list for the FieldTrip project
>        <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] Combine Grand Average
> Message-ID:
>        <CABPNLUoTApRzDeyZGvWFfwJjxQcE_QgTwf+pRJcy-jjh+_E7iA at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Mark,
>
> I am not entirely sure, but I think ft_appendtimelock might be what
> you are looking for. If not, you could probably also just append the
> timelocked information 'by hand':
>
> tl_combined = tl1;
> tl_combined.individual = [tl1.individual; tl2.individual];
>
> But be aware that this could get messy, and you then need to make sure
> the .avg and other fields are still consistent. So, if at all
> possible, stick to ft_appendtimelock :)
>
> Best,
> Eelke
>
> On 16 March 2012 18:05, Mark Noordenbos <mark.noordenbos at gmail.com> wrote:
> > Hi,
> >
> > I'm looking for a function that combines two timelocked Grand Averages
> > (keeping the 'subj_chan_time' dimord).
> > I have for several conditions seperate Grand Averages, but now I need to
> > combine some of them into a new Grand Average while keeping the
> individual
> > data.
> >
> > Does Fieldtrip has a buit-in function to do this?
> >
> > When just calculating the mean, one dimension ('subj' or 'chan' or
> 'time')
> > is always lost.
> >
> > Thanks,
> > Mark
> >
> >
> > --
> > Mark Noordenbos, MSc
> >
> > Radboud University Nijmegen
> > Behavioural Science Institute
> >
> > P.O. Box 9104, Room A05.36
> > 6500 HE Nijmegen
> > The Netherlands
> >
> > Email: m.noordenbos at bsi.ru.nl
> > Telephone: +31 24 3612070
> > Fax:? ? ? ? ? +31 24 3616211
> >
> > http://www.ru.nl
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
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From jm.horschig at donders.ru.nl  Mon Mar 19 13:35:17 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 19 Mar 2012 13:35:17 +0100
Subject: [FieldTrip] Combine Grand Average
In-Reply-To: <CAJT2k_80VhT3oBTNCLipJz5J9PDg2y-DjuRecYWdP9ZaP1ZThQ@mail.gmail.com>
References: <CAJT2k_80VhT3oBTNCLipJz5J9PDg2y-DjuRecYWdP9ZaP1ZThQ@mail.gmail.com>
Message-ID: <4F672805.5060404@donders.ru.nl>

Hi Mark,

I agree with Steve. Though, in order to not re-compute the averages, you 
could create the weighted average yourself. Just make a weight vector 
like this:

/weights = no_trials_cond_A / (no_trials_cond_A+no_trials_cond_B);/

Where /no_trials_cond_A /and /*_b/ contai  the number of trials in 
condition A and B, respectively.
Then you can take the weighted sum of the two grand-averages you have, 
something like:

/    grandavg.individual = condA.individual * weights + condB.individual 
* (1-weights);/

This is mathematically equivalent to re-computing the average on all 
trials (note that I am not sure whether this holds for spectral denisity 
matrices and stuff like that, but for ERPs and plain powerspectra, does).

Best,
Jörn

On 3/19/2012 12:08 PM, Stephen Politzer-Ahles wrote:
> Hi Mark,
>
> Do you mean to combine multiple conditions into a single condition? 
> For that I'm not sure of a built-in function that can do this using 
> grand averages; you might need to re-do ft_timelockanalysis for the 
> new condition and then make new grand averages. Since it's possible 
> that a given subject has more trials contributing to her average for 
> condition A than for condition B, simply averaging the two condition 
> averages together might not be accurate.
>
> Best,
> Steve Politzer-Ahles
>
>     Message: 2
>     Date: Mon, 19 Mar 2012 11:37:47 +0100
>     From: Eelke Spaak <eelke.spaak at donders.ru.nl
>     <mailto:eelke.spaak at donders.ru.nl>>
>     To: Email discussion list for the FieldTrip project
>     <fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>>
>     Subject: Re: [FieldTrip] Combine Grand Average
>     Message-ID:
>     <CABPNLUoTApRzDeyZGvWFfwJjxQcE_QgTwf+pRJcy-jjh+_E7iA at mail.gmail.com <mailto:CABPNLUoTApRzDeyZGvWFfwJjxQcE_QgTwf%2BpRJcy-jjh%2B_E7iA at mail.gmail.com>>
>     Content-Type: text/plain; charset=ISO-8859-1
>
>     Hi Mark,
>
>     I am not entirely sure, but I think ft_appendtimelock might be what
>     you are looking for. If not, you could probably also just append the
>     timelocked information 'by hand':
>
>     tl_combined = tl1;
>     tl_combined.individual = [tl1.individual; tl2.individual];
>
>     But be aware that this could get messy, and you then need to make sure
>     the .avg and other fields are still consistent. So, if at all
>     possible, stick to ft_appendtimelock :)
>
>     Best,
>     Eelke
>
>     On 16 March 2012 18:05, Mark Noordenbos <mark.noordenbos at gmail.com
>     <mailto:mark.noordenbos at gmail.com>> wrote:
>     > Hi,
>     >
>     > I'm looking for a function that combines two timelocked Grand
>     Averages
>     > (keeping the 'subj_chan_time' dimord).
>     > I have for several conditions seperate Grand Averages, but now I
>     need to
>     > combine some of them into a new Grand Average while keeping the
>     individual
>     > data.
>     >
>     > Does Fieldtrip has a buit-in function to do this?
>     >
>     > When just calculating the mean, one dimension ('subj' or 'chan'
>     or 'time')
>     > is always lost.
>     >
>     > Thanks,
>     > Mark
>     >
>     >
>     > --
>     > Mark Noordenbos, MSc
>     >
>     > Radboud University Nijmegen
>     > Behavioural Science Institute
>     >
>     > P.O. Box 9104, Room A05.36
>     > 6500 HE Nijmegen
>     > The Netherlands
>     >
>     > Email: m.noordenbos at bsi.ru.nl <mailto:m.noordenbos at bsi.ru.nl>
>     > Telephone: +31 24 3612070 <tel:%2B31%2024%203612070>
>     > Fax:? ? ? ? ? +31 24 3616211 <tel:%2B31%2024%203616211>
>     >
>     > http://www.ru.nl
>     >
>     >
>     > _______________________________________________
>     > 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

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 giulia.rizza at tiscali.it  Mon Mar 19 16:25:20 2012
From: giulia.rizza at tiscali.it (Giulia Rizza)
Date: Mon, 19 Mar 2012 16:25:20 +0100 (GMT+01:00)
Subject: [FieldTrip] Neuroscan .cnt files
Message-ID: <7171049.98631332170720589.JavaMail.defaultUser@defaultHost>

Dear Fieldtrippers,
hi to everyone and thanks in advance for your time.
I'm not 
an expert and I'd like to share with you a problem I found in reading cnt files 
acquired with Neuroscan.

I read the data with ft_read_data function and I find 
the attached link Plot1, for instance the first channel. It seems that the 
signal is forced to pass per zero every two samples, so I tried to read them  
excluding the even samples and I find the result in Plot2, while excluding the 
odd values I find the result in Plot3.

http://dl.dropbox.com/u/28258961/Plot01.
rar

Unfortunately there are still some problems since the maximum value that 
can be represented (about 900) is smaller than some values in the data and the 
result is that I find a sharp change of sign. How can I fix it?

Thanks to 
anyone who can help me

Giulia


E' nata indoona: chiama, videochiama e messaggia Gratis. Scarica indoona per iPhone, Android e PC: http://www.indoona.com/ 


From yuvharpaz at gmail.com  Mon Mar 19 16:46:04 2012
From: yuvharpaz at gmail.com (Yuval Harpaz)
Date: Mon, 19 Mar 2012 17:46:04 +0200
Subject: [FieldTrip] rejectcomponent after ica for 20 comps only
Message-ID: <CAGQZS_kvLUWndQijop+pjEwj0r2=k=-Efp+WLRs1VzhuMVj2bQ@mail.gmail.com>

Dear ft_emaillist

I want to reject components obtained with with fastica.

if I only run ft_componentanalysis with cfg.numcomponent=20, creating only
20 components, can I still reject a specific component by
ft_rejectcomponent(cfg,comp,data) or will it only reconstruct the date
based on the 20 components I calculated?

thanks,Yuval

-- 

Y.Harpaz

a link to the BIU MEG lab:
http://faculty.biu.ac.il/~goldsa/index.html
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From enzo.brunetti at gmail.com  Mon Mar 19 18:32:34 2012
From: enzo.brunetti at gmail.com (Enzo Brunetti)
Date: Mon, 19 Mar 2012 13:32:34 -0400
Subject: [FieldTrip] Neuroscan .cnt files
In-Reply-To: <7171049.98631332170720589.JavaMail.defaultUser@defaultHost>
References: <7171049.98631332170720589.JavaMail.defaultUser@defaultHost>
Message-ID: <2CD6708A-A08A-4AF0-92BB-B78029DF2B76@gmail.com>

Dear Giulia,
I could not see your dropbox link showing the plot, but a known reported problem with importing .cnt neuroscan files is that the file header does not specify the actual precision of your data (typically 32 bits with new neuroscan systems, 16 bits previously). If you are importing 32 bits data without explicitly defining it previously, you can obtain the type of signals you are talking about (the default importing option is '16bits'). If this is the case, you must to specify this in the cfg input structure of the reader function, as:

cfg.headerformat         =  'ns_cnt32';
cfg.dataformat              =  'ns_cnt32';
cfg.eventformat            =  'ns_cnt32';

in addition to the other specific fields of the structure.

Also, you can visit this link: http://fieldtrip.fcdonders.nl/faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_this for more information.

I hope this could help you.
Best

Dr. Enzo Brunetti F.
---------------------------
Institute of Biomedical Sciences
Faculty of Medicine
University of Chile


On Mar 19, 2012, at 11:25 AM, Giulia Rizza wrote:

> Dear Fieldtrippers,
> hi to everyone and thanks in advance for your time.
> I'm not 
> an expert and I'd like to share with you a problem I found in reading cnt files 
> acquired with Neuroscan.
> 
> I read the data with ft_read_data function and I find 
> the attached link Plot1, for instance the first channel. It seems that the 
> signal is forced to pass per zero every two samples, so I tried to read them  
> excluding the even samples and I find the result in Plot2, while excluding the 
> odd values I find the result in Plot3.
> 
> http://dl.dropbox.com/u/28258961/Plot01.
> rar
> 
> Unfortunately there are still some problems since the maximum value that 
> can be represented (about 900) is smaller than some values in the data and the 
> result is that I find a sharp change of sign. How can I fix it?
> 
> Thanks to 
> anyone who can help me
> 
> Giulia
> 
> 
> E' nata indoona: chiama, videochiama e messaggia Gratis. Scarica indoona per iPhone, Android e PC: http://www.indoona.com/ 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From g.piantoni at nin.knaw.nl  Mon Mar 19 17:59:50 2012
From: g.piantoni at nin.knaw.nl (Gio Piantoni)
Date: Mon, 19 Mar 2012 17:59:50 +0100
Subject: [FieldTrip] rejectcomponent after ica for 20 comps only
In-Reply-To: <CAGQZS_kvLUWndQijop+pjEwj0r2=k=-Efp+WLRs1VzhuMVj2bQ@mail.gmail.com>
References: <CAGQZS_kvLUWndQijop+pjEwj0r2=k=-Efp+WLRs1VzhuMVj2bQ@mail.gmail.com>
Message-ID: <CAHeOcrv=saYUviSjchVn-mdnv53Y4Ky37LsG-hit+E=2CLSy2g@mail.gmail.com>

Hi Yuval,

If you pass data as third argument, the function will substract the
weights of rejected component(s) from your data. So, your data will
have the initial rank minus the number of rejected component. No
reconstruction occurs.

See line 121 of ft_rejectcomponent or try the code below.

nelec = 50;
fs = 1000;
ntrl = 5;

data = [];
data.label = cellfun(@(x)['E' num2str(x)], num2cell(1:nelec), 'uni', 0);
data.fsample = fs;
for i =1:ntrl
  data.trial{i} = randn(nelec, fs);
  data.time{i} = 1/fs:1/fs:1;
end

cfg = [];
cfg.method = 'fastica';
cfg.numcomponent = 10;
comp = ft_componentanalysis(cfg, data);

cfg = [];
cfg.component = 2;
data2 = ft_rejectcomponent(cfg, comp, data); % subtract comp from data
data3 = ft_rejectcomponent(cfg, comp); % reconstruct from comp

rank(data.trial{1}) % full rank
rank(data2.trial{1}) % full rank - 1 rejected
rank(data3.trial{1})  % rank of 'comp' - 1 rejected

On Mon, Mar 19, 2012 at 16:46, Yuval Harpaz <yuvharpaz at gmail.com> wrote:
> Dear ft_emaillist
>
> I want to reject components obtained with with fastica.
>
> if I only run ft_componentanalysis with cfg.numcomponent=20, creating only
> 20 components, can I still reject a specific component by
> ft_rejectcomponent(cfg,comp,data) or will it only reconstruct the date based
> on the 20 components I calculated?
>
> thanks,Yuval
>
> --
>
> Y.Harpaz
>
> a link to the BIU MEG lab:
> http://faculty.biu.ac.il/~goldsa/index.html
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From politzerahless at gmail.com  Mon Mar 19 18:56:21 2012
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Mon, 19 Mar 2012 12:56:21 -0500
Subject: [FieldTrip] fieldtrip Digest, Vol 16, Issue 25
In-Reply-To: <mailman.142.1332174700.1184.fieldtrip@donders.ru.nl>
References: <mailman.142.1332174700.1184.fieldtrip@donders.ru.nl>
Message-ID: <CAJT2k__WBFwXyOujLbn-vm6OGLmrMEWOHqy4BpYE5xUEwp=+eg@mail.gmail.com>

Hi Giulia,

The data certainly do look a bit weird to me, and as Enzo suggests
specifying 32 or 16 bits may help. Also, have you tried reading the data
using ft_preprocessing()<http://fieldtrip.fcdonders.nl/reference/ft_preprocessing>rather
than ft_read_data()? In my experience the high-level function
(ft_preprocessing) is easier to work with and handles a lot of the
complicated stuff for you, so unless you have a special reason to need to
read your data with the low-level functions then you might have more luck
just using ft_preprocessing.

Best,
Steve Politzer-Ahles

Message: 5
> Date: Mon, 19 Mar 2012 13:32:34 -0400
> From: Enzo Brunetti <enzo.brunetti at gmail.com>
> To: Giulia Rizza <giulia.rizza at tiscali.it>,     Email discussion list for
>        the FieldTrip project <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] Neuroscan .cnt files
> Message-ID: <2CD6708A-A08A-4AF0-92BB-B78029DF2B76 at gmail.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Giulia,
> I could not see your dropbox link showing the plot, but a known reported
> problem with importing .cnt neuroscan files is that the file header does
> not specify the actual precision of your data (typically 32 bits with new
> neuroscan systems, 16 bits previously). If you are importing 32 bits data
> without explicitly defining it previously, you can obtain the type of
> signals you are talking about (the default importing option is '16bits').
> If this is the case, you must to specify this in the cfg input structure of
> the reader function, as:
>
> cfg.headerformat         =  'ns_cnt32';
> cfg.dataformat              =  'ns_cnt32';
> cfg.eventformat            =  'ns_cnt32';
>
> in addition to the other specific fields of the structure.
>
> Also, you can visit this link:
> http://fieldtrip.fcdonders.nl/faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_thisfor more information.
>
> I hope this could help you.
> Best
>
> Dr. Enzo Brunetti F.
> ---------------------------
> Institute of Biomedical Sciences
> Faculty of Medicine
> University of Chile
>
>
> On Mar 19, 2012, at 11:25 AM, Giulia Rizza wrote:
>
> > Dear Fieldtrippers,
> > hi to everyone and thanks in advance for your time.
> > I'm not
> > an expert and I'd like to share with you a problem I found in reading
> cnt files
> > acquired with Neuroscan.
> >
> > I read the data with ft_read_data function and I find
> > the attached link Plot1, for instance the first channel. It seems that
> the
> > signal is forced to pass per zero every two samples, so I tried to read
> them
> > excluding the even samples and I find the result in Plot2, while
> excluding the
> > odd values I find the result in Plot3.
> >
> > http://dl.dropbox.com/u/28258961/Plot01.
> > rar
> >
> > Unfortunately there are still some problems since the maximum value that
> > can be represented (about 900) is smaller than some values in the data
> and the
> > result is that I find a sharp change of sign. How can I fix it?
> >
> > Thanks to
> > anyone who can help me
> >
> > Giulia
> >
> >
> > E' nata indoona: chiama, videochiama e messaggia Gratis. Scarica indoona
> per iPhone, Android e PC: http://www.indoona.com/
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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>
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From yuvharpaz at gmail.com  Mon Mar 19 20:49:31 2012
From: yuvharpaz at gmail.com (Yuval Harpaz)
Date: Mon, 19 Mar 2012 21:49:31 +0200
Subject: [FieldTrip] rejectcomponent after ica for 20 comps only
In-Reply-To: <CAHeOcrv=saYUviSjchVn-mdnv53Y4Ky37LsG-hit+E=2CLSy2g@mail.gmail.com>
References: <CAGQZS_kvLUWndQijop+pjEwj0r2=k=-Efp+WLRs1VzhuMVj2bQ@mail.gmail.com>
	<CAHeOcrv=saYUviSjchVn-mdnv53Y4Ky37LsG-hit+E=2CLSy2g@mail.gmail.com>
Message-ID: <CAGQZS_=SbL+U2YumY0HyFc4OpJ2j81199Y_8ke8TddoFoC-29w@mail.gmail.com>

thanks a lot. it clears the matter
Yuval

On 19 March 2012 18:59, Gio Piantoni <g.piantoni at nin.knaw.nl> wrote:

> Hi Yuval,
>
> If you pass data as third argument, the function will substract the
> weights of rejected component(s) from your data. So, your data will
> have the initial rank minus the number of rejected component. No
> reconstruction occurs.
>
> See line 121 of ft_rejectcomponent or try the code below.
>
> nelec = 50;
> fs = 1000;
> ntrl = 5;
>
> data = [];
> data.label = cellfun(@(x)['E' num2str(x)], num2cell(1:nelec), 'uni', 0);
> data.fsample = fs;
> for i =1:ntrl
>  data.trial{i} = randn(nelec, fs);
>  data.time{i} = 1/fs:1/fs:1;
> end
>
> cfg = [];
> cfg.method = 'fastica';
> cfg.numcomponent = 10;
> comp = ft_componentanalysis(cfg, data);
>
> cfg = [];
> cfg.component = 2;
> data2 = ft_rejectcomponent(cfg, comp, data); % subtract comp from data
> data3 = ft_rejectcomponent(cfg, comp); % reconstruct from comp
>
> rank(data.trial{1}) % full rank
> rank(data2.trial{1}) % full rank - 1 rejected
> rank(data3.trial{1})  % rank of 'comp' - 1 rejected
>
> On Mon, Mar 19, 2012 at 16:46, Yuval Harpaz <yuvharpaz at gmail.com> wrote:
> > Dear ft_emaillist
> >
> > I want to reject components obtained with with fastica.
> >
> > if I only run ft_componentanalysis with cfg.numcomponent=20, creating
> only
> > 20 components, can I still reject a specific component by
> > ft_rejectcomponent(cfg,comp,data) or will it only reconstruct the date
> based
> > on the 20 components I calculated?
> >
> > thanks,Yuval
> >
> > --
> >
> > Y.Harpaz
> >
> > a link to the BIU MEG lab:
> > http://faculty.biu.ac.il/~goldsa/index.html
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 

Y.Harpaz

a link to the BIU MEG lab:
http://faculty.biu.ac.il/~goldsa/index.html
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From mark.noordenbos at gmail.com  Tue Mar 20 09:37:51 2012
From: mark.noordenbos at gmail.com (Mark Noordenbos)
Date: Tue, 20 Mar 2012 09:37:51 +0100
Subject: [FieldTrip] Combine Grand Average
Message-ID: <CAJSb8nPtg+d6dFPtWLgNXmasLFXHkOFeHEhrw7FNABMA1pE_fg@mail.gmail.com>

Hi Jörn, Steve and Eelke,

Thanks for the suggestions for combining grand averages.
Unfortunately, ft_appendtimelock did not work for the grand averages.

Probably, the only proper way to this is to make completely new grand
averages with all conditions included, instead of a grand average for each
condition and combine them later.

To quickly view the outcome of combining the grand averages of 2 conditions
a calculated the mean by hand:

datatot.individual = (data1.individual + data2.individual)/2;

Kind regards,
Mark


-- 
Mark Noordenbos, MSc

Radboud University Nijmegen
Behavioural Science Institute

P.O. Box 9104, Room A05.36
6500 HE Nijmegen
The Netherlands

Email: m.noordenbos at bsi.ru.nl
Telephone: +31 24 3612070
Fax:          +31 24 3616211

http://www.ru.nl
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From batrod at gmail.com  Tue Mar 20 18:53:03 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Tue, 20 Mar 2012 12:53:03 -0500
Subject: [FieldTrip] Clusterplot scale?
Message-ID: <CAPy7a9CGu275wjBvMJiUsnaHYSpTpWOwMbhrTovMdvGNXGb26A@mail.gmail.com>

dear Fieldtrippers,

Im using the Montecarlo randomization method with cluster correction to
compare 2 conditions with a t-test.
When i plot the significant cluster with the ft_clusterplot function, it
creates a topoplot with highlighted electrodes.
I was just wondering what values were represented in the topoplot, as it
seems to be the difference between my two conditions, but with a higher
scale.

Rodolphe.
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From jm.horschig at donders.ru.nl  Wed Mar 21 09:45:11 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 21 Mar 2012 09:45:11 +0100
Subject: [FieldTrip] Clusterplot scale?
In-Reply-To: <CAPy7a9CGu275wjBvMJiUsnaHYSpTpWOwMbhrTovMdvGNXGb26A@mail.gmail.com>
References: <CAPy7a9CGu275wjBvMJiUsnaHYSpTpWOwMbhrTovMdvGNXGb26A@mail.gmail.com>
Message-ID: <4F699517.6050407@donders.ru.nl>

Dear Rodolphe,

By default, the corresponding values do not reflect power differences 
directly, but the test-statistic, in your case t-values (that's the 
/stat.stat/ field)
You can see on what scale the plot is by typing /colorbar /in the 
command window or by pressing the colorbar button in the icon bar of the 
matlab figure.

Best,
Jörn


On 3/20/2012 6:53 PM, Rodolphe Nenert wrote:
> dear Fieldtrippers,
>
> Im using the Montecarlo randomization method with cluster correction 
> to compare 2 conditions with a t-test.
> When i plot the significant cluster with the ft_clusterplot function, 
> it creates a topoplot with highlighted electrodes.
> I was just wondering what values were represented in the topoplot, as 
> it seems to be the difference between my two conditions, but with a 
> higher scale.
>
> Rodolphe.
>
>
> _______________________________________________
> 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

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 m.leszczynski.m at googlemail.com  Wed Mar 21 10:51:14 2012
From: m.leszczynski.m at googlemail.com (Marcin)
Date: Wed, 21 Mar 2012 10:51:14 +0100
Subject: [FieldTrip] statfun_depsamplesregrT
Message-ID: <CAAVVtzDY5stRD-XE2Pa5TjrO1L8AJXXSZToy7XhA72hK22bu+w@mail.gmail.com>

Dear Fieldtripers,

Could anyone explain me what is being calculated with the
statfun_depsamplesregrT function, please.

David Groppe (thank you David) suggested in a previous thread on the list
that I might calculate permutation test based on rank correlation to
account for monotonic relationships within the permutation framework. I was
wondering if this is the kind of test that statfun_depsamplesregrT function
calculates.
http://mailman.science.ru.nl/pipermail/fieldtrip/2011-December/004578.html

Best,
Marcin
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From ole.jensen at donders.ru.nl  Wed Mar 21 15:28:58 2012
From: ole.jensen at donders.ru.nl (Ole Jensen)
Date: Wed, 21 Mar 2012 15:28:58 +0100
Subject: [FieldTrip] data analysis competition / Biomag2012
Message-ID: <4F69E5AA.5010507@donders.ru.nl>

Dear colleagues,

We would like to announce (2nd announcement) the data analysis 
competition at the Biomag2012 meeting (Paris, Aug 26-30). Please 
encourage students and postdocs to participate. There were some 
technical glitches in the data after the 1st announcement. They are now 
corrected.

With best wishes,

Ole Jensen and Ali Bahramisharif


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

*Biomag2012 analysis competition - distributed representations
*
http://www.biomag2012.org/content/data-analysis-competition

The decoding of mental states and neuronal representations from brain 
imaging data is a research field in rapid development (Spiers HJ, 
Maguire EA. Decoding human brain activity during real-world experiences. 
Trends Cogn Sci. 2007 ; Haynes JD, Rees G. Decoding mental states from 
brain activity in humans. Nat Rev Neurosci. 2006). These decoding 
approaches have a great potential in MEG research where data are 
recorded from hundreds of sensors with a millisecond time resolution. In 
particular cognitive neuroscience could benefit from further development 
of decoding approaches in order to identify representational specific 
brain activity.
The aim of the competition is to:

  * Promote the development and application of new multivariate analysis
    techniques for decoding of brain activity
  * Make the audience aware of novel approaches
  * Elucidate the pros and cons of the different techniques
      o Which assumptions are behind a given approach?
      o What are the limitations?
  * Attract signal-processing experts from outside the MEG field
  * Encourage a discussion on the cognitive insight the techniques can
    bring about

The deadline for submitting results is Aug 17, 2012.

-- 
Ole Jensen
http://www.neuosc.com

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From vitoria.piai at gmail.com  Wed Mar 21 16:17:24 2012
From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=)
Date: Wed, 21 Mar 2012 16:17:24 +0100
Subject: [FieldTrip] a function for averaging over freq x time x channel
Message-ID: <4F69F104.1000406@gmail.com>

Hi there,

Is there an easy way for averaging over frequency x time x channel if my 
data is the output of ft_freqanalysis with keeptrials = 'no' (so 
chan_freq_time)?

ft_redefinetrial requires rpt to be present, so that's not an option. 
ft_selectdata_old is also complaining about the wrong structure for the 
input data and ft_selectdata_new is outputting exactly the same 
chan_freq_time as the input (I'm using the most recent FT version at the 
DCCN).

I may be missing some really obvious function, but so far I've been 
doing it in the hard way by hand.

Any suggestions are very much appreciated.

Thanks, Vitoria


From jm.horschig at donders.ru.nl  Wed Mar 21 16:21:55 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 21 Mar 2012 16:21:55 +0100
Subject: [FieldTrip] a function for averaging over freq x time x channel
In-Reply-To: <4F69F104.1000406@gmail.com>
References: <4F69F104.1000406@gmail.com>
Message-ID: <4F69F213.5040609@donders.ru.nl>

Hi Vitoria,

try ft_freqdescriptives

Best,
Jörn

On 3/21/2012 4:17 PM, Vitória Magalhães Piai wrote:
> Hi there,
>
> Is there an easy way for averaging over frequency x time x channel if 
> my data is the output of ft_freqanalysis with keeptrials = 'no' (so 
> chan_freq_time)?
>
> ft_redefinetrial requires rpt to be present, so that's not an option. 
> ft_selectdata_old is also complaining about the wrong structure for 
> the input data and ft_selectdata_new is outputting exactly the same 
> chan_freq_time as the input (I'm using the most recent FT version at 
> the DCCN).
>
> I may be missing some really obvious function, but so far I've been 
> doing it in the hard way by hand.
>
> Any suggestions are very much appreciated.
>
> Thanks, Vitoria
> _______________________________________________
> 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

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 jm.horschig at donders.ru.nl  Wed Mar 21 16:32:42 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 21 Mar 2012 16:32:42 +0100
Subject: [FieldTrip] a function for averaging over freq x time x channel
In-Reply-To: <4F69F213.5040609@donders.ru.nl>
References: <4F69F104.1000406@gmail.com> <4F69F213.5040609@donders.ru.nl>
Message-ID: <4F69F49A.5080005@donders.ru.nl>

Hey again,

sorry, it doesn't work with ft_freqdescriptives, then you have to do it 
manually:
squeeze(nanmean(nanmean(nanmean(data.powspctrm, 1), 2), 3))

Best,
Jörn

On 3/21/2012 4:21 PM, "Jörn M. Horschig" wrote:
> Hi Vitoria,
>
> try ft_freqdescriptives
>
> Best,
> Jörn
>
> On 3/21/2012 4:17 PM, Vitória Magalhães Piai wrote:
>> Hi there,
>>
>> Is there an easy way for averaging over frequency x time x channel if 
>> my data is the output of ft_freqanalysis with keeptrials = 'no' (so 
>> chan_freq_time)?
>>
>> ft_redefinetrial requires rpt to be present, so that's not an option. 
>> ft_selectdata_old is also complaining about the wrong structure for 
>> the input data and ft_selectdata_new is outputting exactly the same 
>> chan_freq_time as the input (I'm using the most recent FT version at 
>> the DCCN).
>>
>> I may be missing some really obvious function, but so far I've been 
>> doing it in the hard way by hand.
>>
>> Any suggestions are very much appreciated.
>>
>> Thanks, Vitoria
>> _______________________________________________
>> 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

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 Jan.Hirschmann at med.uni-duesseldorf.de  Wed Mar 21 16:36:39 2012
From: Jan.Hirschmann at med.uni-duesseldorf.de (Jan.Hirschmann at med.uni-duesseldorf.de)
Date: Wed, 21 Mar 2012 16:36:39 +0100
Subject: [FieldTrip] error ft_read_mri
Message-ID: <72E993C35FB11743B79FF9286E5B6D8B03ADFF9E@Mail2-UKD.VMED.UKD>

Dear fieldtrip programmers,

 

with the latest version of fieldtrip I am experiencing problems reading
MRs:

 

a=ft_read_mri('/data/apps/spm/spm8/canonical/avg152T1.nii')

Undefined function or variable "out".

 

Error in fixname (line 55)

while(out(1) == '_'),   out = out(2:end); end;   % remove all underscore
at the begin of the

string

 

Error in ft_hastoolbox (line 366)

  previous.(fixname(toolbox)) = status;

 

Error in ft_read_mri (line 45)

hasmri  = ft_hastoolbox('mri');     % from Darren Weber, see
http://eeg.sourceforge.net/

 

Thanks and all the best,

Jan

--

Jan Hirschmann

MSc. Neuroscience

Institute of Clinical Neuroscience and Medical Psychology

Heinrich Heine University Duesseldorf

Universitaetsstr.  1
40225  Duesseldorf

Tel: 0049 - (0)211 - 81 - 18415

 

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From max-philipp.stenner at med.ovgu.de  Wed Mar 21 19:53:28 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Wed, 21 Mar 2012 18:53:28 +0000
Subject: [FieldTrip] (no subject)
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830CB542@ESEN4.imed.uni-magdeburg.de>

Dear fieldtrip users/developers, 

I'd like to perform time-frequency analysis after computing the planar gradiometer representation of multi-session data and I am wondering whether the order in which the analysis steps are performed matters. The sequence I have used is

ft_megplanar
concatenate data across sessions
ft_average_sens, add the averaged (planar) sensor information to the datapool
ft_freqanalysis
ft_combineplanar

Does that make sense?

Thanks very much, 
best
Max
fieldtrip version: fieldtrip-20111130 on a Windows7 PC


From max-philipp.stenner at med.ovgu.de  Wed Mar 21 23:16:55 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Wed, 21 Mar 2012 22:16:55 +0000
Subject: [FieldTrip] (no subject)
In-Reply-To: <FBEFFA1F493D8944969D2F5AE78E58830CB542@ESEN4.imed.uni-magdeburg.de>
References: <FBEFFA1F493D8944969D2F5AE78E58830CB542@ESEN4.imed.uni-magdeburg.de>
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830CB553@ESEN4.imed.uni-magdeburg.de>

...just to specify the question: I am wondering whether ft_average_sens of data in planar sensor gradiometer representation is problematic

________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]&quot; im Auftrag von &quot;Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de]
Gesendet: Mittwoch, 21. März 2012 19:53
Bis: Email discussion list for the FieldTrip project
Betreff: [FieldTrip] (no subject)

Dear fieldtrip users/developers,

I'd like to perform time-frequency analysis after computing the planar gradiometer representation of multi-session data and I am wondering whether the order in which the analysis steps are performed matters. The sequence I have used is

ft_megplanar
concatenate data across sessions
ft_average_sens, add the averaged (planar) sensor information to the datapool
ft_freqanalysis
ft_combineplanar

Does that make sense?

Thanks very much,
best
Max
fieldtrip version: fieldtrip-20111130 on a Windows7 PC
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From max-philipp.stenner at med.ovgu.de  Wed Mar 21 23:41:21 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Wed, 21 Mar 2012 22:41:21 +0000
Subject: [FieldTrip] (no subject)
In-Reply-To: <FBEFFA1F493D8944969D2F5AE78E58830CB553@ESEN4.imed.uni-magdeburg.de>
References: <FBEFFA1F493D8944969D2F5AE78E58830CB542@ESEN4.imed.uni-magdeburg.de>
	<FBEFFA1F493D8944969D2F5AE78E58830CB553@ESEN4.imed.uni-magdeburg.de>
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830CB561@ESEN4.imed.uni-magdeburg.de>

(i.e. before applying ft_combineplanar)
________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]&quot; im Auftrag von &quot;Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de]
Gesendet: Mittwoch, 21. März 2012 23:16
Bis: Email discussion list for the FieldTrip project
Betreff: Re: [FieldTrip] (no subject)

...just to specify the question: I am wondering whether ft_average_sens of data in planar sensor gradiometer representation is problematic

________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]&quot; im Auftrag von &quot;Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de]
Gesendet: Mittwoch, 21. März 2012 19:53
Bis: Email discussion list for the FieldTrip project
Betreff: [FieldTrip] (no subject)

Dear fieldtrip users/developers,

I'd like to perform time-frequency analysis after computing the planar gradiometer representation of multi-session data and I am wondering whether the order in which the analysis steps are performed matters. The sequence I have used is

ft_megplanar
concatenate data across sessions
ft_average_sens, add the averaged (planar) sensor information to the datapool
ft_freqanalysis
ft_combineplanar

Does that make sense?

Thanks very much,
best
Max
fieldtrip version: fieldtrip-20111130 on a Windows7 PC
_______________________________________________
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 bibi.raquel at gmail.com  Thu Mar 22 04:34:36 2012
From: bibi.raquel at gmail.com (Raquel Bibi)
Date: Wed, 21 Mar 2012 23:34:36 -0400
Subject: [FieldTrip] Combine Grand Average
In-Reply-To: <CAJSb8nPtg+d6dFPtWLgNXmasLFXHkOFeHEhrw7FNABMA1pE_fg@mail.gmail.com>
References: <CAJSb8nPtg+d6dFPtWLgNXmasLFXHkOFeHEhrw7FNABMA1pE_fg@mail.gmail.com>
Message-ID: <CA+Gwb028WOLjw9k9c-c3r6NfovKTG=ukuxroRG5mQPoQ+6XasA@mail.gmail.com>

Mark,
Can you calculate the weighted mean by hand?
(Data1.individual*no_of_trials(data1) +
Data2.individual*no_of_trials(data2)) / (no_trials(data1) +
no_of_trials(data2))

If so, no need to redo!



On Tue, Mar 20, 2012 at 4:37 AM, Mark Noordenbos
<mark.noordenbos at gmail.com>wrote:

> Hi Jörn, Steve and Eelke,
>
> Thanks for the suggestions for combining grand averages.
> Unfortunately, ft_appendtimelock did not work for the grand averages.
>
> Probably, the only proper way to this is to make completely new grand
> averages with all conditions included, instead of a grand average for each
> condition and combine them later.
>
> To quickly view the outcome of combining the grand averages of 2
> conditions a calculated the mean by hand:
>
> datatot.individual = (data1.individual + data2.individual)/2;
>
> Kind regards,
>
> Mark
>
>
> --
> Mark Noordenbos, MSc
>
> Radboud University Nijmegen
> Behavioural Science Institute
>
> P.O. Box 9104, Room A05.36
> 6500 HE Nijmegen
> The Netherlands
>
> Email: m.noordenbos at bsi.ru.nl
> Telephone: +31 24 3612070
> Fax:          +31 24 3616211
>
> http://www.ru.nl
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From jan.schoffelen at donders.ru.nl  Thu Mar 22 09:10:57 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 22 Mar 2012 09:10:57 +0100
Subject: [FieldTrip] error ft_read_mri
In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B03ADFF9E@Mail2-UKD.VMED.UKD>
References: <72E993C35FB11743B79FF9286E5B6D8B03ADFF9E@Mail2-UKD.VMED.UKD>
Message-ID: <F5816B77-88CB-4AA2-9B64-49E9BB83D3CB@donders.ru.nl>

Hi Jan

I cannot reproduce your problem. I'd check the following and try again:
-ensure that you have the latest version of FieldTrip
-ensure that there are no pointers to any spm directory on your matlab-path (apart perhaps from those that are distributed within fieldtrip, i.e. fieldtrip/external/spmXXX)

Cheers,

Jan

On Mar 21, 2012, at 4:36 PM, <Jan.Hirschmann at med.uni-duesseldorf.de> <Jan.Hirschmann at med.uni-duesseldorf.de> wrote:

> Dear fieldtrip programmers,
>  
> with the latest version of fieldtrip I am experiencing problems reading MRs:
>  
> a=ft_read_mri('/data/apps/spm/spm8/canonical/avg152T1.nii')
> Undefined function or variable "out".
>  
> Error in fixname (line 55)
> while(out(1) == '_'),   out = out(2:end); end;   % remove all underscore at the begin of the
> string
>  
> Error in ft_hastoolbox (line 366)
>   previous.(fixname(toolbox)) = status;
>  
> Error in ft_read_mri (line 45)
> hasmri  = ft_hastoolbox('mri');     % from Darren Weber, see http://eeg.sourceforge.net/
>  
> Thanks and all the best,
> Jan
> --
> Jan Hirschmann
> MSc. Neuroscience
> Institute of Clinical Neuroscience and Medical Psychology
> Heinrich Heine University Duesseldorf
> Universitaetsstr.  1
> 40225  Duesseldorf
> Tel: 0049 - (0)211 - 81 - 18415
>  
> _______________________________________________
> 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

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From marco.dahmane at gmail.com  Thu Mar 22 13:13:18 2012
From: marco.dahmane at gmail.com (Marco Dahmane)
Date: Thu, 22 Mar 2012 12:13:18 +0000
Subject: [FieldTrip] Trial-dependant baseline correction
Message-ID: <CAPPdCy__G9a7BL4HJsEbG4eVzYpA5k=pqxyXH5Tm-L=-P3uVrQ@mail.gmail.com>

Dear fellow Fieldtrippers,

I was having a small problem regarding baseline correction in FT.

My situation is rather simple : I have two types of trials, trials A and
trials B. Triggers A are always preceding triggers B, but the delay between
the two is NOT fixed.

I use triggers B to define my trials (for instance -0.5s to +0.5s).
Very straightforward.

However, I would like to use triggers A to define my baseline window. Say I
would like to use the one second preceding each trigger A as the baseline
for the following trial.

Until now the way I was going about it was rather tedious :
a) ft_preprocessing data as one big, long trial (filtering)
b) ft_definetrial to define long trials as starting from trigger A (origin)
to following trigger B (end)
*c) ft_preprocessing to baseline correct*
d) ft_redefinetrial with variable cfg.offset to set origin back to trigger B
e) ft_redefinetrial to take only window [ -0.5s ; +0.5s]

But I'm wondering whether that's not an overkill (especially since the
delay between triggers A and B can be quite long and make the preprocessing
really slow on my old machine).

Any advice is appreciated,

Best regards,
Marco
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From lavado at gmail.com  Thu Mar 22 15:24:42 2012
From: lavado at gmail.com (Ion Lavado)
Date: Thu, 22 Mar 2012 15:24:42 +0100
Subject: [FieldTrip] Sourceanalysis understanding problem
Message-ID: <CAMLwyK6Gi7d_EGxvsCfFGeYM_Pz2HQV8t_2sx8iEMRw9aLxSkA@mail.gmail.com>

Hello, I would like to ask you what does the "cfg.frequency" means in
ft_sourceanalysis. I want to plot a frequency range for example [14 30], do
i have to use cfg.frequency=22? why? It would be perfect if someone could
explain how to make the freqanalysis and the sourceanalysis for a frequency
range for example this one[14 30].

This is the code for my frequency analysis:
cfg = [];
cfg.method    = 'mtmfft';
cfg.output    = 'powandcsd';
cfg.channel   = {'MEG'};
cfg.tapsmofrq = 4;
cfg.foilim    = [14 30];
freq_post = ft_freqanalysis(cfg, words_post);

The i do the sourceanalysis:
cfg              = [];
cfg.frequency    = 22;
cfg.lambda=0;
cfg.method       = 'dics';
cfg.coordsys       = 'neuromag';
cfg.projectnoise = 'yes';
cfg.grad            = freq_pre.grad;
cfg.channel   = {'MEG'};
cfg.grid         = grid;
cfg.reducerank      = 2;
cfg.vol          = vol02;
vol02=ft_convert_units(vol02,'cm');
source_post11= ft_sourceanalysis(cfg, freq_post);


What i get i see that depends only in the cfg.frequency=22, if i change the
previous freqanalysis and use the 22 for the cfg.frequency i get the same
result. Hope someone can help me.

Thanks in advance.

Best,

Ion
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From lavado at gmail.com  Thu Mar 22 17:13:34 2012
From: lavado at gmail.com (Ion Lavado)
Date: Thu, 22 Mar 2012 17:13:34 +0100
Subject: [FieldTrip] is beamforming result correct?
Message-ID: <CAMLwyK4gzzrPbW3qGEfSs6sMz-NwxtsuXRE1J6DURM_Zg7pFbg@mail.gmail.com>

I think the result i got doing the beamforming source reconstruction is not
good as there is lot of activation at the bottom where the cerebellum is.
Can anyone confirm me it is incorrect? Possible mistake?

This is the code i used for the headmodel:

mri = ft_read_mri('/home/ilavado/ilavado/mutiT1/T1_02.mgz');
cfg = [];
cfg.interactive    = 'yes';
cfg.coordsys    = 'neuromag';
mri_real           = ft_volumerealign(cfg,mri);
[segmentedmri]   = ft_volumesegment(cfg, mri_real)
cfg = [];
cfg.sourceunits='cm';
cfg.coordsys       = 'neuromag';
vol02 = ft_prepare_singleshell(cfg, segmentedmri);
ft_plot_vol(vol02);
mri_real = rmfield(mri_real, 'pnt');

sourceDiff = source_post;
sourceDiff.avg.pow = (source_post.avg.pow - source_pre.avg.pow) ./
source_pre.avg.pow;
cfg            = []
cfg.downsample = 2;
sourceDiffInt  = ft_sourceinterpolate(cfg, sourceDiff , mri_real);
cfg = [];
cfg.coordsys      = 'ctf';
cfg.nonlinear     = 'no';
sourceDiffIntNorm = ft_volumenormalise(cfg, sourceDiffInt);

Thank you very much.

Best,

Ion
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From Jarmo.Kontinen at ruhr-uni-bochum.de  Thu Mar 22 17:14:46 2012
From: Jarmo.Kontinen at ruhr-uni-bochum.de (Jarmo Kontinen)
Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
Message-ID: <permail-201203221614466509e8c700002494-Jarmo.Kontinen@msgid.mail.ruhr-uni-bochum.de>

Dear all,
I am trying to import EEG subject averages into Field Trip. The files are
exported with the Brainvision Analyzer in binary form
:subject10_konPro2002.dat and subject10_konPro2002.vhdr.
I have a problem with turning the data into the Field Trip data-structure. I
am following instructions given on this forum on one similar post. What I have
tried is the following:

cfg=[];
cfg.trialdef.eventtype='average'
cfg.dataset='subject10_konPro2002.dat'

 cfg=ft_definetrial(cfg);

Warning: no trialfun was specified, using trialfun_general
> In ft_definetrial at 123
evaluating trialfunction 'trialfun_general'
reading the events from 'subject10_konPro2002.vhdr'
??? Error using ==> ft_definetrial at 176
no trials were defined, see FT_DEFINETRIAL for help

I am grateful for all the help.
Thanks,
Jarmo Kontinen


From Don.Rojas at ucdenver.edu  Thu Mar 22 20:22:47 2012
From: Don.Rojas at ucdenver.edu (Rojas, Don)
Date: Thu, 22 Mar 2012 13:22:47 -0600
Subject: [FieldTrip] is beamforming result correct?
In-Reply-To: <CAMLwyK4gzzrPbW3qGEfSs6sMz-NwxtsuXRE1J6DURM_Zg7pFbg@mail.gmail.com>
References: <CAMLwyK4gzzrPbW3qGEfSs6sMz-NwxtsuXRE1J6DURM_Zg7pFbg@mail.gmail.com>
Message-ID: <4C3A9E0C-C8FB-4B28-9563-8A7942C053B7@ucdenver.edu>

Ion,

I do not think we can say definitively if your result is incorrect or not with the information provided. Can you provide a summary of your task, preprocessing and source analysis steps? There are MEG papers using beamformers that reveal cerebellar activity that is task consistent. If you do not have any a priori reason to expect it, however, then perhaps you are correct.

Best,

Don
-----------------------
Don Rojas, Ph.D.
Associate Professor of Psychiatry
U. of Colorado Denver Anschutz Medical Campus
Director, UCD Magnetoencephalography Lab


On Mar 22, 2012, at 10:13 AM, Ion Lavado wrote:

> I think the result i got doing the beamforming source reconstruction is not good as there is lot of activation at the bottom where the cerebellum is. Can anyone confirm me it is incorrect? Possible mistake?
> 
> This is the code i used for the headmodel:
> 
> mri = ft_read_mri('/home/ilavado/ilavado/mutiT1/T1_02.mgz');
> cfg = [];
> cfg.interactive    = 'yes';
> cfg.coordsys    = 'neuromag';
> mri_real           = ft_volumerealign(cfg,mri); 
> [segmentedmri]   = ft_volumesegment(cfg, mri_real)
> cfg = [];
> cfg.sourceunits='cm';
> cfg.coordsys       = 'neuromag';
> vol02 = ft_prepare_singleshell(cfg, segmentedmri);
> ft_plot_vol(vol02);
> mri_real = rmfield(mri_real, 'pnt');
> 
> sourceDiff = source_post;
> sourceDiff.avg.pow = (source_post.avg.pow - source_pre.avg.pow) ./ source_pre.avg.pow;  
> cfg            = []
> cfg.downsample = 2;
> sourceDiffInt  = ft_sourceinterpolate(cfg, sourceDiff , mri_real);
> cfg = [];
> cfg.coordsys      = 'ctf';
> cfg.nonlinear     = 'no';
> sourceDiffIntNorm = ft_volumenormalise(cfg, sourceDiffInt);
> 
> Thank you very much. 
> 
> Best,
> 
> Ion
> <beam_result.jpg>_______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip






From e.maris at psych.ru.nl  Thu Mar 22 21:12:35 2012
From: e.maris at psych.ru.nl (Eric Maris)
Date: Thu, 22 Mar 2012 21:12:35 +0100 (CET)
Subject: [FieldTrip] statfun_depsamplesregrT
In-Reply-To: <CAAVVtzDY5stRD-XE2Pa5TjrO1L8AJXXSZToy7XhA72hK22bu+w@mail.gmail.com>
References: <CAAVVtzDY5stRD-XE2Pa5TjrO1L8AJXXSZToy7XhA72hK22bu+w@mail.gmail.com>
Message-ID: <035401cd0868$20b27640$621762c0$@maris@psych.ru.nl>

Dear Marcin,

 

 

The statfun_depsamplesregrT calculates a T-statistic for regression
coefficients that are calculated within each of the units-of-observation
(typically, participants) obtained by regressing the subject-specific data
(spatiotemporal, spatio-spectral, spatio-spectro-temporal) on some
predictor variable that varies over the different conditions in which this
participant has provided data (e.g., working-memory load, retention
interval, luminance, contrast, etc). If you doubt the assumed linear
relation between predictor variable and biological data, then you could
write your own statfun_depsamplesrankcorr. To use this test statistic for
cluster-based permutation inference, you need a threshold based on some
reference distribution (which can be parametric, but must not be). 

 

To get this statfun_depsamplesrankcorr running, you will probably have to
take a look in the Fieldtrip code to see how the statistics framework is
structured.

 

Best,

 

Eric Maris

 

 

From: Marcin [mailto:m.leszczynski.m at googlemail.com] 
Sent: woensdag 21 maart 2012 10:51
To: Email discussion list for the FieldTrip project
Subject: [FieldTrip] statfun_depsamplesregrT

 

Dear Fieldtripers,

Could anyone explain me what is being calculated with the
statfun_depsamplesregrT function, please.

David Groppe (thank you David) suggested in a previous thread on the list
that I might calculate permutation test based on rank correlation to
account for monotonic relationships within the permutation framework. I
was wondering if this is the kind of test that statfun_depsamplesregrT
function calculates.
http://mailman.science.ru.nl/pipermail/fieldtrip/2011-December/004578.html

Best,
Marcin

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From g.piantoni at nin.knaw.nl  Fri Mar 23 20:35:22 2012
From: g.piantoni at nin.knaw.nl (Gio Piantoni)
Date: Fri, 23 Mar 2012 20:35:22 +0100
Subject: [FieldTrip] Trial-dependant baseline correction
In-Reply-To: <CAPPdCy__G9a7BL4HJsEbG4eVzYpA5k=pqxyXH5Tm-L=-P3uVrQ@mail.gmail.com>
References: <CAPPdCy__G9a7BL4HJsEbG4eVzYpA5k=pqxyXH5Tm-L=-P3uVrQ@mail.gmail.com>
Message-ID: <CAHeOcru5O5O07Re92i3Eexkj++VHmabqqJ1g7_s9Ww0jFiVN0Q@mail.gmail.com>

Hi Marco,

I don't understand very well if the bottleneck is the number of steps
or the memory/time used in preprocessing (a).

I think that the simplest approach is to use:
1) ft_definetrial (as in your (b))
2) ft_preprocessing (read data and apply preproc options)
3) ft_redefinetrial to take the window [-0.5 0.5] and change the
origin (you can do that in one step if you pass cfg.trl with three
columns: [begin_sample end_sample offset] in sample points)

Otherwise, if you're concerned about memory problems, you could do a
ft_definetrial and preprocessing for A events, and the same for B
events. Then, in Matlab, you average A events and subtract the average
from the B trials.

I think preprocessing on your trials should not take too much memory though.

HTH,
Gio

On Thu, Mar 22, 2012 at 13:13, Marco Dahmane <marco.dahmane at gmail.com> wrote:
> Dear fellow Fieldtrippers,
>
> I was having a small problem regarding baseline correction in FT.
>
> My situation is rather simple : I have two types of trials, trials A and
> trials B. Triggers A are always preceding triggers B, but the delay between
> the two is NOT fixed.
>
> I use triggers B to define my trials (for instance -0.5s to +0.5s).
> Very straightforward.
>
> However, I would like to use triggers A to define my baseline window. Say I
> would like to use the one second preceding each trigger A as the baseline
> for the following trial.
>
> Until now the way I was going about it was rather tedious :
> a) ft_preprocessing data as one big, long trial (filtering)
> b) ft_definetrial to define long trials as starting from trigger A (origin)
> to following trigger B (end)
> *c) ft_preprocessing to baseline correct*
> d) ft_redefinetrial with variable cfg.offset to set origin back to trigger B
> e) ft_redefinetrial to take only window [ -0.5s ; +0.5s]
>
> But I'm wondering whether that's not an overkill (especially since the delay
> between triggers A and B can be quite long and make the preprocessing really
> slow on my old machine).
>
> Any advice is appreciated,
>
> Best regards,
> Marco
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From politzerahless at gmail.com  Sun Mar 25 12:11:28 2012
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sun, 25 Mar 2012 12:11:28 +0200
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
Message-ID: <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg@mail.gmail.com>

Hello Jarmo,

I haven't tried importing Brain Vision files into FieldTrip myself, but
based on the code you sent it looks like the problem may be that you're
missing cfg.trialdef.eventvalue (which is used to tell FieldTrip which
triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim . See
the example at
http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials.

If what you are trying to do is import all trials from all triggers in the
file, I think you have to define your own "trialfun" function to do that
(although I haven't tried this myself so I'm not sure).
http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
information.

Best,
Steve Politzer-Ahles
University of Kansas


Message: 1
> Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> Message-ID:
>        <
> permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de
> >
>
> Content-Type: text/plain; charset=us-ascii
>
> Dear all,
> I am trying to import EEG subject averages into Field Trip. The files are
> exported with the Brainvision Analyzer in binary form
> :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> I have a problem with turning the data into the Field Trip data-structure.
> I
> am following instructions given on this forum on one similar post. What I
> have
> tried is the following:
>
> cfg=[];
> cfg.trialdef.eventtype='average'
> cfg.dataset='subject10_konPro2002.dat'
>
>  cfg=ft_definetrial(cfg);
>
> Warning: no trialfun was specified, using trialfun_general
> > In ft_definetrial at 123
> evaluating trialfunction 'trialfun_general'
> reading the events from 'subject10_konPro2002.vhdr'
> ??? Error using ==> ft_definetrial at 176
> no trials were defined, see FT_DEFINETRIAL for help
>
> I am grateful for all the help.
> Thanks,
> Jarmo Kontinen
>
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From fredericroux at hotmail.de  Mon Mar 26 12:23:50 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Mon, 26 Mar 2012 12:23:50 +0200
Subject: [FieldTrip] SPM path and sourceanalysis on template brain
Message-ID: <DUB113-W76F2D058B3132334525D94B7450@phx.gbl>


Dear all,


I am getting the following error message with the fieldtrip-20120105 version,
and wanted to ask if anyone could tell me:

a) how to prevent it
b) what the consequences of ignoring it will be.

Also I wanted to get some feedback on the possibility of
using a template brain for source localization on data for which
MRI data is missing.

I have a recorded MEG data from n = 98 participants but only have
the MRs of 70 of them. Can I use a template MR to perform
source analysis on the missing data sets?

Looking forward to any kind of suggestions.
Have a nice day,

Fred


-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From ivano_triggiani at yahoo.it  Mon Mar 26 14:14:47 2012
From: ivano_triggiani at yahoo.it (Ivano Triggiani)
Date: Mon, 26 Mar 2012 13:14:47 +0100 (BST)
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
In-Reply-To: <mailman.1.1332756017.8892.fieldtrip@donders.ru.nl>
References: <mailman.1.1332756017.8892.fieldtrip@donders.ru.nl>
Message-ID: <1332764087.47250.YahooMailNeo@web132103.mail.ird.yahoo.com>

Dear Jarmo,

Filedtrip needs a definition of segments of interest. For example reading a trigger channel or something else to cut the EEG recording into trials. If I have understood what you want to do is to get an average of general EEG (for example resting state EEG closed eyes). But you have to indicate which average you want to obtain, for example you can tell fieldtrip to divide EEG into epochs of 3 seconds and then to make an average of all of them.
What you wrote is the request of an average, but you are not specifing of what.
Fof example you can write a trial function that provides a trl matrix, i.e.:
0 3 0

3 6 0
6 9 0
9 12 0
12 13 0
...

where first column is the start sample in seconds (you have to multiply it for sample rate), the second column is the end sample and the third is the offset (in this case is always zero), or look at 
http://fieldtrip.fcdonders.nl/tutorial/preprocessing#use_your_own_function_for_trial_selection

best wishes,
Ivano



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




"No man can wear one face to himself 
and another to the multitude,
without finally getting bewildered 
as to which one is true."


Nathaniel Hawthorne


________________________________
 Da: "fieldtrip-request at donders.ru.nl" <fieldtrip-request at donders.ru.nl>
A: fieldtrip at donders.ru.nl 
Inviato: Lunedì 26 Marzo 2012 12:00
Oggetto: fieldtrip Digest, Vol 16, Issue 33
 
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Today's Topics:

   1. Re: Problem with FT_DEFINETRIAL (Stephen Politzer-Ahles)


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

Message: 1
Date: Sun, 25 Mar 2012 12:11:28 +0200
From: Stephen Politzer-Ahles <politzerahless at gmail.com>
To: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL
Message-ID:
    <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello Jarmo,

I haven't tried importing Brain Vision files into FieldTrip myself, but
based on the code you sent it looks like the problem may be that you're
missing cfg.trialdef.eventvalue (which is used to tell FieldTrip which
triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim . See
the example at
http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials.

If what you are trying to do is import all trials from all triggers in the
file, I think you have to define your own "trialfun" function to do that
(although I haven't tried this myself so I'm not sure).
http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
information.

Best,
Steve Politzer-Ahles
University of Kansas


Message: 1
> Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> Message-ID:
>        <
> permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de
> >
>
> Content-Type: text/plain; charset=us-ascii
>
> Dear all,
> I am trying to import EEG subject averages into Field Trip. The files are
> exported with the Brainvision Analyzer in binary form
> :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> I have a problem with turning the data into the Field Trip data-structure.
> I
> am following instructions given on this forum on one similar post. What I
> have
> tried is the following:
>
> cfg=[];
> cfg.trialdef.eventtype='average'
> cfg.dataset='subject10_konPro2002.dat'
>
>  cfg=ft_definetrial(cfg);
>
> Warning: no trialfun was specified, using trialfun_general
> > In ft_definetrial at 123
> evaluating trialfunction 'trialfun_general'
> reading the events from 'subject10_konPro2002.vhdr'
> ??? Error using ==> ft_definetrial at 176
> no trials were defined, see FT_DEFINETRIAL for help
>
> I am grateful for all the help.
> Thanks,
> Jarmo Kontinen
>
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------------------------------

_______________________________________________
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End of fieldtrip Digest, Vol 16, Issue 33
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From fredericroux at hotmail.de  Mon Mar 26 14:47:22 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Mon, 26 Mar 2012 14:47:22 +0200
Subject: [FieldTrip] beamforming with rank deficient covariance matrix
Message-ID: <DUB113-W8242FDFA7507E17608A292B7450@phx.gbl>



Dear all,

I have a question related to the rank of the covariance matrix
used for the beamformer.

I preprocessed my data using ICA to reject EOG and ECG component (typically
between 2-4 components). This however, leads to a reduction in the rank
of the covariance matrix and I get a warning using ft_sourceanalysis
saying that my covariance matrix is rank deficient because rank(COV) < Nchannels.

I would like to know, how much of a problem and how serious this can be.

The way I understand things, this should only cause trouble if the number
of active sources exceeds the number of linearly independent rows of the covariance matrix?
Is this assumption correct? 

Is there some step in the ft_sourceanalyis pipeline that assumes that the number of
sources is equal to the number of channels, and that could bias the computation
of the beamformer? I mean in that case I would have more sources than channels
and thus the beamformer would fail.

Would be great if someone could help me to figure this out.

Cheers,
Fred




-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From max-philipp.stenner at med.ovgu.de  Mon Mar 26 14:51:08 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Mon, 26 Mar 2012 12:51:08 +0000
Subject: [FieldTrip] ft_sourceanalysis
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830CB840@ESEN4.imed.uni-magdeburg.de>

Dear fieldtrip developers and users, 

I am computing single trial LCMV beamforming moments with ft_sourceanalysis and cfg.rawtrial = 'yes'. I chose cfg.rawtrial because my fieldtrip version (fieldtrip-lite-20111130) reports a bug when using cfg.singletrial.

Am I right that the single-trial covariance matrices will not affect the moments when using precomputed filters (precomputed on the basis of the covariance matrices from "keeptrial = no" timelockdata across all experimental conditions) on "keeptrial = yes" - timelock data (sorted according to conditions) with cfg.rawtrial = 'yes'?
(I am not interested in power (which is changed to NaN by lcmv_beamforming anyways) or noise).

Thanks very much 
Max

fieldtrip-lite-20111130 on a Windows7 PC


From Jarmo.Kontinen at ruhr-uni-bochum.de  Mon Mar 26 15:09:23 2012
From: Jarmo.Kontinen at ruhr-uni-bochum.de (Jarmo Kontinen)
Date: Mon, 26 Mar 2012 15:09:23 +0200 (CEST)
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
In-Reply-To: <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg@mail.gmail.com>
Message-ID: <permail-201203261309236509e8c70000654b-Jarmo.Kontinen@msgid.mail.ruhr-uni-bochum.de>


Dear Stephen,
Thanks for your reply. I  have added the  missing field you sugegsted, but FT
still gives the same error-message.

Maybe I was also unclear what I want to do in the first place. The data we
have is already preprocessed ( filtered, segmented etc.) with the Analyzer.
Also, we have averaged the ERP's for each subject and each experimental
condition over all the trials. I would like to import these averaged ERP's
into FT and do some statisitics on the data. The problem is that I do not know
how to get required data-structure to use the FT-functions.

Best,
Jarmo


Stephen Politzer-Ahles schrieb am 2012-03-25:
> Hello Jarmo,

> I haven't tried importing Brain Vision files into FieldTrip myself,
> but
> based on the code you sent it looks like the problem may be that
> you're
> missing cfg.trialdef.eventvalue (which is used to tell FieldTrip
> which
> triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim
> . See
> the example at
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials.

> If what you are trying to do is import all trials from all triggers
> in the
> file, I think you have to define your own "trialfun" function to do
> that
> (although I haven't tried this myself so I'm not sure).
> http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
> information.

> Best,
> Steve Politzer-Ahles
> University of Kansas


> Message: 1
> > Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> > From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> > To: <fieldtrip at donders.ru.nl>
> > Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> > Message-ID:
> >        <
> > permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de


> > Content-Type: text/plain; charset=us-ascii

> > Dear all,
> > I am trying to import EEG subject averages into Field Trip. The
> > files are
> > exported with the Brainvision Analyzer in binary form
> > :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> > I have a problem with turning the data into the Field Trip
> > data-structure.
> > I
> > am following instructions given on this forum on one similar post.
> > What I
> > have
> > tried is the following:

> > cfg=[];
> > cfg.trialdef.eventtype='average'
> > cfg.dataset='subject10_konPro2002.dat'

> >  cfg=ft_definetrial(cfg);

> > Warning: no trialfun was specified, using trialfun_general
> > > In ft_definetrial at 123
> > evaluating trialfunction 'trialfun_general'
> > reading the events from 'subject10_konPro2002.vhdr'
> > ??? Error using ==> ft_definetrial at 176
> > no trials were defined, see FT_DEFINETRIAL for help

> > I am grateful for all the help.
> > Thanks,
> > Jarmo Kontinen



From Maria.Pefkou at unige.ch  Mon Mar 26 18:01:00 2012
From: Maria.Pefkou at unige.ch (Maria Pefkou)
Date: Mon, 26 Mar 2012 18:01:00 +0200
Subject: [FieldTrip] Create BEM model for EEG source localisation
Message-ID: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>

Dear FieldTrip users,

I started using the toolbox fairly recently to analyse EEG data and I have
huge trouble making a BEM model, which I need for source localisation.
Following the online tutorial, I processed my subjects' individual
structural MRIs in FreeSurfer and MNE and managed to prepare the
triangulated mesh. However, my problem is the volume conduction model. I
can get a singleshell one, using the ft_prepare_singleshell function, but
as far as I understand it is excusively used for MEG data. I came to this
conclusion because when I try to compute the forward model, given that I
provide information about the electrodes position, I always get the
following error:

"unsupported volume conductor model for EEG".
I guess this is because the vol.type is 'nolte' and there is no such case
for EEG data, at least not in the ft_prepare_vol_sens.m function, which is
automatically called.

I have tried to prepare a BEM model using the ft_prepare_headmodel function
with cfg.method='bemcp' or cfg.method='dipoli' but I was unsuccessful.
The problem is that, after having tried various functions/options, I lost
the general picture and I'm running in circles... The question is: I have a
segmented mri, how can I get a BEM model out of this? I must be missing a
fundamental part of the procedure but I can't quite find out what it is.
Any suggestions/help would be very much appreciated.

Thank you in advance,
Maria Pefkou

------------------------------------------
Research Assistant
Functional Brain Mapping Lab
University of Geneva
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From Maria.Pefkou at unige.ch  Mon Mar 26 18:05:36 2012
From: Maria.Pefkou at unige.ch (Maria Pefkou)
Date: Mon, 26 Mar 2012 18:05:36 +0200
Subject: [FieldTrip] Create BEM model for EEG source localisation
In-Reply-To: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>
References: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>
Message-ID: <CAJ5HwaumWvg4CT5-3MPEO5=H=YWK5kkU-wY2xJR8Fithb7dsRA@mail.gmail.com>

I forgot to mention before that right now I'm running fieldtrip-20120325
under Ubuntu 10.04.

On 26 March 2012 18:01, Maria Pefkou <Maria.Pefkou at unige.ch> wrote:

> Dear FieldTrip users,
>
> I started using the toolbox fairly recently to analyse EEG data and I have
> huge trouble making a BEM model, which I need for source localisation.
> Following the online tutorial, I processed my subjects' individual
> structural MRIs in FreeSurfer and MNE and managed to prepare the
> triangulated mesh. However, my problem is the volume conduction model. I
> can get a singleshell one, using the ft_prepare_singleshell function, but
> as far as I understand it is excusively used for MEG data. I came to this
> conclusion because when I try to compute the forward model, given that I
> provide information about the electrodes position, I always get the
> following error:
>
> "unsupported volume conductor model for EEG".
> I guess this is because the vol.type is 'nolte' and there is no such case
> for EEG data, at least not in the ft_prepare_vol_sens.m function, which is
> automatically called.
>
> I have tried to prepare a BEM model using the ft_prepare_headmodel
> function with cfg.method='bemcp' or cfg.method='dipoli' but I was
> unsuccessful.
> The problem is that, after having tried various functions/options, I lost
> the general picture and I'm running in circles... The question is: I have a
> segmented mri, how can I get a BEM model out of this? I must be missing a
> fundamental part of the procedure but I can't quite find out what it is.
> Any suggestions/help would be very much appreciated.
>
> Thank you in advance,
> Maria Pefkou
>
> ------------------------------------------
> Research Assistant
> Functional Brain Mapping Lab
> University of Geneva
>
>
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From k.muesch at uke.uni-hamburg.de  Mon Mar 26 18:45:35 2012
From: k.muesch at uke.uni-hamburg.de (=?iso-8859-1?Q?Kathrin_M=FCsch?=)
Date: Mon, 26 Mar 2012 18:45:35 +0200
Subject: [FieldTrip] inconsistent results from dipolefitting and beamforming
Message-ID: <5D2500F2-F9AB-41B0-8BA1-25B18E08A5A5@uke.uni-hamburg.de>

Hi Fieldtrip users,

I am trying to apply a beamformer to simulated data to check whether my headmodels are correct. While ft_dipolefit localizes the dipole in the original position, the beamformer results in a source at a totally different position (see figure 1). I kept everything as similar as possible to the example scripts (forward simulation & dipole fit, forward simulation & beamformer) but used individual gradiometer positions, grid and volume of a single subject (CTF space) and plotted the source in a template grid (SPM space). If I run the dipolesimulation with the individual gradiometer structure and the template headmodel vol and template grid, the dipole and the source result in the same position, although the grad and vol are not in the same coordinate system (figure 2). And importantly, shouldn't the dipole be in the right hemisphere anyway with the coordinates 5/2/3? I appended the code below.

Could the different coordinate systems lead to the inconsistent results of dipolefitting and beamforming? Will the dipolesimulation be in the same coordinate system as the volume or gradiometer structure I feed in (CTF space, in my case)? How could I use the dipolesimulation, dipolefitting and beamforming to properly check my headmodels?

I tried so many things now but I couldn't find the error. Any help is very appreciated.

Best,
Kathrin



These are the variables I used:

vol = headmodel of individual subject in CTF space (cm)
data.grad = gradiometer structure of individual subject in CTF space (cm)
mnigrid = grid of individual subject in CTF space (cm)
template_grid = grid of template brain in SPM space (cm)
mri = spm8 template brain in SMP space


%% compute forward simulated data + apply diplole fit
cfg     = [];
cfg.vol = vol;
cfg.grad = data.grad;
cfg.channel = 'MEG';
cfg.dip.pos = [5 2 3]; % pos of dipole in cm
cfg.dip.mom = [1 0 0]';
cfg.dip.frequency = 10;
cfg.ntrials = 20;
cfg.relnoise = 10;
raw = ft_dipolesimulation(cfg);
 
% compute the data covariance matrix, which will capture the activity of
% the simulated dipole
cfg = [];
cfg.covariance = 'yes';
avg = ft_timelockanalysis(cfg, raw);
 
% apply dipolefit
cfg = [];
cfg.vol = vol;
cfg.grad = data.grad;
cfg.dip.pos = [0 0 0];
cfg.gridsearch = 'no';
dip = ft_dipolefitting(cfg, avg);
 
cfg = [];
cfg.location = dip.dip.pos *10;
figure, ft_sourceplot(cfg,mri)

 
% do the beamformer source reconstuction on a 1 cm grid
cfg = [];
cfg.channel = 'MEG';
cfg.vol = vol;
cfg.grad = data.grad;
cfg.grid  = mnigrid;
cfg.method = 'lcmv';
cfg.projectnoise = 'yes'; 
source = ft_sourceanalysis(cfg, avg);

% compute the neural activity index, i.e. projected power divided by
% projected noise
cfg = [];
cfg.powmethod = 'none'; % keep the power as estimated from the data covariance, i.e. the induced power
source = ft_sourcedescriptives(cfg, source);
 
interp = ft_sourceinterpolate([], source, mri);
 
cfg = [];
cfg.method = 'ortho';
cfg.interactive = 'yes';
cfg.funparameter = 'nai';
cfg.funcolorlim = [1.5 4];  % the voxel in the center of the volume conductor messes up the autoscaling
figure, ft_sourceplot(cfg, interp);
 






_____________________________________
Kathrin Müsch

Dept. of Neurophysiology and Pathophysiology
University Medical Center Hamburg-Eppendorf
Martinistr. 52
20246 Hamburg
Germany
Phone: +49-40-7410-54680
Fax: +49-40-7410-57752
E-Mail: k.muesch at uke.uni-hamburg.de
_____________________________________


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

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg

Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus 
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From smoratti at psi.ucm.es  Mon Mar 26 16:13:00 2012
From: smoratti at psi.ucm.es (Stephan Moratti)
Date: Mon, 26 Mar 2012 16:13:00 +0200
Subject: [FieldTrip] beamforming with rank deficient covariance matrix
In-Reply-To: <DUB113-W8242FDFA7507E17608A292B7450@phx.gbl>
References: <DUB113-W8242FDFA7507E17608A292B7450@phx.gbl>
Message-ID: <9BF0E297-D3D1-41F4-A2BF-D9940E50E51C@psi.ucm.es>

Dear Fred,

In case of reduced rank people usually do regularization specifying  a lambda value (cfg.lcmv.lambda ='5%').

Best,

Stephan

El 26/03/2012, a las 14:47, Frederic Roux escribió:

> 
> Dear all,
> 
> I have a question related to the rank of the covariance matrix
> used for the beamformer.
> 
> I preprocessed my data using ICA to reject EOG and ECG component (typically
> between 2-4 components). This however, leads to a reduction in the rank
> of the covariance matrix and I get a warning using ft_sourceanalysis
> saying that my covariance matrix is rank deficient because rank(COV) < Nchannels.
> 
> I would like to know, how much of a problem and how serious this can be.
> 
> The way I understand things, this should only cause trouble if the number
> of active sources exceeds the number of linearly independent rows of the covariance matrix?
> Is this assumption correct? 
> 
> Is there some step in the ft_sourceanalyis pipeline that assumes that the number of
> sources is equal to the number of channels, and that could bias the computation
> of the beamformer? I mean in that case I would have more sources than channels
> and thus the beamformer would fail.
> 
> Would be great if someone could help me to figure this out.
> 
> Cheers,
> Fred
> 
> 
> 
> 
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


________________________________________________________
Stephan Moratti, PhD

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

Universidad Complutense de Madrid
Facultad de Psicología
Departamento de Psicología Básica I
Campus de Somosaguas
28223 Pozuelo de Alarcón (Madrid)
Spain

and

Center for Biomedical Technology
Laboratory for Cognitive and Computational Neuroscience
Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)
Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982


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From jan.schoffelen at donders.ru.nl  Mon Mar 26 21:42:19 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Mon, 26 Mar 2012 21:42:19 +0200
Subject: [FieldTrip] Create BEM model for EEG source localisation
In-Reply-To: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>
References: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>
Message-ID: <29B44597-C214-468C-A291-ABCDEEA6E099@donders.ru.nl>

Hi Maria,

You could have a look at:

http://fieldtrip.fcdonders.nl/tutorial/headmodel

and

http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg

Hopefully this will give you some inspiration.

Best,

Jan-Mathijs

On Mar 26, 2012, at 6:01 PM, Maria Pefkou wrote:

> Dear FieldTrip users,
> 
> I started using the toolbox fairly recently to analyse EEG data and I have huge trouble making a BEM model, which I need for source localisation.
> Following the online tutorial, I processed my subjects' individual structural MRIs in FreeSurfer and MNE and managed to prepare the triangulated mesh. However, my problem is the volume conduction model. I can get a singleshell one, using the ft_prepare_singleshell function, but as far as I understand it is excusively used for MEG data. I came to this conclusion because when I try to compute the forward model, given that I provide information about the electrodes position, I always get the following error: 
> 
> "unsupported volume conductor model for EEG".
> I guess this is because the vol.type is 'nolte' and there is no such case for EEG data, at least not in the ft_prepare_vol_sens.m function, which is automatically called.
> 
> I have tried to prepare a BEM model using the ft_prepare_headmodel function with cfg.method='bemcp' or cfg.method='dipoli' but I was unsuccessful.
> The problem is that, after having tried various functions/options, I lost the general picture and I'm running in circles... The question is: I have a segmented mri, how can I get a BEM model out of this? I must be missing a fundamental part of the procedure but I can't quite find out what it is.
> Any suggestions/help would be very much appreciated.
> 
> Thank you in advance,
> Maria Pefkou
> 
> ------------------------------------------
> Research Assistant
> Functional Brain Mapping Lab
> University of Geneva
> 
> _______________________________________________
> 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




From jan.schoffelen at donders.ru.nl  Mon Mar 26 21:52:11 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Mon, 26 Mar 2012 21:52:11 +0200
Subject: [FieldTrip] inconsistent results from dipolefitting and
	beamforming
In-Reply-To: <5D2500F2-F9AB-41B0-8BA1-25B18E08A5A5@uke.uni-hamburg.de>
References: <5D2500F2-F9AB-41B0-8BA1-25B18E08A5A5@uke.uni-hamburg.de>
Message-ID: <E931E86A-3F5A-4998-A098-3DC9091C72CF@donders.ru.nl>

Dear Kathrin,

Note that you cannot just mix geometrical objects which are defined in different coordinate systems within a simulation / source reconstruction.
The code cannot make the distinction about the coordinate systems, and assumes that all geometrical objects that go into a function are defined within the same coordinate system (i.e. x,y,z position mean the same in all objects). This also goes for the mri used for the interpolation. You should use an MRI volume that has a transformation matrix attached to it that transforms from voxel space into CTF coordinate system, rather than into MNI space. The result of a faulty interpolation would lead among others to the x and y axis being exchanged. I think you should look into this direction for a solution. 
By the way, (5,2,3) is indeed in the right hemisphere, but how it shows up on the screen depends on whether the anatomy is shown in radiological or neurological convention.

Best,

Jan-Mathijs

On Mar 26, 2012, at 6:45 PM, Kathrin Müsch wrote:

> Hi Fieldtrip users,
> 
> I am trying to apply a beamformer to simulated data to check whether my headmodels are correct. While ft_dipolefit localizes the dipole in the original position, the beamformer results in a source at a totally different position (see figure 1). I kept everything as similar as possible to the example scripts (forward simulation & dipole fit, forward simulation & beamformer) but used individual gradiometer positions, grid and volume of a single subject (CTF space) and plotted the source in a template grid (SPM space). If I run the dipolesimulation with the individual gradiometer structure and the template headmodel vol and template grid, the dipole and the source result in the same position, although the grad and vol are not in the same coordinate system (figure 2). And importantly, shouldn't the dipole be in the right hemisphere anyway with the coordinates 5/2/3? I appended the code below.
> 
> Could the different coordinate systems lead to the inconsistent results of dipolefitting and beamforming? Will the dipolesimulation be in the same coordinate system as the volume or gradiometer structure I feed in (CTF space, in my case)? How could I use the dipolesimulation, dipolefitting and beamforming to properly check my headmodels?
> 
> I tried so many things now but I couldn't find the error. Any help is very appreciated.
> 
> Best,
> Kathrin
> 
> 
> 
> These are the variables I used:
> 
> vol = headmodel of individual subject in CTF space (cm)
> data.grad = gradiometer structure of individual subject in CTF space (cm)
> mnigrid = grid of individual subject in CTF space (cm)
> template_grid = grid of template brain in SPM space (cm)
> mri = spm8 template brain in SMP space
> 
> 
> %% compute forward simulated data + apply diplole fit
> cfg     = [];
> cfg.vol = vol;
> cfg.grad = data.grad;
> cfg.channel = 'MEG';
> cfg.dip.pos = [5 2 3]; % pos of dipole in cm
> cfg.dip.mom = [1 0 0]';
> cfg.dip.frequency = 10;
> cfg.ntrials = 20;
> cfg.relnoise = 10;
> raw = ft_dipolesimulation(cfg);
>  
> % compute the data covariance matrix, which will capture the activity of
> % the simulated dipole
> cfg = [];
> cfg.covariance = 'yes';
> avg = ft_timelockanalysis(cfg, raw);
>  
> % apply dipolefit
> cfg = [];
> cfg.vol = vol;
> cfg.grad = data.grad;
> cfg.dip.pos = [0 0 0];
> cfg.gridsearch = 'no';
> dip = ft_dipolefitting(cfg, avg);
>  
> cfg = [];
> cfg.location = dip.dip.pos *10;
> figure, ft_sourceplot(cfg,mri)
> 
>  
> % do the beamformer source reconstuction on a 1 cm grid
> cfg = [];
> cfg.channel = 'MEG';
> cfg.vol = vol;
> cfg.grad = data.grad;
> cfg.grid  = mnigrid;
> cfg.method = 'lcmv';
> cfg.projectnoise = 'yes'; 
> source = ft_sourceanalysis(cfg, avg);
> 
> % compute the neural activity index, i.e. projected power divided by
> % projected noise
> cfg = [];
> cfg.powmethod = 'none'; % keep the power as estimated from the data covariance, i.e. the induced power
> source = ft_sourcedescriptives(cfg, source);
>  
> interp = ft_sourceinterpolate([], source, mri);
>  
> cfg = [];
> cfg.method = 'ortho';
> cfg.interactive = 'yes';
> cfg.funparameter = 'nai';
> cfg.funcolorlim = [1.5 4];  % the voxel in the center of the volume conductor messes up the autoscaling
> figure, ft_sourceplot(cfg, interp);
>  
> 
> <individual.png>
> 
> 
> <template.png>
> 
> 
> _____________________________________
> Kathrin Müsch
> 
> Dept. of Neurophysiology and Pathophysiology
> University Medical Center Hamburg-Eppendorf
> Martinistr. 52
> 20246 Hamburg
> Germany
> Phone: +49-40-7410-54680
> Fax: +49-40-7410-57752
> E-Mail: k.muesch at uke.uni-hamburg.de
> _____________________________________
> 
> 
> --
> Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):
> 
> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg
> 
> Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus
> _______________________________________________
> 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

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From wljj09 at gmail.com  Mon Mar 26 22:06:52 2012
From: wljj09 at gmail.com (Jing Wang)
Date: Mon, 26 Mar 2012 22:06:52 +0200
Subject: [FieldTrip] about ft_appendspike
Message-ID: <CABKH8xZdF2QZsL_WXR2iiSw8GjYnjMBLvaeJ5bmD5n=X9Dh7Xw@mail.gmail.com>

Dear fieldtrip developers and users,

I am trying to append spikes to local field potential with ft_appendspike.

The local field potential data have five channels, but the spikes data have
12 channels. They have some trials. According to the ft_appenddata, the
channels will be concatenated within each trial when the input datasets
have different channels.

However, my purpose is to append the first 2 channel of spike data on the
first channel of local field potential data. And to append the third
channel of spike data on the second channel of local field potential data,
and so on. How can I do with ft_appendspike?

Thank you very much! I am grateful for all the help!

Jing
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From lavado at gmail.com  Tue Mar 27 11:19:12 2012
From: lavado at gmail.com (Ion Lavado)
Date: Tue, 27 Mar 2012 11:19:12 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band, concept problem
Message-ID: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>

Hello, i'm having problems trying the beamformer analysis with a frequency
band of interest. I would like to have for example an interval like [8 14]
Hz. My concept problem is about the cfg.frequency and
cfg.tapsmofrq  values. (it must be a escalar, but i want a frequency band).

%FREQ ANALYSIS
cfg = [];
cfg.method    = 'mtmfft';
cfg.output    = 'powandcsd';
cfg.tapsmofrq = 5;
cfg.foilim    = [8 14];
freq_words_alpha = ft_freqanalysis(cfg, words);


%SOURCE ANALYSIS
cfg              = [];
cfg.frequency    = 11;
cfg.lambda=0;
cfg.method       = 'dics';
cfg.coordsys       = 'neuromag';
cfg.projectnoise = 'yes';
cfg.grad            =  freq_words_alpha.grad;
cfg.channel   = {'MEG'};
cfg.grid         = grid;
cfg.reducerank      = 2;
cfg.vol          = vol02;
vol02=ft_convert_units(vol02,'cm');
source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );


I use a cfg.frequency of 11 but i don't have really clear what i'm doing as
a get the same result using cfg.frequency=11 but a freqanalysis in [10 12].
I would be very grateful if someone could solve my doubt.

Best wishes,

Mikel
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From fredericroux at hotmail.de  Tue Mar 27 12:14:45 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Tue, 27 Mar 2012 12:14:45 +0200
Subject: [FieldTrip] question to the fieldtrip developers - multiple spm
 versions in fieldtrip
Message-ID: <DUB113-W12B64F64480B0A75AB493EB74A0@phx.gbl>



Dear all,

I would like to ask again if the fact of getting a warning
that different spm versions will confuse fieldtrip
can have consequences in the ft_sourceanalysis pipeline.

I am using version 2012-01-05 which has SPM2 and SPM8
in the external folder.

It would be great if someone from the development-team could tell me

a) why this is a problem
b) how to circumvent it


I renamed the spm.m file into spm.m.bak in the SPM2 folder so that
only the spm.m file from the SPM8 folder is used. However, it would
be great if someone could tell me if this is a workaround or not.


Best regards,
Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From smoratti at psi.ucm.es  Tue Mar 27 12:38:19 2012
From: smoratti at psi.ucm.es (Stephan Moratti)
Date: Tue, 27 Mar 2012 12:38:19 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band,
	concept problem
In-Reply-To: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
References: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
Message-ID: <EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>

Dear Mikel,

I understand that you should do a mtmfft with a center frequency of interest (in your case cfg.foil = [11 11]) and then you do a frequency smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you need a time window big enough to allow such a smoothing. The CSD should represent a frequency window of 8 to 14 Hz then. Then you put the result of the mtmfft into the dics beamformer.

Best,

Stephan
 
El 27/03/2012, a las 11:19, Ion Lavado escribió:

> Hello, i'm having problems trying the beamformer analysis with a frequency band of interest. I would like to have for example an interval like [8 14] Hz. My concept problem is about the cfg.frequency and cfg.tapsmofrq  values. (it must be a escalar, but i want a frequency band). 
> 
> %FREQ ANALYSIS
> cfg = [];
> cfg.method    = 'mtmfft';
> cfg.output    = 'powandcsd';
> cfg.tapsmofrq = 5;
> cfg.foilim    = [8 14];
> freq_words_alpha = ft_freqanalysis(cfg, words);
> 
> 
> %SOURCE ANALYSIS
> cfg              = []; 
> cfg.frequency    = 11;  
> cfg.lambda=0;
> cfg.method       = 'dics';
> cfg.coordsys       = 'neuromag';
> cfg.projectnoise = 'yes';
> cfg.grad            =  freq_words_alpha.grad;
> cfg.channel   = {'MEG'}; 
> cfg.grid         = grid; 
> cfg.reducerank      = 2;
> cfg.vol          = vol02;
> vol02=ft_convert_units(vol02,'cm');
> source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
> 
> 
> I use a cfg.frequency of 11 but i don't have really clear what i'm doing as a get the same result using cfg.frequency=11 but a freqanalysis in [10 12]. I would be very grateful if someone could solve my doubt.
> 
> Best wishes,
> 
> Mikel
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


________________________________________________________
Stephan Moratti, PhD

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

Universidad Complutense de Madrid
Facultad de Psicología
Departamento de Psicología Básica I
Campus de Somosaguas
28223 Pozuelo de Alarcón (Madrid)
Spain

and

Center for Biomedical Technology
Laboratory for Cognitive and Computational Neuroscience
Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)
Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982


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From lavado at gmail.com  Tue Mar 27 12:46:35 2012
From: lavado at gmail.com (Ion Lavado)
Date: Tue, 27 Mar 2012 12:46:35 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band,
	concept problem
In-Reply-To: <EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>
References: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
	<EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>
Message-ID: <CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>

Thank you Stephan, just one thing, why i need a time window big enough? so
i'm just studying the frequency.

Best,

Mikel

2012/3/27 Stephan Moratti <smoratti at psi.ucm.es>

> Dear Mikel,
>
> I understand that you should do a mtmfft with a center frequency of
> interest (in your case cfg.foil = [11 11]) and then you do a frequency
> smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you need a time window big
> enough to allow such a smoothing. The CSD should represent a frequency
> window of 8 to 14 Hz then. Then you put the result of the mtmfft into the
> dics beamformer.
>
> Best,
>
> Stephan
>
> El 27/03/2012, a las 11:19, Ion Lavado escribió:
>
> Hello, i'm having problems trying the beamformer analysis with a frequency
> band of interest. I would like to have for example an interval like [8 14]
> Hz. My concept problem is about the cfg.frequency and
> cfg.tapsmofrq  values. (it must be a escalar, but i want a frequency band).
>
> %FREQ ANALYSIS
> cfg = [];
> cfg.method    = 'mtmfft';
> cfg.output    = 'powandcsd';
> cfg.tapsmofrq = 5;
> cfg.foilim    = [8 14];
> freq_words_alpha = ft_freqanalysis(cfg, words);
>
>
> %SOURCE ANALYSIS
> cfg              = [];
> cfg.frequency    = 11;
> cfg.lambda=0;
> cfg.method       = 'dics';
> cfg.coordsys       = 'neuromag';
> cfg.projectnoise = 'yes';
> cfg.grad            =  freq_words_alpha.grad;
> cfg.channel   = {'MEG'};
> cfg.grid         = grid;
> cfg.reducerank      = 2;
> cfg.vol          = vol02;
> vol02=ft_convert_units(vol02,'cm');
> source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
>
>
> I use a cfg.frequency of 11 but i don't have really clear what i'm doing
> as a get the same result using cfg.frequency=11 but a freqanalysis in [10
> 12]. I would be very grateful if someone could solve my doubt.
>
> Best wishes,
>
> Mikel
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> ________________________________________________________
> Stephan Moratti, PhD
>
> see also: http://web.me.com/smoratti/
>
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
> and
>
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
>
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
>
>
>
> _______________________________________________
> 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 Mar 27 13:14:56 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 27 Mar 2012 13:14:56 +0200
Subject: [FieldTrip] SPM path and sourceanalysis on template brain
In-Reply-To: <DUB113-W76F2D058B3132334525D94B7450@phx.gbl>
References: <DUB113-W76F2D058B3132334525D94B7450@phx.gbl>
Message-ID: <4F71A130.7070705@donders.ru.nl>

Dear Frederic,

I meant to send this mail already yesterday - but at least you cleared 
up the issue I had with your first mail ;)
Original mail:

Although you forgot to actually paste the error message into the mail 
you sent, I assume that you get a warning that mentions something like 
"Multiple occurences of SPM have been found on your path". If this is 
the error, you are using 
addpath(genpath('WhereeverFieldTripIsStoredOnYourMachine')), but should 
just do addpath('WhereeverFieldTripIsStoredOnYourMachine') and then call 
ft_defaults. Otherwise, your source reconstruction might be a result of 
different version of SPM, which might lead to faulty behaviour, because 
functions of different versions are not designed to be compatible with 
each other.

Best,
Jörn

On 3/26/2012 12:23 PM, Frederic Roux wrote:
> Dear all,
>
>
> I am getting the following error message with the fieldtrip-20120105 
> version,
> and wanted to ask if anyone could tell me:
>
> a) how to prevent it
> b) what the consequences of ignoring it will be.
>
> Also I wanted to get some feedback on the possibility of
> using a template brain for source localization on data for which
> MRI data is missing.
>
> I have a recorded MEG data from n = 98 participants but only have
> the MRs of 70 of them. Can I use a template MR to perform
> source analysis on the missing data sets?
>
> Looking forward to any kind of suggestions.
> Have a nice day,
>
> Fred
>
>
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
>
>
>
>
> _______________________________________________
> 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

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 Jarmo.Kontinen at ruhr-uni-bochum.de  Tue Mar 27 13:24:43 2012
From: Jarmo.Kontinen at ruhr-uni-bochum.de (Jarmo Kontinen)
Date: Tue, 27 Mar 2012 13:24:43 +0200 (CEST)
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
In-Reply-To: <1332764087.47250.YahooMailNeo@web132103.mail.ird.yahoo.com>
Message-ID: <permail-201203271124436509e8c7000033ba-Jarmo.Kontinen@msgid.mail.ruhr-uni-bochum.de>


Dear Ivano,
I had some problem with email, so if I am replying to you twice, I apologize.

 I was maybe a  bit unclear maybe in my first post. My files already contain
 averaged data.
Problem is to get the right data-structure to use the existing FT-functions to
do analysis on the data.

Best,
Jarmo

Ivano Triggiani schrieb am 2012-03-26:
> Dear Jarmo,

> Filedtrip needs a definition of segments of interest. For example
> reading a trigger channel or something else to cut the EEG recording
> into trials. If I have understood what you want to do is to get an
> average of general EEG (for example resting state EEG closed eyes).
> But you have to indicate which average you want to obtain, for
> example you can tell fieldtrip to divide EEG into epochs of 3 seconds
> and then to make an average of all of them.
> What you wrote is the request of an average, but you are not
> specifing of what.
> Fof example you can write a trial function that provides a trl
> matrix, i.e.:
> 0 3 0

> 3 6 0
> 6 9 0
> 9 12 0
> 12 13 0
> ...

> where first column is the start sample in seconds (you have to
> multiply it for sample rate), the second column is the end sample and
> the third is the offset (in this case is always zero), or look at
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#use_your_own_function_for_trial_selection

> best wishes,
> Ivano



> ------------------------------------------------------------------------




> "No man can wear one face to himself
> and another to the multitude,
> without finally getting bewildered
> as to which one is true."


> Nathaniel Hawthorne


> ________________________________
>  Da: "fieldtrip-request at donders.ru.nl"
>  <fieldtrip-request at donders.ru.nl>
> A: fieldtrip at donders.ru.nl
> Inviato: Lunedì 26 Marzo 2012 12:00
> Oggetto: fieldtrip Digest, Vol 16, Issue 33

> Send fieldtrip mailing list submissions to
>     fieldtrip at donders.ru.nl

> To subscribe or unsubscribe via the World Wide Web, visit
>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>     fieldtrip-request at donders.ru.nl

> You can reach the person managing the list at
>     fieldtrip-owner at donders.ru.nl

> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."


> Today's Topics:

>    1. Re: Problem with FT_DEFINETRIAL (Stephen Politzer-Ahles)


> ----------------------------------------------------------------------

> Message: 1
> Date: Sun, 25 Mar 2012 12:11:28 +0200
> From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL
> Message-ID:
>    
> <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"

> Hello Jarmo,

> I haven't tried importing Brain Vision files into FieldTrip myself,
> but
> based on the code you sent it looks like the problem may be that
> you're
> missing cfg.trialdef.eventvalue (which is used to tell FieldTrip
> which
> triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim
> . See
> the example at
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials.

> If what you are trying to do is import all trials from all triggers
> in the
> file, I think you have to define your own "trialfun" function to do
> that
> (although I haven't tried this myself so I'm not sure).
> http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
> information.

> Best,
> Steve Politzer-Ahles
> University of Kansas


> Message: 1
> > Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> > From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> > To: <fieldtrip at donders.ru.nl>
> > Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> > Message-ID:
> >        <
> > permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de


> > Content-Type: text/plain; charset=us-ascii

> > Dear all,
> > I am trying to import EEG subject averages into Field Trip. The
> > files are
> > exported with the Brainvision Analyzer in binary form
> > :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> > I have a problem with turning the data into the Field Trip
> > data-structure.
> > I
> > am following instructions given on this forum on one similar post.
> > What I
> > have
> > tried is the following:

> > cfg=[];
> > cfg.trialdef.eventtype='average'
> > cfg.dataset='subject10_konPro2002.dat'

> >  cfg=ft_definetrial(cfg);

> > Warning: no trialfun was specified, using trialfun_general
> > > In ft_definetrial at 123
> > evaluating trialfunction 'trialfun_general'
> > reading the events from 'subject10_konPro2002.vhdr'
> > ??? Error using ==> ft_definetrial at 176
> > no trials were defined, see FT_DEFINETRIAL for help

> > I am grateful for all the help.
> > Thanks,
> > Jarmo Kontinen

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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 16, Issue 33
> *****************************************



From jm.horschig at donders.ru.nl  Tue Mar 27 13:27:27 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 27 Mar 2012 13:27:27 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band,
	concept problem
In-Reply-To: <CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>
References: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
	<EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>
	<CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>
Message-ID: <4F71A41F.4080807@donders.ru.nl>

Hi Ion,

A frequency is by definition at least a peak and a trough(up flank and 
down flank), making it one cycle (think of sinusoid here). Thus, you 
could say that one needs at least one cycle of a certain frequency such 
that it is eligible to talk about a 'frequency'. Just in case you don't 
know it already, you might want to look things up as Rayleigh frequency, 
Nyquist frequency, and I would suggest that you read (or start reading) 
the digitial signal processing book: http://www.dspguide.com/

Note that a true oscillation is usually considered to last at least 
three cycles (of course, opinions differ her - I go with four). The 
length of the window of interest reflects the number of cycles that can 
be estimated. For source reconstruction, make sure cfg.toilim is as long 
as the number of cycles you want to estimate, e.g. when using cfg.foi = 
10, then cfg.toilim(2)-cfg.toilim(1) should be at least 400ms when you 
want an estimate of 4 cycles.

Hope it helps!
Best,
Jörn



On 3/27/2012 12:46 PM, Ion Lavado wrote:
> Thank you Stephan, just one thing, why i need a time window big 
> enough? so i'm just studying the frequency.
>
> Best,
>
> Mikel
>
> 2012/3/27 Stephan Moratti <smoratti at psi.ucm.es 
> <mailto:smoratti at psi.ucm.es>>
>
>     Dear Mikel,
>
>     I understand that you should do a mtmfft with a center frequency
>     of interest (in your case cfg.foil = [11 11]) and then you do a
>     frequency smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you
>     need a time window big enough to allow such a smoothing. The CSD
>     should represent a frequency window of 8 to 14 Hz then. Then you
>     put the result of the mtmfft into the dics beamformer.
>
>     Best,
>
>     Stephan
>
>     El 27/03/2012, a las 11:19, Ion Lavado escribió:
>
>>     Hello, i'm having problems trying the beamformer analysis with a
>>     frequency band of interest. I would like to have for example an
>>     interval like [8 14] Hz. My concept problem is about the
>>     cfg.frequency and cfg.tapsmofrq  values. (it must be a escalar,
>>     but i want a frequency band).
>>
>>     %FREQ ANALYSIS
>>     cfg = [];
>>     cfg.method    = 'mtmfft';
>>     cfg.output    = 'powandcsd';
>>     cfg.tapsmofrq = 5;
>>     cfg.foilim    = [8 14];
>>     freq_words_alpha = ft_freqanalysis(cfg, words);
>>
>>
>>     %SOURCE ANALYSIS
>>     cfg              = [];
>>     cfg.frequency    = 11;
>>     cfg.lambda=0;
>>     cfg.method       = 'dics';
>>     cfg.coordsys       = 'neuromag';
>>     cfg.projectnoise = 'yes';
>>     cfg.grad            =  freq_words_alpha.grad;
>>     cfg.channel   = {'MEG'};
>>     cfg.grid         = grid;
>>     cfg.reducerank      = 2;
>>     cfg.vol          = vol02;
>>     vol02=ft_convert_units(vol02,'cm');
>>     source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
>>
>>
>>     I use a cfg.frequency of 11 but i don't have really clear what
>>     i'm doing as a get the same result using cfg.frequency=11 but a
>>     freqanalysis in [10 12]. I would be very grateful if someone
>>     could solve my doubt.
>>
>>     Best wishes,
>>
>>     Mikel
>>     _______________________________________________
>>     fieldtrip mailing list
>>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>     ________________________________________________________
>     Stephan Moratti, PhD
>
>     see also: http://web.me.com/smoratti/
>
>     Universidad Complutense de Madrid
>     Facultad de Psicología
>     Departamento de Psicología Básica I
>     Campus de Somosaguas
>     28223 Pozuelo de Alarcón (Madrid)
>     Spain
>
>     and
>
>     Center for Biomedical Technology
>     Laboratory for Cognitive and Computational Neuroscience
>     Parque Científico y Tecnológico de la Universidad Politecnica de
>     Madrid
>     Campus Montegancedo
>     28223 Pozuelo de Alarcón (Madrid)
>     Spain
>
>
>     email: smoratti at psi.ucm.es <mailto:smoratti at psi.ucm.es>
>     Tel.: +34 679219982 <tel:%2B34%20679219982>
>
>
>
>     _______________________________________________
>     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

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 Ulrich.Pomper at charite.de  Tue Mar 27 15:00:32 2012
From: Ulrich.Pomper at charite.de (Pomper, Ulrich)
Date: Tue, 27 Mar 2012 15:00:32 +0200
Subject: [FieldTrip] one-sample cluster test
Message-ID: <4F71B9F0.8080106@charite.de>

Dear list members,

this topic was discussed some time in 2008, but it seems to me no 
conclusion was found.

I would like to find source activity that differs significantly from 
zero. I could run a one sample t-test for every voxel and end up having 
a huge MC problem, or (preferably) use some kind of cluster based 
permutation statistics. However, the option for a one sample cluster 
test is not implemented in FT.

Would it be correct to test the data from my experimental condition 
against a set of data containing all zeros using a cluster based 
permutation test?

Any help is very much appreciated!
Best, Ulrich



From mark.noordenbos at gmail.com  Tue Mar 27 15:35:00 2012
From: mark.noordenbos at gmail.com (Mark Noordenbos)
Date: Tue, 27 Mar 2012 15:35:00 +0200
Subject: [FieldTrip] one-sample cluster test
Message-ID: <CAJSb8nMMcxO0xxW8+6z1rAswYReKKPxq+3Rc0Htaz-dyoXELJA@mail.gmail.com>

Hi Ulrich,

There is a function 'statfun_actvsblT' to test your activity against the
baseline. However, this function only accepts input with dimord
'chan_freq_time'.
Maybe, you can create your own function based on 'statfun_actvsblT' to test
the activity against zero.

Kind regards,
Mark

Op 27 maart 2012 15:00 schreef <fieldtrip-request at donders.ru.nl> het
volgende:

> Send fieldtrip mailing list submissions to
>        fieldtrip at donders.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>        fieldtrip-request at donders.ru.nl
>
> You can reach the person managing the list at
>        fieldtrip-owner at donders.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>   1. Re: Problem with FT_DEFINETRIAL (Jarmo Kontinen)
>   2. Re: Beamforming analysis in frequency band,       concept problem
>      (J?rn M. Horschig)
>   3. one-sample cluster test (Pomper, Ulrich)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 27 Mar 2012 13:24:43 +0200 (CEST)
> From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> To: Ivano Triggiani <ivano_triggiani at yahoo.it>, Email discussion list
>        for the FieldTrip project <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL
> Message-ID:
>        <
> permail-201203271124436509e8c7000033ba-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de
> >
>
> Content-Type: text/plain; charset=iso-8859-1
>
>
> Dear Ivano,
> I had some problem with email, so if I am replying to you twice, I
> apologize.
>
>  I was maybe a  bit unclear maybe in my first post. My files already
> contain
>  averaged data.
> Problem is to get the right data-structure to use the existing
> FT-functions to
> do analysis on the data.
>
> Best,
> Jarmo
>
> Ivano Triggiani schrieb am 2012-03-26:
> > Dear Jarmo,
>
> > Filedtrip needs a definition of segments of interest. For example
> > reading a trigger channel or something else to cut the EEG recording
> > into trials. If I have understood what you want to do is to get an
> > average of general EEG (for example resting state EEG closed eyes).
> > But you have to indicate which average you want to obtain, for
> > example you can tell fieldtrip to divide EEG into epochs of 3 seconds
> > and then to make an average of all of them.
> > What you wrote is the request of an average, but you are not
> > specifing of what.
> > Fof example you can write a trial function that provides a trl
> > matrix, i.e.:
> > 0 3 0
>
> > 3 6 0
> > 6 9 0
> > 9 12 0
> > 12 13 0
> > ...
>
> > where first column is the start sample in seconds (you have to
> > multiply it for sample rate), the second column is the end sample and
> > the third is the offset (in this case is always zero), or look at
> >
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#use_your_own_function_for_trial_selection
>
> > best wishes,
> > Ivano
>
>
>
> > ------------------------------------------------------------------------
>
>
>
>
> > "No man can wear one face to himself
> > and another to the multitude,
> > without finally getting bewildered
> > as to which one is true."
>
>
> > Nathaniel Hawthorne
>
>
> > ________________________________
> >  Da: "fieldtrip-request at donders.ru.nl"
> >  <fieldtrip-request at donders.ru.nl>
> > A: fieldtrip at donders.ru.nl
> > Inviato: Luned? 26 Marzo 2012 12:00
> > Oggetto: fieldtrip Digest, Vol 16, Issue 33
>
> > Send fieldtrip mailing list submissions to
> > ??? fieldtrip at donders.ru.nl
>
> > To subscribe or unsubscribe via the World Wide Web, visit
> > ??? http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > ??? fieldtrip-request at donders.ru.nl
>
> > You can reach the person managing the list at
> > ??? fieldtrip-owner at donders.ru.nl
>
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
>
>
> > Today's Topics:
>
> > ?  1. Re: Problem with FT_DEFINETRIAL (Stephen Politzer-Ahles)
>
>
> > ----------------------------------------------------------------------
>
> > Message: 1
> > Date: Sun, 25 Mar 2012 12:11:28 +0200
> > From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> > To: fieldtrip at donders.ru.nl
> > Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL
> > Message-ID:
> > ???
> > <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
>
> > Hello Jarmo,
>
> > I haven't tried importing Brain Vision files into FieldTrip myself,
> > but
> > based on the code you sent it looks like the problem may be that
> > you're
> > missing cfg.trialdef.eventvalue (which is used to tell FieldTrip
> > which
> > triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim
> > . See
> > the example at
> >
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials
> .
>
> > If what you are trying to do is import all trials from all triggers
> > in the
> > file, I think you have to define your own "trialfun" function to do
> > that
> > (although I haven't tried this myself so I'm not sure).
> > http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
> > information.
>
> > Best,
> > Steve Politzer-Ahles
> > University of Kansas
>
>
> > Message: 1
> > > Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> > > From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> > > To: <fieldtrip at donders.ru.nl>
> > > Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> > > Message-ID:
> > >? ? ? ? <
> > >
> permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de
>
>
> > > Content-Type: text/plain; charset=us-ascii
>
> > > Dear all,
> > > I am trying to import EEG subject averages into Field Trip. The
> > > files are
> > > exported with the Brainvision Analyzer in binary form
> > > :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> > > I have a problem with turning the data into the Field Trip
> > > data-structure.
> > > I
> > > am following instructions given on this forum on one similar post.
> > > What I
> > > have
> > > tried is the following:
>
> > > cfg=[];
> > > cfg.trialdef.eventtype='average'
> > > cfg.dataset='subject10_konPro2002.dat'
>
> > >? cfg=ft_definetrial(cfg);
>
> > > Warning: no trialfun was specified, using trialfun_general
> > > > In ft_definetrial at 123
> > > evaluating trialfunction 'trialfun_general'
> > > reading the events from 'subject10_konPro2002.vhdr'
> > > ??? Error using ==> ft_definetrial at 176
> > > no trials were defined, see FT_DEFINETRIAL for help
>
> > > I am grateful for all the help.
> > > Thanks,
> > > Jarmo Kontinen
>
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >  <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120325/df4ce70a/attachment-0001.html
> >
>
> > ------------------------------
>
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> > End of fieldtrip Digest, Vol 16, Issue 33
> > *****************************************
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 27 Mar 2012 13:27:27 +0200
> From: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> To: fieldtrip at donders.ru.nl
> Subject: Re: [FieldTrip] Beamforming analysis in frequency band,
>        concept problem
> Message-ID: <4F71A41F.4080807 at donders.ru.nl>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Ion,
>
> A frequency is by definition at least a peak and a trough(up flank and
> down flank), making it one cycle (think of sinusoid here). Thus, you
> could say that one needs at least one cycle of a certain frequency such
> that it is eligible to talk about a 'frequency'. Just in case you don't
> know it already, you might want to look things up as Rayleigh frequency,
> Nyquist frequency, and I would suggest that you read (or start reading)
> the digitial signal processing book: http://www.dspguide.com/
>
> Note that a true oscillation is usually considered to last at least
> three cycles (of course, opinions differ her - I go with four). The
> length of the window of interest reflects the number of cycles that can
> be estimated. For source reconstruction, make sure cfg.toilim is as long
> as the number of cycles you want to estimate, e.g. when using cfg.foi =
> 10, then cfg.toilim(2)-cfg.toilim(1) should be at least 400ms when you
> want an estimate of 4 cycles.
>
> Hope it helps!
> Best,
> J?rn
>
>
>
> On 3/27/2012 12:46 PM, Ion Lavado wrote:
> > Thank you Stephan, just one thing, why i need a time window big
> > enough? so i'm just studying the frequency.
> >
> > Best,
> >
> > Mikel
> >
> > 2012/3/27 Stephan Moratti <smoratti at psi.ucm.es
> > <mailto:smoratti at psi.ucm.es>>
> >
> >     Dear Mikel,
> >
> >     I understand that you should do a mtmfft with a center frequency
> >     of interest (in your case cfg.foil = [11 11]) and then you do a
> >     frequency smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you
> >     need a time window big enough to allow such a smoothing. The CSD
> >     should represent a frequency window of 8 to 14 Hz then. Then you
> >     put the result of the mtmfft into the dics beamformer.
> >
> >     Best,
> >
> >     Stephan
> >
> >     El 27/03/2012, a las 11:19, Ion Lavado escribi?:
> >
> >>     Hello, i'm having problems trying the beamformer analysis with a
> >>     frequency band of interest. I would like to have for example an
> >>     interval like [8 14] Hz. My concept problem is about the
> >>     cfg.frequency and cfg.tapsmofrq  values. (it must be a escalar,
> >>     but i want a frequency band).
> >>
> >>     %FREQ ANALYSIS
> >>     cfg = [];
> >>     cfg.method    = 'mtmfft';
> >>     cfg.output    = 'powandcsd';
> >>     cfg.tapsmofrq = 5;
> >>     cfg.foilim    = [8 14];
> >>     freq_words_alpha = ft_freqanalysis(cfg, words);
> >>
> >>
> >>     %SOURCE ANALYSIS
> >>     cfg              = [];
> >>     cfg.frequency    = 11;
> >>     cfg.lambda=0;
> >>     cfg.method       = 'dics';
> >>     cfg.coordsys       = 'neuromag';
> >>     cfg.projectnoise = 'yes';
> >>     cfg.grad            =  freq_words_alpha.grad;
> >>     cfg.channel   = {'MEG'};
> >>     cfg.grid         = grid;
> >>     cfg.reducerank      = 2;
> >>     cfg.vol          = vol02;
> >>     vol02=ft_convert_units(vol02,'cm');
> >>     source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
> >>
> >>
> >>     I use a cfg.frequency of 11 but i don't have really clear what
> >>     i'm doing as a get the same result using cfg.frequency=11 but a
> >>     freqanalysis in [10 12]. I would be very grateful if someone
> >>     could solve my doubt.
> >>
> >>     Best wishes,
> >>
> >>     Mikel
> >>     _______________________________________________
> >>     fieldtrip mailing list
> >>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
> >>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
> >     ________________________________________________________
> >     Stephan Moratti, PhD
> >
> >     see also: http://web.me.com/smoratti/
> >
> >     Universidad Complutense de Madrid
> >     Facultad de Psicolog?a
> >     Departamento de Psicolog?a B?sica I
> >     Campus de Somosaguas
> >     28223 Pozuelo de Alarc?n (Madrid)
> >     Spain
> >
> >     and
> >
> >     Center for Biomedical Technology
> >     Laboratory for Cognitive and Computational Neuroscience
> >     Parque Cient?fico y Tecnol?gico de la Universidad Politecnica de
> >     Madrid
> >     Campus Montegancedo
> >     28223 Pozuelo de Alarc?n (Madrid)
> >     Spain
> >
> >
> >     email: smoratti at psi.ucm.es <mailto:smoratti at psi.ucm.es>
> >     Tel.: +34 679219982 <tel:%2B34%20679219982>
> >
> >
> >
> >     _______________________________________________
> >     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
>
>
> --
> J?rn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
>
> 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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> >
>
> ------------------------------
>
> Message: 3
> Date: Tue, 27 Mar 2012 15:00:32 +0200
> From: "Pomper, Ulrich" <Ulrich.Pomper at charite.de>
> To: Email discussion list for the FieldTrip project
>        <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] one-sample cluster test
> Message-ID: <4F71B9F0.8080106 at charite.de>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear list members,
>
> this topic was discussed some time in 2008, but it seems to me no
> conclusion was found.
>
> I would like to find source activity that differs significantly from
> zero. I could run a one sample t-test for every voxel and end up having
> a huge MC problem, or (preferably) use some kind of cluster based
> permutation statistics. However, the option for a one sample cluster
> test is not implemented in FT.
>
> Would it be correct to test the data from my experimental condition
> against a set of data containing all zeros using a cluster based
> permutation test?
>
> Any help is very much appreciated!
> Best, Ulrich
>
>
>
> ------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> End of fieldtrip Digest, Vol 16, Issue 39
> *****************************************
>
>
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From jm.horschig at donders.ru.nl  Tue Mar 27 15:48:07 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 27 Mar 2012 15:48:07 +0200
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <4F71B9F0.8080106@charite.de>
References: <4F71B9F0.8080106@charite.de>
Message-ID: <4F71C517.9010906@donders.ru.nl>

Dear Ulrich,


First of all, you might want to use the Neural Activity Index (NAI), as 
also described in the tutorial:
http://fieldtrip.fcdonders.nl/tutorial/beamformer#source_analysiswithout_contrasting_condition

Then, to answer your question, I am tempted to say that this would be an 
invalid approach when dealing with power, so in frequency-space. Power 
obviously has a lower bound, so that the average of any random 
collection of power values will never be 0. Though, what you are 
suggesting is the same as a regular t-test, isn't it?
In case you are dealing e.g. with am LCMV beamformer, I am not quite 
sure, but the null-hypothesis you suggested (amplitude==0)  sounds fair.

In any case, building a surrogate distribution same mean and variance 
than your data might be a better way to deal with your problem. That 
should be easily doable in Matlab without any need to implement this in 
FieldTrip. And note that the MC problem is always present, but a 
cluster-based correction (similar to Bonferroni, but correcting by the 
number of voxels in the cluster not by the number of all voxels) sounds 
legitimate to me. Afair, that's how it's done in FT.

Best,
Jörn




On 3/27/2012 3:00 PM, Pomper, Ulrich wrote:
> Dear list members,
>
> this topic was discussed some time in 2008, but it seems to me no
> conclusion was found.
>
> I would like to find source activity that differs significantly from
> zero. I could run a one sample t-test for every voxel and end up having
> a huge MC problem, or (preferably) use some kind of cluster based
> permutation statistics. However, the option for a one sample cluster
> test is not implemented in FT.
>
> Would it be correct to test the data from my experimental condition
> against a set of data containing all zeros using a cluster based
> permutation test?
>
> Any help is very much appreciated!
> Best, Ulrich
>
> _______________________________________________
> 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

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 tessa.vanleeuwen at fcdonders.ru.nl  Tue Mar 27 18:27:25 2012
From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen)
Date: Tue, 27 Mar 2012 18:27:25 +0200 (CEST)
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <189719464.70211.1332863376495.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <1710162166.70656.1332865645305.JavaMail.root@draco.zimbra.ru.nl>

Dear Fieldtrip experts,

I have noticed enhanced coherence (sensor level) in my data after applying ICA during preprocessing, removing only 1 EOG component. Of course the (mainly quantitatively) enhanced coherence could be due to the removal of (artifact induced) noise from the data. But this increase also occured when applying ICA to previously cleaned data, implying changes induced by ICA somehow affect coherence.

One of the aims of our project is to compute coherence/connectivity measures at the source level. Since connectivity measures are often difficult to interpret as they are, I would like to ask whether anyone has experience with connectivity analyses after preprocessing that involved ICA. Are people aware of possible influences of ICA on connectivity measures and is there a way to deal with this? Or would it be advisable NOT to use ICA when later looking at coherence/connectivity at the source level? 

We initially aim to compare across conditions (data that have been preprocessed together and from which the same ICA component has been removed). But we also have different experimental groups for which we would like to qualitatively compare active networks during our task.

Thank you in advance for any input, it is highly appreciated.

Best wishes,
Tessa


---

Tessa van Leeuwen, PhD
postdoctoral researcher

Department of Neurophysiology
Max Planck Institute for Brain Research


From toncho11 at gmail.com  Tue Mar 27 19:13:18 2012
From: toncho11 at gmail.com (Anton Andreev)
Date: Tue, 27 Mar 2012 19:13:18 +0200
Subject: [FieldTrip] Time stamp per sample
Message-ID: <CAG3TGCN+1ZV7zaAbGKvm8j3M1arg8pQXRgrfSLaof2hVp7G-vg@mail.gmail.com>

Hi,

I have a question about the fieldtrip buffer.
Does the protocol provides information about the time every sample has been
taken?

I would like to produce a chunk of data for 300ms or 1 second for example.
I can build such chunk if I simply sort out samples that are in the time
range of 1 second starting with the time stamp of the first one. Then again
for 1 second and ....

Thanks,
Anton
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From eelke.spaak at donders.ru.nl  Tue Mar 27 20:20:28 2012
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Tue, 27 Mar 2012 20:20:28 +0200
Subject: [FieldTrip] question regarding FieldTrip
In-Reply-To: <CAGhHk+itOwLA7rv42X1tbLH=-wYBYwincRSRUdHFM+AvaMAiJw@mail.gmail.com>
References: <CAGhHk+itOwLA7rv42X1tbLH=-wYBYwincRSRUdHFM+AvaMAiJw@mail.gmail.com>
Message-ID: <CABPNLUp9EpsGqqv6pgQPnPrjn09FE1oqcwtO2QUVLrVZn4XQ2Q@mail.gmail.com>

Dear Ilya,

You probably intended to post to the FieldTrip mailing list, so I am
also forwarding my reply to the list. If you are not registered on the
list, please do so (http://fieldtrip.fcdonders.nl/discussion_list).

Your question suggests to me that you are not using FieldTrip-style
data structures. All FT functions are designed to work with such
structures, so you should convert your data to an FT data structure
first. You can have a look at these FAQs on the Wiki for suggestions:
http://fieldtrip.fcdonders.nl/faq/how_are_the_various_data_structures_defined
and http://fieldtrip.fcdonders.nl/faq/how_can_i_import_my_own_dataformat
. Also, you should probably have a look at the tutorial documentation
(http://fieldtrip.fcdonders.nl/tutorial), specifically the one on
time-frequency analysis.

Hope this helps,
Best,

Eelke

On 27 March 2012 19:13, ilya monosov <ilya.monosov at gmail.com> wrote:
> Hello,
> i have a quick question. thank you so much in advance. if i have a matrix of
> single trial lfps (10 by 10,000) .. meaning that i have 10 trials that are
> 10,000 msec long,
> and i want to get single trial frequency power matrixes for each trial and
> also the average (and perhaps do stats, but most likely not as i am doing
> this to just get
> a quick impression of LFP frequency behavior in locations where i recorded
> single neurons), what commands would i use for FieldTrip?
>
> i have tried but i am getting strange errors that lead me to believe that my
> input format is wrong.
>
> Thank you very much
> ilya


From batrod at gmail.com  Tue Mar 27 18:36:54 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Tue, 27 Mar 2012 11:36:54 -0500
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <1710162166.70656.1332865645305.JavaMail.root@draco.zimbra.ru.nl>
References: <189719464.70211.1332863376495.JavaMail.root@draco.zimbra.ru.nl>
	<1710162166.70656.1332865645305.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <CAPy7a9C0Av7RaH7QTsvErDBU-rf-Buu2x0EvfF5+mk=wGn=XnA@mail.gmail.com>

Dear Tessa,
would it be possible to give some precision about your analyzes.

1) After your first "cleaning", do you test coherence on particular
components or your entire data minus the "EOG" component?

2) When you say that you redo ICA on cleaned data (of course, an ICA
analysis made on a result of a previous ICA analysis with components
removed is a bad idea), do you remove another component or do you  test
your coherence on particular components?

Rodolphe

On Tue, Mar 27, 2012 at 11:27 AM, Tessa van Leeuwen <
tessa.vanleeuwen at fcdonders.ru.nl> wrote:

> Dear Fieldtrip experts,
>
> I have noticed enhanced coherence (sensor level) in my data after applying
> ICA during preprocessing, removing only 1 EOG component. Of course the
> (mainly quantitatively) enhanced coherence could be due to the removal of
> (artifact induced) noise from the data. But this increase also occured when
> applying ICA to previously cleaned data, implying changes induced by ICA
> somehow affect coherence.
>
> One of the aims of our project is to compute coherence/connectivity
> measures at the source level. Since connectivity measures are often
> difficult to interpret as they are, I would like to ask whether anyone has
> experience with connectivity analyses after preprocessing that involved
> ICA. Are people aware of possible influences of ICA on connectivity
> measures and is there a way to deal with this? Or would it be advisable NOT
> to use ICA when later looking at coherence/connectivity at the source level?
>
> We initially aim to compare across conditions (data that have been
> preprocessed together and from which the same ICA component has been
> removed). But we also have different experimental groups for which we would
> like to qualitatively compare active networks during our task.
>
> Thank you in advance for any input, it is highly appreciated.
>
> Best wishes,
> Tessa
>
>
> ---
>
> Tessa van Leeuwen, PhD
> postdoctoral researcher
>
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From batrod at gmail.com  Tue Mar 27 19:36:36 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Tue, 27 Mar 2012 12:36:36 -0500
Subject: [FieldTrip] optimum number of cycles
Message-ID: <CAPy7a9B64dcStbT9eEOZ4BR-HXq4WbkQ8LmzeqYxKNrnAooQqw@mail.gmail.com>

Dear filedtrippers, i had a question regarding the time-frequency analysis,
such as the one that can be found on the tutorial :
http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis

In the fixed-widow example, using a hanning taper, it is said that a fixed
widow of 500 ms can estimate power of different frequency bands like 2 Hz,
4Hz, etc...
However, for 2 Hz it means only 1 cycle.

In the frequency-dependent window length, 7 cycles per frequency bands are
used.

My questions are, is it ok to estimate a power with one cycle? What could
be the optimum number of cycles? Is ot ok to compare the power of different
frequency bands that have been estimated using a different number of cycles?

Thanks a lot,

Rodolphe.
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From smoratti at psi.ucm.es  Tue Mar 27 22:33:36 2012
From: smoratti at psi.ucm.es (smoratti at psi.ucm.es)
Date: Tue, 27 Mar 2012 22:33:36 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band,
	concept problem
In-Reply-To: <CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>
References: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
	<EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>
	<CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>
Message-ID: <E0D49E5B-2248-466C-A88D-0ECFB2E57851@psi.ucm.es>

Hi Mikel,

I think Jörn gave you already the answer. You need enough time points to accurately estimate the oscillations of a frequency. For example in wavelet analysis (morlet) people use at least 5 cycles.

Best,

Stephan

________________________________________________________
Stephan Moratti, PhD

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

Universidad Complutense de Madrid
Facultad de Psicología
Departamento de Psicología Básica I
Campus de Somosaguas
28223 Pozuelo de Alarcón (Madrid)
Spain

and

Center for Biomedical Technology
Laboratory for Cognitive and Computational Neuroscience
Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)
Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982

El 27/03/2012, a las 12:46, Ion Lavado escribió:

> Thank you Stephan, just one thing, why i need a time window big enough? so i'm just studying the frequency.
> 
> Best,
> 
> Mikel
> 
> 2012/3/27 Stephan Moratti <smoratti at psi.ucm.es>
> Dear Mikel,
> 
> I understand that you should do a mtmfft with a center frequency of interest (in your case cfg.foil = [11 11]) and then you do a frequency smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you need a time window big enough to allow such a smoothing. The CSD should represent a frequency window of 8 to 14 Hz then. Then you put the result of the mtmfft into the dics beamformer.
> 
> Best,
> 
> Stephan
>  
> El 27/03/2012, a las 11:19, Ion Lavado escribió:
> 
>> Hello, i'm having problems trying the beamformer analysis with a frequency band of interest. I would like to have for example an interval like [8 14] Hz. My concept problem is about the cfg.frequency and cfg.tapsmofrq  values. (it must be a escalar, but i want a frequency band). 
>> 
>> %FREQ ANALYSIS
>> cfg = [];
>> cfg.method    = 'mtmfft';
>> cfg.output    = 'powandcsd';
>> cfg.tapsmofrq = 5;
>> cfg.foilim    = [8 14];
>> freq_words_alpha = ft_freqanalysis(cfg, words);
>> 
>> 
>> %SOURCE ANALYSIS
>> cfg              = []; 
>> cfg.frequency    = 11;  
>> cfg.lambda=0;
>> cfg.method       = 'dics';
>> cfg.coordsys       = 'neuromag';
>> cfg.projectnoise = 'yes';
>> cfg.grad            =  freq_words_alpha.grad;
>> cfg.channel   = {'MEG'}; 
>> cfg.grid         = grid; 
>> cfg.reducerank      = 2;
>> cfg.vol          = vol02;
>> vol02=ft_convert_units(vol02,'cm');
>> source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
>> 
>> 
>> I use a cfg.frequency of 11 but i don't have really clear what i'm doing as a get the same result using cfg.frequency=11 but a freqanalysis in [10 12]. I would be very grateful if someone could solve my doubt.
>> 
>> Best wishes,
>> 
>> Mikel
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> ________________________________________________________
> Stephan Moratti, PhD
> 
> see also: http://web.me.com/smoratti/
> 
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> and
> 
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> 
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
> 
> 
> 
> _______________________________________________
> 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 tessa.vanleeuwen at fcdonders.ru.nl  Tue Mar 27 23:34:33 2012
From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen)
Date: Tue, 27 Mar 2012 23:34:33 +0200 (CEST)
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <CAPy7a9C0Av7RaH7QTsvErDBU-rf-Buu2x0EvfF5+mk=wGn=XnA@mail.gmail.com>
Message-ID: <1832235848.73257.1332884073180.JavaMail.root@draco.zimbra.ru.nl>

Dear Rodolphe, Thank you for your response, I tried to clarify below. > 1) After your first "cleaning", do you test coherence on particular
> components or your entire data minus the "EOG" component?
I tested the coherence on the entire dataset after removal of the EOG component. > 2) When you say that you redo ICA on cleaned data (of course, an ICA
> analysis made on a result of a previous ICA analysis with components
> removed is a bad idea), do you remove another component or do you test
> your coherence on particular components?
Sorry, I could have been more clear about this. I initially compared two versions of the same dataset: one in which all trials containing a blink were removed from the dataset after manual inspection; another version in which only trials with a blink during the actual stimulus period were removed manually and the rest of the trials, including trials with blinks outside the stimulus window, were 'cleaned' with ICA, i.e. the EOG component was removed. Eye-balling coherence in occipital channels, this was increased in the ICA-cleaned version. To check whether the increase in coherence could have been explained by an increased number of retained trials in the ICA-cleaned-version, I also applied the unmixing matrix obtained from the ICA to the manually cleaned version of the data, i.e., in which only smaller eye-movements or unidentified EOG artifacts would have been remaining after manual inspection. Now of course I could have been over-removing non-existent noise in this case, but also here the same difference in coherence appeared, now with the same number of trials in both condition. When I look at the time-frequency representations from both versions, these look highly similar, only small intensity differences can be seen. I only used a small amount of data to test this and these results might therefore not be completely reliable. But I know other people have experienced similar problems with altered coherence and I was wondering whether any effect of ICA-preprocessing on coherence/connectivity measures was generally known on the list and in the literature. Perhaps the removal of common noise with ICA can already explain the differences? Best wishes, Tessa > Rodolphe
> On Tue, Mar 27, 2012 at 11:27 AM, Tessa van Leeuwen <
> tessa.vanleeuwen at fcdonders.ru.nl > wrote:
> > Dear Fieldtrip experts,
> > I have noticed enhanced coherence (sensor level) in my data after
> > applying ICA during preprocessing, removing only 1 EOG component. Of
> > course the (mainly quantitatively) enhanced coherence could be due
> > to
> > the removal of (artifact induced) noise from the data. But this
> > increase also occured when applying ICA to previously cleaned data,
> > implying changes induced by ICA somehow affect coherence.
> > One of the aims of our project is to compute coherence/connectivity
> > measures at the source level. Since connectivity measures are often
> > difficult to interpret as they are, I would like to ask whether
> > anyone
> > has experience with connectivity analyses after preprocessing that
> > involved ICA. Are people aware of possible influences of ICA on
> > connectivity measures and is there a way to deal with this? Or would
> > it be advisable NOT to use ICA when later looking at
> > coherence/connectivity at the source level?
> > We initially aim to compare across conditions (data that have been
> > preprocessed together and from which the same ICA component has been
> > removed). But we also have different experimental groups for which
> > we
> > would like to qualitatively compare active networks during our task.
> > Thank you in advance for any input, it is highly appreciated.
> > Best wishes,
> > Tessa
> > ---
> > Tessa van Leeuwen, PhD
> > postdoctoral researcher
> > Department of Neurophysiology
> > Max Planck Institute for Brain Research
> > _______________________________________________
> > 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 yoni.levy at inserm.fr  Wed Mar 28 00:40:25 2012
From: yoni.levy at inserm.fr (yoni.levy at inserm.fr)
Date: Wed, 28 Mar 2012 00:40:25 +0200
Subject: [FieldTrip] actvsblT test statistic when running ft_freqstatistics
Message-ID: <20120328004025.8z450t1fk04wc8gk@imp.inserm.fr>

I am running the ft_freqstatistics using the actvsblT option, so as to  
statistically test activation period with baseline activity. For this,  
I followed the "Within trial experiments" tutorial in fieldtrip  
(http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq#within_trial_experiments).
The tutorial emphasizes that one should select equal length time  
windows. However, the number of trials in both conditions (activation  
and baseline) remains unequal. Therefore, when I run ft_freqstatistics  
with the design mentioned in the tutorial (inserting only the number  
of trials of the activation condition), I receive the following error  
message:
"the number of observations in the design does not match the number of  
observations in the data"

Is there an error in the turorial, or is the script intended to create  
two frequency output-files, with different total number of trials.

Thanks in advance,
Yoni


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





From batrod at gmail.com  Wed Mar 28 02:20:42 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Tue, 27 Mar 2012 19:20:42 -0500
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <1832235848.73257.1332884073180.JavaMail.root@draco.zimbra.ru.nl>
References: <CAPy7a9C0Av7RaH7QTsvErDBU-rf-Buu2x0EvfF5+mk=wGn=XnA@mail.gmail.com>
	<1832235848.73257.1332884073180.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <CAPy7a9CkPgza79Tg7fFykksYQhsfgVRkK63Hq4Q=uN+iO6Y4kQ@mail.gmail.com>

Dear Tessa,

ok this is more clear now.
ICA is a wonderful tool which can easily become your worst enemy in data
analyzing.

By removing yourself certains epochs with blinks before doing an ICA, its
is possible that you remove relevant data that can be used by your ICA
algorithm to better separate components.  Certain people would argue that
even filtering your data before ICA can be a bad idea.
Therefore, when you apply the ICA on your "cleaned" data, there is more
chance that the component that will reflect the most what is left from
blinks will also contains more relevant data.
This data removal could potentially decrease your data variability
therefore increase your coherence.
Also, the number of epochs you keep after your cleaning (which should be
different from ICA compared to visual removal) could potentially explain
such a difference.

Hope this helps,

Rodolphe


On Tue, Mar 27, 2012 at 4:34 PM, Tessa van Leeuwen <
tessa.vanleeuwen at fcdonders.ru.nl> wrote:

> Dear Rodolphe,
>
> Thank you for your response, I tried to clarify below.
>
>
> 1) After your first "cleaning", do you test coherence on particular
> components or your entire data minus the "EOG" component?
>
> I tested the coherence on the entire dataset after removal of the EOG
> component.
>
> 2) When you say that you redo ICA on cleaned data (of course, an ICA
> analysis made on a result of a previous ICA analysis with components
> removed is a bad idea), do you remove another component or do you  test
> your coherence on particular components?
>
> Sorry, I could have been more clear about this. I initially compared two
> versions of the same dataset: one in which all trials containing a blink
> were removed from the dataset after manual inspection; another version in
> which only trials with a blink during the actual stimulus period were
> removed manually and the rest of the trials, including trials with blinks
> outside the stimulus window, were 'cleaned' with ICA, i.e. the EOG
> component was removed. Eye-balling coherence in occipital channels, this
> was increased in the ICA-cleaned version.
>
> To check whether the increase in coherence could have been explained by an
> increased number of retained trials in the ICA-cleaned-version, I also
> applied the unmixing matrix obtained from the ICA to the manually cleaned
> version of the data, i.e., in which only smaller eye-movements or
> unidentified EOG artifacts would have been remaining after manual
> inspection. Now of course I could have been over-removing non-existent
> noise in this case, but also here the same difference in coherence
> appeared, now with the same number of trials in both condition. When I look
> at the time-frequency representations from both versions, these look highly
> similar, only small intensity differences can be seen.
>
> I only used a small amount of data to test this and these results might
> therefore not be completely reliable. But I know other people have
> experienced similar problems with altered coherence and I was wondering
> whether any effect of ICA-preprocessing on coherence/connectivity measures
> was generally known on the list and in the literature. Perhaps the removal
> of common noise with ICA can already explain the differences?
>
> Best wishes,
> Tessa
>
>
> Rodolphe
>
> On Tue, Mar 27, 2012 at 11:27 AM, Tessa van Leeuwen <
> tessa.vanleeuwen at fcdonders.ru.nl> wrote:
>
>> Dear Fieldtrip experts,
>>
>> I have noticed enhanced coherence (sensor level) in my data after
>> applying ICA during preprocessing, removing only 1 EOG component. Of course
>> the (mainly quantitatively) enhanced coherence could be due to the removal
>> of (artifact induced) noise from the data. But this increase also occured
>> when applying ICA to previously cleaned data, implying changes induced by
>> ICA somehow affect coherence.
>>
>> One of the aims of our project is to compute coherence/connectivity
>> measures at the source level. Since connectivity measures are often
>> difficult to interpret as they are, I would like to ask whether anyone has
>> experience with connectivity analyses after preprocessing that involved
>> ICA. Are people aware of possible influences of ICA on connectivity
>> measures and is there a way to deal with this? Or would it be advisable NOT
>> to use ICA when later looking at coherence/connectivity at the source level?
>>
>> We initially aim to compare across conditions (data that have been
>> preprocessed together and from which the same ICA component has been
>> removed). But we also have different experimental groups for which we would
>> like to qualitatively compare active networks during our task.
>>
>> Thank you in advance for any input, it is highly appreciated.
>>
>> Best wishes,
>> Tessa
>>
>>
>> ---
>>
>> Tessa van Leeuwen, PhD
>> postdoctoral researcher
>>
>> Department of Neurophysiology
>> Max Planck Institute for Brain Research
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From sysoevao at psychiatry.wustl.edu  Wed Mar 28 04:01:22 2012
From: sysoevao at psychiatry.wustl.edu (Sysoeva, Olga Vladimirovna)
Date: Wed, 28 Mar 2012 02:01:22 +0000
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <CAPy7a9CkPgza79Tg7fFykksYQhsfgVRkK63Hq4Q=uN+iO6Y4kQ@mail.gmail.com>
References: <CAPy7a9C0Av7RaH7QTsvErDBU-rf-Buu2x0EvfF5+mk=wGn=XnA@mail.gmail.com>
	<1832235848.73257.1332884073180.JavaMail.root@draco.zimbra.ru.nl>,
	<CAPy7a9CkPgza79Tg7fFykksYQhsfgVRkK63Hq4Q=uN+iO6Y4kQ@mail.gmail.com>
Message-ID: <41C83D63782BE149B1B984A58E866D8FE82D@CITEMB2D.cits.wustl.edu>

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From politzerahless at gmail.com  Wed Mar 28 06:58:34 2012
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Tue, 27 Mar 2012 23:58:34 -0500
Subject: [FieldTrip] question to the fieldtrip developers - multiple spm
 versions in fieldtrip
Message-ID: <CAJT2k_-jbUesSdb1b3Y6TaTQwx7P8oFw6nMGoVz-Qjw=VAX26Q@mail.gmail.com>

Hi Frederic,

As far as I know, those SPM errors are a consequence of adding all the
subdirectories of FieldTrip to your MATLAB path; see
http://fieldtrip.fcdonders.nl/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path.
If you add just the main Fieldtrip directory instead of all
subdirectories, you shouldn't get the error. I haven't tried
ft_sourceanalysis myself so I'm not sure if this issue has any consequences
when running that.

Best,
Steve

----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 27 Mar 2012 12:14:45 +0200
> From: Frederic Roux <fredericroux at hotmail.de>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] question to the fieldtrip developers - multiple
>        spm versions in fieldtrip
> Message-ID: <DUB113-W12B64F64480B0A75AB493EB74A0 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
> Dear all,
>
> I would like to ask again if the fact of getting a warning
> that different spm versions will confuse fieldtrip
> can have consequences in the ft_sourceanalysis pipeline.
>
> I am using version 2012-01-05 which has SPM2 and SPM8
> in the external folder.
>
> It would be great if someone from the development-team could tell me
>
> a) why this is a problem
> b) how to circumvent it
>
>
> I renamed the spm.m file into spm.m.bak in the SPM2 folder so that
> only the spm.m file from the SPM8 folder is used. However, it would
> be great if someone could tell me if this is a workaround or not.
>
>
> Best regards,
> Fred
>
> --
> Fr?d?ric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
>
>
>
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From m.leszczynski.m at googlemail.com  Wed Mar 28 08:22:23 2012
From: m.leszczynski.m at googlemail.com (Marcin)
Date: Wed, 28 Mar 2012 08:22:23 +0200
Subject: [FieldTrip] statfun_depsamplesregrT
In-Reply-To: <4f6b87bf.86600e0a.3f3a.ffff8106SMTPIN_ADDED@mx.google.com>
References: <CAAVVtzDY5stRD-XE2Pa5TjrO1L8AJXXSZToy7XhA72hK22bu+w@mail.gmail.com>
	<4f6b87bf.86600e0a.3f3a.ffff8106SMTPIN_ADDED@mx.google.com>
Message-ID: <CAAVVtzAJe6zEuu-wR_6MX8c7bSekX+k0v=H43TAnGRMt2yz=2g@mail.gmail.com>

Dear Dr. Maris,

thanks for your reply.
If I get you right you say that whether I use the statfun_depsamplesregrT
or use/write statfun_depsamplesrankcorr depends on assumed (apriori)
relation between the predictor variable (experimental condition) and the
data. If I assume linearity (i.e. in the case of WM load:  ERP/TF(1) <
ERP/TF(2) < ERP/TF(3) < ERP/TF(4)) I might use the statfun_depsamplesregrT.
If I doubt linearity (i.e.WM load ERP/TF(1) < ERP/TF(2) <= ERP/TF(3) <
ERP/TF(4)) I should use the statfun_depsamplesrankcorr. Is this correct?

I am not sure if I underestood your point about reference distribution. Are
you saying that for the cluster-based permutation inference I need to
threshold on a reference distribution which might be either parametric or
non-parametric? If this is the case. What does it depend on whether I use
parametric or non parametric reference distribution?

Thank you again for your time and your help.

Best,
Marcin

W dniu 22 marca 2012 21:12 użytkownik Eric Maris <e.maris at psych.ru.nl>napisał:

> Dear Marcin,****
>
> ** **
>
> ** **
>
> The statfun_depsamplesregrT calculates a T-statistic for regression
> coefficients that are calculated within each of the units-of-observation
> (typically, participants) obtained by regressing the subject-specific data
> (spatiotemporal, spatio-spectral, spatio-spectro-temporal) on some
> predictor variable that varies over the different conditions in which this
> participant has provided data (e.g., working-memory load, retention
> interval, luminance, contrast, etc). If you doubt the assumed linear
> relation between predictor variable and biological data, then you could
> write your own statfun_depsamplesrankcorr. To use this test statistic for
> cluster-based permutation inference, you need a threshold based on some
> reference distribution (which can be parametric, but must not be). ****
>
> ** **
>
> To get this statfun_depsamplesrankcorr running, you will probably have to
> take a look in the Fieldtrip code to see how the statistics framework is
> structured.****
>
> ** **
>
> Best,****
>
> ** **
>
> Eric Maris****
>
> ** **
>
> ** **
>
> *From:* Marcin [mailto:m.leszczynski.m at googlemail.com]
> *Sent:* woensdag 21 maart 2012 10:51
> *To:* Email discussion list for the FieldTrip project
> *Subject:* [FieldTrip] statfun_depsamplesregrT****
>
> ** **
>
> Dear Fieldtripers,
>
> Could anyone explain me what is being calculated with the
> statfun_depsamplesregrT function, please.
>
> David Groppe (thank you David) suggested in a previous thread on the list
> that I might calculate permutation test based on rank correlation to
> account for monotonic relationships within the permutation framework. I was
> wondering if this is the kind of test that statfun_depsamplesregrT function
> calculates.
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-December/004578.html
>
> Best,
> Marcin****
>
> _______________________________________________
> 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  Wed Mar 28 09:32:30 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 28 Mar 2012 09:32:30 +0200
Subject: [FieldTrip] optimum number of cycles
In-Reply-To: <CAPy7a9B64dcStbT9eEOZ4BR-HXq4WbkQ8LmzeqYxKNrnAooQqw@mail.gmail.com>
References: <CAPy7a9B64dcStbT9eEOZ4BR-HXq4WbkQ8LmzeqYxKNrnAooQqw@mail.gmail.com>
Message-ID: <4F72BE8E.7020603@donders.ru.nl>

Hi Rodolphe,

I don't think that your questions have a 'best' answer, but see below 
for my opinion.

> In the fixed-widow example, using a hanning taper, it is said that a 
> fixed widow of 500 ms can estimate power of different frequency bands 
> like 2 Hz, 4Hz, etc...
> However, for 2 Hz it means only 1 cycle.
>
> In the frequency-dependent window length, 7 cycles per frequency bands 
> are used.
>
> My questions are, is it ok to estimate a power with one cycle?

I would say no, but it depends on what trade-off between precision in 
time and frequency space you want to achieve. Of course it can be done, 
but the estimate is much more unreliable than when taking more cycles.

>  What could be the optimum number of cycles?

It depends on your question and frequency band. I would use at least 
three to five cycles for the most prominent frequencies(theta, alpha, 
beta), maybe two for very low frequencies (delta and below) and at least 
six or seven for higher frequencies (>40Hz). Some people use a fixed 
window length for the gamma-range and frequency smoothing around 10Hz, 
independent of the exact frequency (see e.g. the Neuron paper by Siegel 
et al., 2008, they use 250ms and 12Hz smoothing)

> Is ot ok to compare the power of different frequency bands that have 
> been estimated using a different number of cycles?

Yes and no, because different frequency bands have different 
characteristics, and are influenced differently by the 1/f noise. Taking 
more cycles for a higher frequency band and less for lower sounds 
logical, given that a signal low SNR requires more smoothing to reliably 
estimate the frequency content. However, frequencies bands are due to 
this 1/f noise different in power, e.g. alpha band activity will always 
have more power than gamma band activity.

>
> Thanks a lot,

You're welcome.

Best,
Jörn

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

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 jm.horschig at donders.ru.nl  Wed Mar 28 09:41:29 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 28 Mar 2012 09:41:29 +0200
Subject: [FieldTrip] Time stamp per sample
In-Reply-To: <CAG3TGCN+1ZV7zaAbGKvm8j3M1arg8pQXRgrfSLaof2hVp7G-vg@mail.gmail.com>
References: <CAG3TGCN+1ZV7zaAbGKvm8j3M1arg8pQXRgrfSLaof2hVp7G-vg@mail.gmail.com>
Message-ID: <4F72C0A9.7040604@donders.ru.nl>

Hi Anton,

This depends on the decimation rate that you specify, see here:
http://fieldtrip.fcdonders.nl/development/realtime/ctf?s[]=acq2ftx#downsampling_channel_selection_applying_gains

You can use ft_read_header(buffer) to read out the sampling frequency 
and then call ft_read_data to read the data. Here, you can specify a 
begin and an endsample, which define the length of the data the function 
returns. Prior, you can call ft_read_event to get the time stamp of the 
trigger value of interest. If you are interested in continuously reading 
data in without relying on certain events, you can don't need to call 
ft_read_event.

In FieldTrip, there are some example functions that you can look at, 
/e.g. //ft_realtime_asynchronous/ or/ft_realtime_synchronous/, see also 
here:
http://fieldtrip.fcdonders.nl/tutorial/realtime

 From what you wrote I get that the asynchronous type is what you aim for.

Best,
Jörn



On 3/27/2012 7:13 PM, Anton Andreev wrote:
> Hi,
>
> I have a question about the fieldtrip buffer.
> Does the protocol provides information about the time every sample has 
> been taken?
>
> I would like to produce a chunk of data for 300ms or 1 second for 
> example.
> I can build such chunk if I simply sort out samples that are in the 
> time range of 1 second starting with the time stamp of the first one. 
> Then again for 1 second and ....
>
> Thanks,
> Anton
>
>
> _______________________________________________
> 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

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 tessa.vanleeuwen at fcdonders.ru.nl  Wed Mar 28 10:59:58 2012
From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen)
Date: Wed, 28 Mar 2012 10:59:58 +0200 (CEST)
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <41C83D63782BE149B1B984A58E866D8FE82D@CITEMB2D.cits.wustl.edu>
Message-ID: <2130657903.77844.1332925198031.JavaMail.root@draco.zimbra.ru.nl>

Dear Olga, Thank you very much for your reply, this is very useful information! Because my trials are short I do not have sufficient data to let ICA compute all 275 possible components from my 275 channels - I use component reduction and estimate 80 components. This could then very well be the reason why coherence is altered after ICA. It makes sense that the interpolation would destroy any original phase relationships that are there. Thanks! Best wishes, Tessa ----- Original Message -----
> From: "Olga Vladimirovna Sysoeva" <sysoevao at psychiatry.wustl.edu>
> To: "Email discussion list for the FieldTrip project"
> <fieldtrip at donders.ru.nl>
> Sent: Wednesday, March 28, 2012 4:01:22 AM
> Subject: Re: [FieldTrip] coherence/connectivity measures after
> applying ICA
> Hi, Tessa,
> I do not have much experience for myself with coherence, but I'm very
> interested in the question you raised. Here is what I've seen in
> R.Thatcher's tutorial on Adulteration of Phase Relations when using
> Independent Components Analysis/Blind Identification and other
> Regression Methods to “Correct for Artifact
> http://www.appliedneuroscience.com/Tutorial%20on%20ICA%20Phase%20Adulteration.pdf
> .
> "Let us consider the rejection of eye movement artifact (EOG) using
> the ICA method which is the mathematical basis for Blind Source
> analysis. The ICA method decomposes a time series into a set of
> globally independent time series. Mathematically ICA can invert the
> equation and exactly reproduce the original time series based on the
> mathematical components. In this case the originally measured time or
> phase differences between each electrode are preserved and the
> cross-spectrum is unaltered.
> However, everything changes when the ICA or PCA or Blind Source, etc.
> methods are used to remove artifact by reconstructing 19 channels
> based on a smaller set of components, e.g., 17 or 18 channels and then
> deleting or omitting the EOG “components” to reconstruct 19 channels.
> This is because a regression process (interpolation) is used to
> minimize the deviation of the original 19 channel time series from the
> 17 or 18 “components” by which the remainder is used as weights to
> produce a second time series that has altered all of the phase
> relations in the original time series. The regression uses the average
> of the entire time series and therefore “smoothes” time or phase at
> each time point. Averaging a time series and computing deviations
> (whether information min-max, equimax, or simple linear regression)
> and then using the result to weight each time point by averages
> thereby smoothes each data point’s phase relations at each moment of
> time, distorting coherence, and destroys the time and phase relations
> present in the original time series."
> Hope it can help...
> Best Regards,
> Olga
> Olga Sysoeva,
> Research Associate, PhD
> Washington University School of Medicine
> Campus Box 8134
> 660 South Euclid Ave
> Saint Louis, MO 63110-9909
> From: fieldtrip-bounces at donders.ru.nl
> [fieldtrip-bounces at donders.ru.nl] on behalf of Rodolphe Nenert
> [batrod at gmail.com]
> Sent: Tuesday, March 27, 2012 7:20 PM
> To: Email discussion list for the FieldTrip project
> Subject: Re: [FieldTrip] coherence/connectivity measures after
> applying ICA
> Dear Tessa,
> ok this is more clear now.
> ICA is a wonderful tool which can easily become your worst enemy in
> data analyzing.
> By removing yourself certains epochs with blinks before doing an ICA,
> its is possible that you remove relevant data that can be used by your
> ICA algorithm to better separate components. Certain people would
> argue that even filtering your data before ICA can be a bad idea.
> Therefore, when you apply the ICA on your "cleaned" data, there is
> more chance that the component that will reflect the most what is left
> from blinks will also contains more relevant data.
> This data removal could potentially decrease your data variability
> therefore increase your coherence.
> Also, the number of epochs you keep after your cleaning (which should
> be different from ICA compared to visual removal) could potentially
> explain such a difference.
> Hope this helps,
> Rodolphe
> On Tue, Mar 27, 2012 at 4:34 PM, Tessa van Leeuwen <
> tessa.vanleeuwen at fcdonders.ru.nl > wrote:
> > Dear Rodolphe,
> > Thank you for your response, I tried to clarify below.
> > > 1) After your first "cleaning", do you test coherence on
> > > particular
> > > components or your entire data minus the "EOG" component?
> > I tested the coherence on the entire dataset after removal of the
> > EOG
> > component.
> > > 2) When you say that you redo ICA on cleaned data (of course, an
> > > ICA
> > > analysis made on a result of a previous ICA analysis with
> > > components
> > > removed is a bad idea), do you remove another component or do you
> > > test
> > > your coherence on particular components?
> > Sorry, I could have been more clear about this. I initially compared
> > two versions of the same dataset: one in which all trials containing
> > a
> > blink were removed from the dataset after manual inspection; another
> > version in which only trials with a blink during the actual stimulus
> > period were removed manually and the rest of the trials, including
> > trials with blinks outside the stimulus window, were 'cleaned' with
> > ICA, i.e. the EOG component was removed. Eye-balling coherence in
> > occipital channels, this was increased in the ICA-cleaned version.
> > To check whether the increase in coherence could have been explained
> > by an increased number of retained trials in the
> > ICA-cleaned-version,
> > I also applied the unmixing matrix obtained from the ICA to the
> > manually cleaned version of the data, i.e., in which only smaller
> > eye-movements or unidentified EOG artifacts would have been
> > remaining
> > after manual inspection. Now of course I could have been
> > over-removing
> > non-existent noise in this case, but also here the same difference
> > in
> > coherence appeared, now with the same number of trials in both
> > condition. When I look at the time-frequency representations from
> > both
> > versions, these look highly similar, only small intensity
> > differences
> > can be seen.
> > I only used a small amount of data to test this and these results
> > might therefore not be completely reliable. But I know other people
> > have experienced similar problems with altered coherence and I was
> > wondering whether any effect of ICA-preprocessing on
> > coherence/connectivity measures was generally known on the list and
> > in
> > the literature. Perhaps the removal of common noise with ICA can
> > already explain the differences?
> > Best wishes,
> > Tessa
> > > Rodolphe
> > > On Tue, Mar 27, 2012 at 11:27 AM, Tessa van Leeuwen <
> > > tessa.vanleeuwen at fcdonders.ru.nl > wrote:
> > > > Dear Fieldtrip experts,
> > > > I have noticed enhanced coherence (sensor level) in my data
> > > > after
> > > > applying ICA during preprocessing, removing only 1 EOG
> > > > component.
> > > > Of
> > > > course the (mainly quantitatively) enhanced coherence could be
> > > > due
> > > > to
> > > > the removal of (artifact induced) noise from the data. But this
> > > > increase also occured when applying ICA to previously cleaned
> > > > data,
> > > > implying changes induced by ICA somehow affect coherence.
> > > > One of the aims of our project is to compute
> > > > coherence/connectivity
> > > > measures at the source level. Since connectivity measures are
> > > > often
> > > > difficult to interpret as they are, I would like to ask whether
> > > > anyone
> > > > has experience with connectivity analyses after preprocessing
> > > > that
> > > > involved ICA. Are people aware of possible influences of ICA on
> > > > connectivity measures and is there a way to deal with this? Or
> > > > would
> > > > it be advisable NOT to use ICA when later looking at
> > > > coherence/connectivity at the source level?
> > > > We initially aim to compare across conditions (data that have
> > > > been
> > > > preprocessed together and from which the same ICA component has
> > > > been
> > > > removed). But we also have different experimental groups for
> > > > which
> > > > we
> > > > would like to qualitatively compare active networks during our
> > > > task.
> > > > Thank you in advance for any input, it is highly appreciated.
> > > > Best wishes,
> > > > Tessa
> > > > ---
> > > > Tessa van Leeuwen, PhD
> > > > postdoctoral researcher
> > > > Department of Neurophysiology
> > > > Max Planck Institute for Brain Research
> > > > _______________________________________________
> > > > 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
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If
> you are not the intended recipient, be advised that any unauthorized
> use, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If
> you are not the intended recipient, be advised that any unauthorized
> use, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From dieter.devlaminck at inria.fr  Wed Mar 28 11:26:15 2012
From: dieter.devlaminck at inria.fr (Dieter Devlaminck)
Date: Wed, 28 Mar 2012 11:26:15 +0200 (CEST)
Subject: [FieldTrip] warning: the trial definition in the configuration is
 inconsistent with the actual data
In-Reply-To: <763718776.653827.1332926546901.JavaMail.root@zmbs2.inria.fr>
Message-ID: <1286872503.653958.1332926775888.JavaMail.root@zmbs2.inria.fr>


Dear All, 

When I try to invoke the 'ft_topoplotER(cfg,GA_FC)' command, I get the following warning 

Warning: the trial definition in the configuration is inconsistent with the actual data 

This happens both with the tutorial data as with my own data and is apparently caused by the fact that in the data structure there is a field 'previous' which in turn contains a field 'trl' which contains information on all triggers found in my original data. As I only take the average of the trials corresponding to certain target stimuli with ft_timelockanalysis (using 'cfg.trials = find(data.cfg.trl(:,end));') and then try to make a plot of that, fieldtrip finds an inconsistency in the dimensions and then does some kind of reconstruction, stating the following 

Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording 

This worries me a bit as I do not know exactly what it is doing although the tutorial plot seemed to be the same as the one on the website. What can I do to avoid this warning? 

I use fieldtrip version 20120308 and matlab R2010b on fedora 14. 

Thanks in advance, 
Best regards, 
Dieter Devlaminck 
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From eelke.spaak at donders.ru.nl  Wed Mar 28 11:39:05 2012
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Wed, 28 Mar 2012 11:39:05 +0200
Subject: [FieldTrip] warning: the trial definition in the configuration
 is inconsistent with the actual data
In-Reply-To: <1286872503.653958.1332926775888.JavaMail.root@zmbs2.inria.fr>
References: <763718776.653827.1332926546901.JavaMail.root@zmbs2.inria.fr>
	<1286872503.653958.1332926775888.JavaMail.root@zmbs2.inria.fr>
Message-ID: <CABPNLUozQGCeGXm3DkH5eVrG5155RsBncFpjCfTwfTbPnSSmOg@mail.gmail.com>

Dear Dieter,

You have correctly tracked down the cause of the warning: the actual
data is inconsistent with a trl-matrix found somewhere in your
data.cfg (.previous) tree.

The reason you are getting these warnings is that certain FieldTrip
functions (apparently including ft_topoplotER and/or some of its
dependencies) require a data.sampleinfo field in your data structure
that is consistent with the actual data. In general, data.sampleinfo
is an Nx2 matrix containing, for each trial in the data, the indices
of the begin and end sample of that trial, with respect to the
original data set (on disk). If such a consistent data.sampleinfo does
not exist, as is the case with your data, fieldtrip will simply
reconstruct this sampleinfo by using 1 as the begin sample of trial 1,
and k as its end sample, where k is the number of samples in trial 1.
Trial 2 will be numbered from k+1 to k+n, where n is trial 2's length,
etc. This allows all FT functions depending on sampleinfo to function
adequately. Thus, given that you understand where the warning comes
from (as is the case), you should not worry about it and can safely
ignore it.

Do keep in mind, though (also for other people on the list, who might
find this post in the future), that you cannot interpret the
reconstructed sampleinfo in terms of the original recording anymore.
This is not an issue with the plotting functions (since you do not
directly use the manipulated data anyway), but might become relevant
when you e.g. use ft_databrowser or ft_artifact_zvalue, which can
return segments of interest in your data, specified in begin and end
samples.

Best,
Eelke

On 28 March 2012 11:26, Dieter Devlaminck <dieter.devlaminck at inria.fr> wrote:
> Dear All,
>
> When I try to invoke the 'ft_topoplotER(cfg,GA_FC)' command, I get the
> following warning
>
> Warning: the trial definition in the configuration is inconsistent with the
> actual data
>
> This happens both with the tutorial data as with my own data and is
> apparently caused by the fact that in the data structure there is a field
> 'previous' which in turn contains a field 'trl' which contains information
> on all triggers found in my original data. As I only take the average of the
> trials corresponding to certain target stimuli with ft_timelockanalysis
> (using 'cfg.trials = find(data.cfg.trl(:,end));') and then try to make a
> plot of that, fieldtrip finds an inconsistency in the dimensions and then
> does some kind of reconstruction, stating the following
>
> Warning: reconstructing sampleinfo by assuming that the trials are
> consecutive segments of a continuous recording
>
> This worries me a bit as I do not know exactly what it is doing although the
> tutorial plot seemed to be the same as the one on the website. What can I do
> to avoid this warning?
>
> I use fieldtrip version 20120308 and matlab R2010b on fedora 14.
>
> Thanks in advance,
> Best regards,
> Dieter Devlaminck
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From dieter.devlaminck at inria.fr  Wed Mar 28 13:07:34 2012
From: dieter.devlaminck at inria.fr (Dieter Devlaminck)
Date: Wed, 28 Mar 2012 13:07:34 +0200 (CEST)
Subject: [FieldTrip] warning: the trial definition in the configuration
 is inconsistent with the actual data
In-Reply-To: <CABPNLUozQGCeGXm3DkH5eVrG5155RsBncFpjCfTwfTbPnSSmOg@mail.gmail.com>
Message-ID: <1504836263.656522.1332932854634.JavaMail.root@zmbs2.inria.fr>

Dear Eelke,

Thank you for answering so quickly.

> Do keep in mind, though (also for other people on the list, who might
> find this post in the future), that you cannot interpret the
> reconstructed sampleinfo in terms of the original recording anymore.
> This is not an issue with the plotting functions (since you do not
> directly use the manipulated data anyway), but might become relevant
> when you e.g. use ft_databrowser or ft_artifact_zvalue, which can
> return segments of interest in your data, specified in begin and end
> samples.

Indeed, this is the main reason why I asked this question, as it might have repercussions when calling other methods.

Is there a reason why the sampleinfo field disappears when calling the ft_timelockanalysis method? The field is still present in my data after calling the ft_redefinetrial method. I assume the normal operation is that the sampleinfo field is still present as it is normally used by subsequent methods?

A second thing I noticed is that now that I read my file with ft_preprocessing as one continuous trial and then partition my data into trials with ft_definetrials and ft_redefinetrials that the trialinfo (where I set some custom labels with my own trialfun) field has disappeared. If I first call ft_definetrials and the ft_preprocessing the trialinfo field is still there.

Best regards,
Dieter Devlaminck

----- Oorspronkelijk bericht -----
> Van: "Eelke Spaak" <eelke.spaak at donders.ru.nl>
> Aan: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
> Verzonden: Woensdag 28 maart 2012 11:39:05
> Onderwerp: Re: [FieldTrip] warning: the trial definition in the configuration is inconsistent with the actual data
> Dear Dieter,
> 
> You have correctly tracked down the cause of the warning: the actual
> data is inconsistent with a trl-matrix found somewhere in your
> data.cfg (.previous) tree.
> 
> The reason you are getting these warnings is that certain FieldTrip
> functions (apparently including ft_topoplotER and/or some of its
> dependencies) require a data.sampleinfo field in your data structure
> that is consistent with the actual data. In general, data.sampleinfo
> is an Nx2 matrix containing, for each trial in the data, the indices
> of the begin and end sample of that trial, with respect to the
> original data set (on disk). If such a consistent data.sampleinfo does
> not exist, as is the case with your data, fieldtrip will simply
> reconstruct this sampleinfo by using 1 as the begin sample of trial 1,
> and k as its end sample, where k is the number of samples in trial 1.
> Trial 2 will be numbered from k+1 to k+n, where n is trial 2's length,
> etc. This allows all FT functions depending on sampleinfo to function
> adequately. Thus, given that you understand where the warning comes
> from (as is the case), you should not worry about it and can safely
> ignore it.
> 
> Do keep in mind, though (also for other people on the list, who might
> find this post in the future), that you cannot interpret the
> reconstructed sampleinfo in terms of the original recording anymore.
> This is not an issue with the plotting functions (since you do not
> directly use the manipulated data anyway), but might become relevant
> when you e.g. use ft_databrowser or ft_artifact_zvalue, which can
> return segments of interest in your data, specified in begin and end
> samples.
> 
> Best,
> Eelke
> 
> On 28 March 2012 11:26, Dieter Devlaminck <dieter.devlaminck at inria.fr>
> wrote:
> > Dear All,
> >
> > When I try to invoke the 'ft_topoplotER(cfg,GA_FC)' command, I get
> > the
> > following warning
> >
> > Warning: the trial definition in the configuration is inconsistent
> > with the
> > actual data
> >
> > This happens both with the tutorial data as with my own data and is
> > apparently caused by the fact that in the data structure there is a
> > field
> > 'previous' which in turn contains a field 'trl' which contains
> > information
> > on all triggers found in my original data. As I only take the
> > average of the
> > trials corresponding to certain target stimuli with
> > ft_timelockanalysis
> > (using 'cfg.trials = find(data.cfg.trl(:,end));') and then try to
> > make a
> > plot of that, fieldtrip finds an inconsistency in the dimensions and
> > then
> > does some kind of reconstruction, stating the following
> >
> > Warning: reconstructing sampleinfo by assuming that the trials are
> > consecutive segments of a continuous recording
> >
> > This worries me a bit as I do not know exactly what it is doing
> > although the
> > tutorial plot seemed to be the same as the one on the website. What
> > can I do
> > to avoid this warning?
> >
> > I use fieldtrip version 20120308 and matlab R2010b on fedora 14.
> >
> > Thanks in advance,
> > Best regards,
> > Dieter Devlaminck
> >
> > _______________________________________________
> > 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 akiko.ikkai at gmail.com  Thu Mar 29 00:22:46 2012
From: akiko.ikkai at gmail.com (Akiko Ikkai)
Date: Wed, 28 Mar 2012 18:22:46 -0400
Subject: [FieldTrip] beamformer results smaller than brain
Message-ID: <CAKwx6Qc-TBiKARXJmJewk2Ob-CMZpTyXijCJ71iuOYGkH0ZbQA@mail.gmail.com>

Hi Fieldtrip users,

I'm hoping that someone could give me advice on segmentation and beamformer
on EEG data. I have EEG data set based on 128 channel cap. Thanks to the
help I got in mid-Feb, I'm now able to create a decent
segmentation (seg_results image attached) and volume conduction model.
However, when I run beamformer based on these models, resulting beamforming
image is often smaller than the brain (beamformer_result attached).
Particularly posterior parietal and occipital map is NaN.

I have tried going back to segmentation and expanded brain by
using imdilate after ft_volumesegment such as:

newbrain = imdilate(seg2.brain,strel_bol(1)); % seg2.brain is original
brain tissue from segmentation

seg2.brain = newbrain;
seg2.seg = seg2.scalp + seg2.skull*3 + seg2.brain*6;

and run ft_prepare_mesh_new on seg2. Of course, I have to make sure there
is no intersect between different tissue types, so using imdilate has
limitation.

Could someone explain why this shrinkage might be happening, and how I
could fix it?

Thanks in advance! Akiko

-- 
Akiko Ikkai, Ph.D.
Postdoctoral Fellow
Department of Psychological and Brain Sciences
Johns Hopkins University
Ames Hall, 3400 N. Charles St.
Baltimore, MD 21218
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From a.stolk at fcdonders.ru.nl  Thu Mar 29 10:19:47 2012
From: a.stolk at fcdonders.ru.nl (Stolk, A.)
Date: Thu, 29 Mar 2012 10:19:47 +0200 (CEST)
Subject: [FieldTrip] beamformer results smaller than brain
In-Reply-To: <CAKwx6Qc-TBiKARXJmJewk2Ob-CMZpTyXijCJ71iuOYGkH0ZbQA@mail.gmail.com>
Message-ID: <1939595059.215032.1333009187080.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Akiko, I'm not sure whether this is causing it, but w hat size inwardshift did you use when preparing your sourcemodel? Also check this page on our wiki: http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space Best, Arjen ----- Oorspronkelijk bericht -----
> Van: "Akiko Ikkai" <akiko.ikkai at gmail.com>
> Aan: fieldtrip at donders.ru.nl
> Verzonden: Donderdag 29 maart 2012 00:22:46
> Onderwerp: [FieldTrip] beamformer results smaller than brain
> Hi Fieldtrip users,
> I'm hoping that someone could give me advice on segmentation and
> beamformer on EEG data. I have EEG data set based on 128 channel cap.
> Thanks to the help I got in mid-Feb, I'm now able to create a decent
> segmentation (seg_results image attached) and volume conduction model.
> However, when I run beamformer based on these models, resulting
> beamforming image is often smaller than the brain (beamformer_result
> attached). Particularly posterior parietal and occipital map is NaN. 
> I have tried going back to segmentation and expanded brain by
> using imdilate after ft_volumesegment such as:
> newbrain = imdilate(seg2.brain,strel_bol(1)); % seg2.brain is original
> brain tissue from segmentation
> seg2.brain = newbrain;
> seg2.seg = seg2.scalp + seg2.skull*3 + seg2.brain*6;
> and run ft_prepare_mesh_new on seg2. Of course, I have to make sure
> there is no intersect between different tissue types, so using
> imdilate has limitation. 
> Could someone explain why this shrinkage might be happening, and how I
> could fix it? 
> Thanks in advance! Akiko
> --
> Akiko Ikkai, Ph.D.
> Postdoctoral Fellow
> Department of Psychological and Brain Sciences
> Johns Hopkins University
> Ames Hall, 3400 N. Charles St.
> Baltimore, MD 21218
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From g.piantoni at nin.knaw.nl  Thu Mar 29 11:13:19 2012
From: g.piantoni at nin.knaw.nl (Gio Piantoni)
Date: Thu, 29 Mar 2012 11:13:19 +0200
Subject: [FieldTrip] beamformer results smaller than brain
In-Reply-To: <CAKwx6Qc-TBiKARXJmJewk2Ob-CMZpTyXijCJ71iuOYGkH0ZbQA@mail.gmail.com>
References: <CAKwx6Qc-TBiKARXJmJewk2Ob-CMZpTyXijCJ71iuOYGkH0ZbQA@mail.gmail.com>
Message-ID: <CAHeOcruuVvKPDwhwXfozS8s6VciGf8T_stFcjYLMjOEvVOJiMg@mail.gmail.com>

Hi Akiko,

Your headmodel looks pretty good and your beamformer plot seems to
cover most of the gray matter.

However, it's good to check the location of your dipoles in respect to
your headmodel. For example, you can plot the .pos field of your
leadfield. Something like:

ft_plot_mesh(bnd(3), 'facealpha', .5)
hold on
plot3(lead.pos(:,1), lead.pos(:,2), lead.pos(:,3), '.')

It might well be that your grid is too coarse and some dipoles just
happen to be over the edge of the brain. Remember that your
"beamformer_result.png" is just an interpolation of the values of this
dipole grid.

You can either try to make your grid more refined (but remember that
your computation time will significantly increase). Or you can
manipulate the way dipoles are considered inside or outside the brain
with "inwardshift" for ft_prepare_leadfield (although I'd advise
against using a negative value as some dipoles might really end up
outside of your brain mesh, with some numerical instabilities).
Another option (the easiest) is to nudge your grid by, say, a few
millimeters, so that the parietal dipoles will be just inside the
brain mesh.

HTH,

Gio

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

+31 20 5665492
gio at gpiantoni.com
www.gpiantoni.com

On Thu, Mar 29, 2012 at 00:22, Akiko Ikkai <akiko.ikkai at gmail.com> wrote:
> Hi Fieldtrip users,
>
> I'm hoping that someone could give me advice on segmentation and beamformer
> on EEG data. I have EEG data set based on 128 channel cap. Thanks to the
> help I got in mid-Feb, I'm now able to create a decent
> segmentation (seg_results image attached) and volume conduction model.
> However, when I run beamformer based on these models, resulting beamforming
> image is often smaller than the brain (beamformer_result attached).
> Particularly posterior parietal and occipital map is NaN.
>
> I have tried going back to segmentation and expanded brain by using imdilate
> after ft_volumesegment such as:
>
> newbrain = imdilate(seg2.brain,strel_bol(1)); % seg2.brain is original brain
> tissue from segmentation
>
> seg2.brain = newbrain;
>
> seg2.seg = seg2.scalp + seg2.skull*3 + seg2.brain*6;
>
> and run ft_prepare_mesh_new on seg2. Of course, I have to make sure there is
> no intersect between different tissue types, so using imdilate has
> limitation.
>
> Could someone explain why this shrinkage might be happening, and how I could
> fix it?
>
> Thanks in advance! Akiko
>
> --
> Akiko Ikkai, Ph.D.
> Postdoctoral Fellow
> Department of Psychological and Brain Sciences
> Johns Hopkins University
> Ames Hall, 3400 N. Charles St.
> Baltimore, MD 21218
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From fredericroux at hotmail.de  Thu Mar 29 12:37:59 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 12:37:59 +0200
Subject: [FieldTrip] segmented volume not aligned with individual mri
Message-ID: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>


Dear all,

I am trying to create mni-aligned grids in individual head-space
and have followed the code provided in the corresponding example-script 
on the fieldtrip site to the line.

However when I plot the segmented volume it looks as if something
is going wrong. I am attaching the plots of the gray and white matter,
as well as of the csf.

I tried flipping the dimensions as suggested in the example script, however
this had zero effect.

My code looks like this.

addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
ft_defaults;

mri = ft_read_mri([path2files,'ID_V2.mri']);

cfg = [];
cfg.coordsys = 'ctf';
cfg.downsample = 2;
seg = ft_volumesegment(cfg,mri);

seg.transform = mri.transform;
seg.anatomy = mri.anatomy;

figure;
cfg = [];
ft_sourceplot(cfg,seg);
figure;
cfg = [];
cfg.funparameter = 'gray';

ft_sourceplot(cfg,seg);

figure;

cfg = [];

cfg.funparameter = 'white';


ft_sourceplot(cfg,seg);


figure;

cfg = [];

cfg.funparameter = 'csf';


ft_sourceplot(cfg,seg);



Anybody an idea why this is happening?
Any help would be highly appreciated.

Fred
-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From ali at cs.ru.nl  Thu Mar 29 12:46:54 2012
From: ali at cs.ru.nl (Ali Bahramisharif)
Date: Thu, 29 Mar 2012 12:46:54 +0200
Subject: [FieldTrip] segmented volume not aligned with individual mri
In-Reply-To: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>
References: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>
Message-ID: <165141044b7f16d8ba3fa0bc824d2c59.squirrel@squirrel.science.ru.nl>

Dear Fred,

Why do you enforce:

seg.transform = mri.transform;

after segmentation? I do not do it, and it looks fine!

Cheers,
Ali

>
> Dear all,
>
> I am trying to create mni-aligned grids in individual head-space
> and have followed the code provided in the corresponding example-script
> on the fieldtrip site to the line.
>
> However when I plot the segmented volume it looks as if something
> is going wrong. I am attaching the plots of the gray and white matter,
> as well as of the csf.
>
> I tried flipping the dimensions as suggested in the example script,
> however
> this had zero effect.
>
> My code looks like this.
>
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
> ft_defaults;
>
> mri = ft_read_mri([path2files,'ID_V2.mri']);
>
> cfg = [];
> cfg.coordsys = 'ctf';
> cfg.downsample = 2;
> seg = ft_volumesegment(cfg,mri);
>
> seg.transform = mri.transform;
> seg.anatomy = mri.anatomy;
>
> figure;
> cfg = [];
> ft_sourceplot(cfg,seg);
> figure;
> cfg = [];
> cfg.funparameter = 'gray';
>
> ft_sourceplot(cfg,seg);
>
> figure;
>
> cfg = [];
>
> cfg.funparameter = 'white';
>
>
> ft_sourceplot(cfg,seg);
>
>
> figure;
>
> cfg = [];
>
> cfg.funparameter = 'csf';
>
>
> ft_sourceplot(cfg,seg);
>
>
>
> Anybody an idea why this is happening?
> Any help would be highly appreciated.
>
> Fred
> --
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
>
>
>  		 	   		  _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Address:
        HG02.517
        Intelligent Systems
        Radboud University Nijmegen
        Heyendaalseweg 135
        6525 AJ Nijmegen
        The Netherlands

http://www.cs.ru.nl/~ali
Tel.:   +31 (0)24 36 52634



From jan.schoffelen at donders.ru.nl  Thu Mar 29 13:22:40 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 29 Mar 2012 13:22:40 +0200
Subject: [FieldTrip] segmented volume not aligned with individual mri
In-Reply-To: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>
References: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>
Message-ID: <9CDB7D6C-A8FC-4000-A234-3CD5913EBD12@donders.ru.nl>

Hi Fred,

You specify the seg to be downsampled. Therefore, I guess that the seg.dim and the mri.dim don't match anymore. Nor will the dimensions of the mri.anatomy match those of the seg.gray/white/csf. Also, as Ali suggests, the transformation matrices cannot be exchanged anymore.
I suspect that if you do: cfg = []; cfg.downsample = 2; mri2=ft_volumedownsample(cfg, mri); seg.anatomy = mri2.anatomy (and leave out seg.transform = mri.transform) that things will look a bit better.

JM

On Mar 29, 2012, at 12:37 PM, Frederic Roux wrote:

> Dear all,
> 
> I am trying to create mni-aligned grids in individual head-space
> and have followed the code provided in the corresponding example-script 
> on the fieldtrip site to the line.
> 
> However when I plot the segmented volume it looks as if something
> is going wrong. I am attaching the plots of the gray and white matter,
> as well as of the csf.
> 
> I tried flipping the dimensions as suggested in the example script, however
> this had zero effect.
> 
> My code looks like this.
> 
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
> ft_defaults;
> 
> mri = ft_read_mri([path2files,'ID_V2.mri']);
> 
> cfg = [];
> cfg.coordsys = 'ctf';
> cfg.downsample = 2;
> seg = ft_volumesegment(cfg,mri);
> 
> seg.transform = mri.transform;
> seg.anatomy = mri.anatomy;
> 
> figure;
> cfg = [];
> ft_sourceplot(cfg,seg);
> figure;
> cfg = [];
> cfg.funparameter = 'gray';
> ft_sourceplot(cfg,seg);
> figure;
> cfg = [];
> cfg.funparameter = 'white';
> ft_sourceplot(cfg,seg);
> figure;
> cfg = [];
> cfg.funparameter = 'csf';
> ft_sourceplot(cfg,seg);
> 
> Anybody an idea why this is happening?
> Any help would be highly appreciated.
> 
> Fred
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 
> <segmented_1.jpg>_______________________________________________
> 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

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From fredericroux at hotmail.de  Thu Mar 29 16:05:18 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 16:05:18 +0200
Subject: [FieldTrip] segmentation and individual grids
Message-ID: <DUB113-W1130856191D4A2E13FDACDCB7480@phx.gbl>


Dear Ali, Dear JM,

thanks a lot for your help.

According to your suggestions I have modified
my code as following:

mri = ft_read_mir('MRI_FILE_V2.mri');

cfg = [];
cfg.downsample = 2;
cfg.coordsys = 'ctf';

mri = ft_volume_downsample(cfg,mri);

cfg = [];
cfg.coordsys = 'ctf';
seg = ft_volumesegment(cfg,mri);
seg.anatomy = mri.anatomy;

Now the comparison of the segmented volumes and the MRI look fine,
but it seems that there is still a problem when I compute the individual grids (see attached figure).

I am also attaching the code I am using.

Would be great if you could help me to get this working.

Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From jan.schoffelen at donders.ru.nl  Thu Mar 29 16:17:00 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 29 Mar 2012 16:17:00 +0200
Subject: [FieldTrip] Fwd: segmentation and individual grids
References: <DUB113-W1130856191D4A2E13FDACDCB7480@phx.gbl>
Message-ID: <E9FA494C-82EA-4CCE-8951-1B020914FB2B@donders.ru.nl>

Hi Fred,

I forwarded your question to the list, so that other people get the opportunity to answer, and/or benefit from the answer ;-).

JM


Begin forwarded message:

> From: Frederic Roux <fredericroux at hotmail.de>
> Date: March 29, 2012 4:05:18 PM GMT+02:00
> To: <fieldtrip at donders.ru.nl>, <jan.schoffelen at donders.ru.nl>, <ali at cs.ru.nl>
> Subject: segmentation and individual grids
> Reply-To: <fredericrouxw at gmail.com>
> 
> Dear Ali, Dear JM,
> 
> thanks a lot for your help.
> 
> According to your suggestions I have modified
> my code as following:
> 
> mri = ft_read_mir('MRI_FILE_V2.mri');
> 
> cfg = [];
> cfg.downsample = 2;
> cfg.coordsys = 'ctf';
> 
> mri = ft_volume_downsample(cfg,mri);
> 
> cfg = [];
> cfg.coordsys = 'ctf';
> seg = ft_volumesegment(cfg,mri);
> seg.anatomy = mri.anatomy;
> 
> Now the comparison of the segmented volumes and the MRI look fine,
> but it seems that there is still a problem when I compute the individual grids (see attached figure).
> 
> I am also attaching the code I am using.
> 
> Would be great if you could help me to get this working.
> 
> Fred
> 
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 

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

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From fredericroux at hotmail.de  Thu Mar 29 17:45:52 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 17:45:52 +0200
Subject: [FieldTrip] alignment channel array, head model & individual grid
Message-ID: <DUB113-W104C6E0B399243CBB06024BB7480@phx.gbl>


Dear all,

I have trouble finding the right alignment for my head models and individual grids
with the MEG channel array.

The code I use is the following:

addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/fieltdrip_private/');
ft_defaults;

spm2path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm2/';
spm8path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm8/';

rmpath(spm2path,spm8path);


mri = ft_read_mri('ID_V2.mri');

cfg = [];
cfg.coordsys = 'ctf';
seg = ft_volumesegment(cfg,mri);

cfg = [];
hdm = ft_prepare_singleshell(cfg,seg);

cfg = [];
cfg.template = '/data/common/SPM8current/spm8/canonical/single_subj_T1.nii';
cfg.coordsys = 'ctf';
cfg.nonlinear = 'no';

norm = ft_volumenormalise(cfg,mri);

load template_grid.mat % template created from the SPM8 single_subj_T1.nii template located in the canonical folder of SPM8

grid = [];
grid.pos = warp_apply(inv(norm.cfg.final), template_grid.pos, 'homogenous')/10;
grid.inside = template_gird.inside;
grid.outside = template_grid.outside;

transfrom_ctf2spm = norm.cfg.final;

figure;
hold on;
ft_plot_sens(ft_read_sens('ID.ds'));
ft_plot_vol(hdm);
ft_plot_mesh(grid.pos(grid.inside,:));


Would be great if you could help me to figure out what is going wrong here.

Best,
Fred


-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From fredericroux at hotmail.de  Thu Mar 29 18:39:01 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 18:39:01 +0200
Subject: [FieldTrip] alignment channel array, head model & individual grid
Message-ID: <DUB113-W824234F69AD703490B557DB7480@phx.gbl>


I forgot to the mention that the left plot shows the headmodel and the channel array
whereas the rigth plot shows the grid and the channel array.

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From fredericroux at hotmail.de  Thu Mar 29 19:03:02 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 19:03:02 +0200
Subject: [FieldTrip] fieldtrip Digest, Vol 16, Issue 51
In-Reply-To: <mailman.715.1333035969.902.fieldtrip@donders.ru.nl>
References: <mailman.715.1333035969.902.fieldtrip@donders.ru.nl>
Message-ID: <DUB113-W63BCB0620F89F65ED05E6DB7480@phx.gbl>


Hi Julian,

thank you for response. That did indeed solve the problem.
I had commented out the section where everything is converted
from mm to cm.

Now the grid is at least on the same scale as the head model.
However, when I compare the template grid (Figure1) with
the individual grid (Figure6) it seems as if there is still a difference.

Is this normal and a consequence of the warping or should the
plot look different?

Best, Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225




> From: fieldtrip-request at donders.ru.nl
> Subject: fieldtrip Digest, Vol 16, Issue 51
> To: fieldtrip at donders.ru.nl
> Date: Thu, 29 Mar 2012 17:46:09 +0200
> 
> Send fieldtrip mailing list submissions to
> 	fieldtrip at donders.ru.nl
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> 	fieldtrip-request at donders.ru.nl
> 
> You can reach the person managing the list at
> 	fieldtrip-owner at donders.ru.nl
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
> 
> 
> Today's Topics:
> 
>    1. alignment channel array, head model & individual grid
>       (Frederic Roux)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 29 Mar 2012 17:45:52 +0200
> From: Frederic Roux <fredericroux at hotmail.de>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] alignment channel array, head model & individual
> 	grid
> Message-ID: <DUB113-W104C6E0B399243CBB06024BB7480 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 
> Dear all,
> 
> I have trouble finding the right alignment for my head models and individual grids
> with the MEG channel array.
> 
> The code I use is the following:
> 
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/fieltdrip_private/');
> ft_defaults;
> 
> spm2path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm2/';
> spm8path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm8/';
> 
> rmpath(spm2path,spm8path);
> 
> 
> mri = ft_read_mri('ID_V2.mri');
> 
> cfg = [];
> cfg.coordsys = 'ctf';
> seg = ft_volumesegment(cfg,mri);
> 
> cfg = [];
> hdm = ft_prepare_singleshell(cfg,seg);
> 
> cfg = [];
> cfg.template = '/data/common/SPM8current/spm8/canonical/single_subj_T1.nii';
> cfg.coordsys = 'ctf';
> cfg.nonlinear = 'no';
> 
> norm = ft_volumenormalise(cfg,mri);
> 
> load template_grid.mat % template created from the SPM8 single_subj_T1.nii template located in the canonical folder of SPM8
> 
> grid = [];
> grid.pos = warp_apply(inv(norm.cfg.final), template_grid.pos, 'homogenous')/10;
> grid.inside = template_gird.inside;
> grid.outside = template_grid.outside;
> 
> transfrom_ctf2spm = norm.cfg.final;
> 
> figure;
> hold on;
> ft_plot_sens(ft_read_sens('ID.ds'));
> ft_plot_vol(hdm);
> ft_plot_mesh(grid.pos(grid.inside,:));
> 
> 
> Would be great if you could help me to figure out what is going wrong here.
> 
> Best,
> Fred
> 
> 
> -- 
> Fr?d?ric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 
>  		 	   		  
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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 16, Issue 51
> *****************************************
 		 	   		  
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From Ulrich.Pomper at charite.de  Fri Mar 30 10:37:06 2012
From: Ulrich.Pomper at charite.de (Pomper, Ulrich)
Date: Fri, 30 Mar 2012 10:37:06 +0200
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <203022dc538e40168d5b72ded3195dcc@EXCCAHT-1.mail.uke.ads>
References: <4F71B9F0.8080106@charite.de>
	<203022dc538e40168d5b72ded3195dcc@EXCCAHT-1.mail.uke.ads>
Message-ID: <4F7570B2.5040707@charite.de>

Thanks Mark + Jörn for the replies!
I'll have a look at the NAI.

On 27.03.2012 15:48, "Jörn M. Horschig" wrote:

Dear Ulrich,


First of all, you might want to use the Neural Activity Index (NAI), as
also described in the tutorial:
http://fieldtrip.fcdonders.nl/tutorial/beamformer#source_analysiswithout_contrasting_condition

Then, to answer your question, I am tempted to say that this would be an
invalid approach when dealing with power, so in frequency-space. Power
obviously has a lower bound, so that the average of any random
collection of power values will never be 0.

That sounds plausible for raw power data, but actually, I want to compare whether my power change to baseline activity is different from zero (maybe that wasn't evident in my first post). I think that's a correct approach.




Though, what you are
suggesting is the same as a regular t-test, isn't it?
In case you are dealing e.g. with am LCMV beamformer, I am not quite
sure, but the null-hypothesis you suggested (amplitude==0)  sounds fair.

In any case, building a surrogate distribution same mean and variance
than your data might be a better way to deal with your problem. That
should be easily doable in Matlab without any need to implement this in
FieldTrip. And note that the MC problem is always present, but a
cluster-based correction (similar to Bonferroni, but correcting by the
number of voxels in the cluster not by the number of all voxels) sounds
legitimate to me. Afair, that's how it's done in FT.

Are you sure? I am not aware of any correction to the alpha level that is done by the cluster-based correction in FT. Afaik all it does is look for a certain number of significant voxels that are close in time, freq and space.
Best, Ulrich

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From yoni.levy at inserm.fr  Fri Mar 30 10:40:25 2012
From: yoni.levy at inserm.fr (yoni.levy at inserm.fr)
Date: Fri, 30 Mar 2012 10:40:25 +0200
Subject: [FieldTrip] actvsblT test statistic when running ft_freqstatistic
Message-ID: <20120330104025.kbc1vye188wwcoc8@imp.inserm.fr>

Dear All,

Would anyone know how to run ft_freqstatistics using the actvsblT?

I intend to statistically test activation period with baseline  
activity. For this, I followed the "Within trial experiments" tutorial  
in fieldtrip
(http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq#within_trial_experiments).
The tutorial emphasizes that one should select equal length time
windows. However, the number of trials in both conditions (activation
and baseline) remains unequal. Therefore, when I run ft_freqstatistics
with the design mentioned in the tutorial (inserting only the number
of trials of the activation condition), I receive the following error
message:
"the number of observations in the design does not match the number of
observations in the data"

Is there an error in the turorial, or is the script intended to create
two frequency output-files, with different total number of trials.

Any advice would be appreciated,

Thanks,

Yoni

----
Yoni Levy, Ph.D.,
INSERM U825,
Address: Pavillon BAUDOT / CHU Purpan,
Place du Docteur Joseph Baylac,
31024 TOULOUSE cédex 3, FRANCE.
E-Mail : yoni.levy at inserm.fr

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





From Ulrich.Pomper at charite.de  Fri Mar 30 10:56:52 2012
From: Ulrich.Pomper at charite.de (Pomper, Ulrich)
Date: Fri, 30 Mar 2012 10:56:52 +0200
Subject: [FieldTrip] =?utf-8?q?Postdoctoral_Position_-_Charit=C3=A9_Berlin?=
In-Reply-To: <8B8CE00B-155C-41D9-9F50-16EA83EB9314@charite.de>
References: <8B8CE00B-155C-41D9-9F50-16EA83EB9314@charite.de>
Message-ID: <4F757554.10703@charite.de>

The Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin invites applications for a Post-doctoral position.

A Starting Grant of the European Research Council (ERC) will fund the position. The main objective of this ERC research program is to examine neural and neurochemical markers of multisensory integration and to test a new hypothesis that considers dynamic interplay of synchronized neural populations as a key to multisensory processes. The studies within this program include healthy subjects and patients with schizophrenia, as an example of a mental disorder with deficits in multisensory integration. Multisensory processes will be examined in a series of experiments requiring both bottom-up and top-down processing.

Applicants should have a background in psychology, medicine, biology, physics, engineering, or neuroscience. Experience in human EEG/MEG studies, Matlab programming skills, as well as German language skills for interacting with patients are prerequisites for the position. An interest in neurophysiological studies including clinical populations is expected.

Applicants are asked to submit their CV, a motivation letter, 2 names of referees, and documentation of relevant qualifications (e.g., copies of diplomas and/or transcripts of grades) until April 15, 2012, electronically to:

Daniel Senkowski, Department of Psychiatry and Psychotherapy, Charité, University Medicine Berlin, 10115 Berlin, Germany, Phone: +49-30-2311-2738, Fax: +49-30-2311-2209, www.danielsenkowski.com<http://www.danielsenkowski.com/>, daniel.senkowski at charite.de<mailto:daniel.senkowski at charite.de>






---------------------------------------------------------------
Daniel Senkowski, Ph.D

Head of the Multisensory Integration research group
Department of Psychiatry and Psychotherapy
Charité, University Medicine Berlin
St. Hedwig Hospital, Große Hamburger Str. 5-11
10115 Berlin, Germany
Phone: +49-30-2311-2738
Fax:      +49-30-2311-2209
http://psy-ccm.charite.de/en/research/neuroimaging/multisensory_integration

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From jm.horschig at donders.ru.nl  Fri Mar 30 15:38:43 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Fri, 30 Mar 2012 15:38:43 +0200
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <4F7570B2.5040707@charite.de>
References: <4F71B9F0.8080106@charite.de>
	<203022dc538e40168d5b72ded3195dcc@EXCCAHT-1.mail.uke.ads>
	<4F7570B2.5040707@charite.de>
Message-ID: <4F75B763.9010906@donders.ru.nl>

Hi Ulrich,

>
> Are you sure? I am not aware of any correction to the alpha level that 
> is done by the cluster-based correction in FT. Afaik all it does is 
> look for a certain number of significant voxels that are close in 
> time, freq and space.

Oh indeed, I was mixing things up there. I couldn't find anything 
mentioned like this neither in the code nor in the Maris&Oostenveld 
paper. Then it was probably something I remembered from another 
test/tool, or I was mixing thoughts of mine with a simplistic 
explanation of random field theory. In any way, my apologies for the 
confusion.

Best,
Jörn


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

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 samarakm at mail.uc.edu  Fri Mar 30 21:04:42 2012
From: samarakm at mail.uc.edu (Samarasinghe, Kasun (samarakm))
Date: Fri, 30 Mar 2012 19:04:42 +0000
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <4F71B9F0.8080106@charite.de>
References: <4F71B9F0.8080106@charite.de>
Message-ID: <158540F0F1AD27479479077742EA83C515EA8C66@CH1PRD0102MB148.prod.exchangelabs.com>

Dear Fieldtrip members,

I am trying to construct a generic head model by following the tutorial "Build a geometrical description of the volume conduction model of the head". For some reason, I cannot download the zipped MRI file in the location : '"ftp://ftp.fcdonders.nl/pub/fieldtrip/". Any help regarding the correct location of this file would be appreciated.

Thank you,
Kasun

--------------------------------------------
Kasun M Samarasinghe
Doctoral Student
Electrical Engineering - Systems Track
University of Cincinnati








From samarakm at mail.uc.edu  Fri Mar 30 21:09:50 2012
From: samarakm at mail.uc.edu (Samarasinghe, Kasun (samarakm))
Date: Fri, 30 Mar 2012 19:09:50 +0000
Subject: [FieldTrip] Failure to access the MRI file in the Tutorial section
Message-ID: <158540F0F1AD27479479077742EA83C515EA8C74@CH1PRD0102MB148.prod.exchangelabs.com>

Dear Fieldtrip members,

I am trying to construct a generic head model by following the tutorial "Build a geometrical description of the volume conduction model of the head". For some reason, I cannot download the zipped MRI file in the location : '"ftp://ftp.fcdonders.nl/pub/fieldtrip/". Any help regarding the correct location of this file would be appreciated.

Please disregard my previous email since it had the wrong title.

Thank you,
Kasun

--------------------------------------------
Kasun M Samarasinghe
Doctoral Student
Electrical Engineering - Systems Track
University of Cincinnati



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From batrod at gmail.com  Fri Mar 30 21:24:56 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Fri, 30 Mar 2012 14:24:56 -0500
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <158540F0F1AD27479479077742EA83C515EA8C66@CH1PRD0102MB148.prod.exchangelabs.com>
References: <4F71B9F0.8080106@charite.de>
	<158540F0F1AD27479479077742EA83C515EA8C66@CH1PRD0102MB148.prod.exchangelabs.com>
Message-ID: <CAPy7a9CfQRDROZ6U_ksCddV8pMVyGdB--Uxhr1y3k6Lz3kKsoQ@mail.gmail.com>

Hi Kasun,

what software do you use to access this adress?
I know Chrome has issue with ftp, but Firefox handle that well. (I just
remade a test).

Rodolphe

On Fri, Mar 30, 2012 at 2:04 PM, Samarasinghe, Kasun (samarakm) <
samarakm at mail.uc.edu> wrote:

> Dear Fieldtrip members,
>
> I am trying to construct a generic head model by following the tutorial
> "Build a geometrical description of the volume conduction model of the
> head". For some reason, I cannot download the zipped MRI file in the
> location : '"ftp://ftp.fcdonders.nl/pub/fieldtrip/". Any help regarding
> the correct location of this file would be appreciated.
>
> Thank you,
> Kasun
>
> --------------------------------------------
> Kasun M Samarasinghe
> Doctoral Student
> Electrical Engineering - Systems Track
> University of Cincinnati
>
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From samarakm at mail.uc.edu  Fri Mar 30 21:42:27 2012
From: samarakm at mail.uc.edu (Samarasinghe, Kasun (samarakm))
Date: Fri, 30 Mar 2012 19:42:27 +0000
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <CAPy7a9CfQRDROZ6U_ksCddV8pMVyGdB--Uxhr1y3k6Lz3kKsoQ@mail.gmail.com>
References: <4F71B9F0.8080106@charite.de>
	<158540F0F1AD27479479077742EA83C515EA8C66@CH1PRD0102MB148.prod.exchangelabs.com>,
	<CAPy7a9CfQRDROZ6U_ksCddV8pMVyGdB--Uxhr1y3k6Lz3kKsoQ@mail.gmail.com>
Message-ID: <158540F0F1AD27479479077742EA83C515EA8C98@CH1PRD0102MB148.prod.exchangelabs.com>



Hi Rodolphe,



Yes, I can access using Firefox now, and thank you for your prompt response. I was using Chrome earlier, and yes it seems to have issues with the server.



Thank you again,

Kasun

--------------------------------------------
Kasun M Samarasinghe
Doctoral Student
Electrical Engineering - Systems Track
University of Cincinnati

________________________________
From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Rodolphe Nenert [batrod at gmail.com]
Sent: Friday, March 30, 2012 3:24 PM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] one-sample cluster test

Hi Kasun,

what software do you use to access this adress?
I know Chrome has issue with ftp, but Firefox handle that well. (I just remade a test).

Rodolphe

On Fri, Mar 30, 2012 at 2:04 PM, Samarasinghe, Kasun (samarakm) <samarakm at mail.uc.edu<mailto:samarakm at mail.uc.edu>> wrote:
Dear Fieldtrip members,

I am trying to construct a generic head model by following the tutorial "Build a geometrical description of the volume conduction model of the head". For some reason, I cannot download the zipped MRI file in the location : '"ftp://ftp.fcdonders.nl/pub/fieldtrip/". Any help regarding the correct location of this file would be appreciated.

Thank you,
Kasun

--------------------------------------------
Kasun M Samarasinghe
Doctoral Student
Electrical Engineering - Systems Track
University of Cincinnati






_______________________________________________
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 fredericroux at hotmail.de  Sat Mar 31 13:10:31 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Sat, 31 Mar 2012 13:10:31 +0200
Subject: [FieldTrip] restrict source reconstruction to gray matter
Message-ID: <DUB113-W1405024A1BD2BE5FF28CE14B74E0@phx.gbl>



Dear all,

I read that it is possible to restrict source reconstruction to gray matter.
Can anyone give me a hint on where can I find example code on how to do it?

I was searching for it on the fieldtrip-webstite but couldn't find anything.

Any help would as always be highly appreciated.

Fred



-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From jan.schoffelen at donders.ru.nl  Sat Mar 31 13:30:02 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Sat, 31 Mar 2012 13:30:02 +0200
Subject: [FieldTrip] restrict source reconstruction to gray matter
In-Reply-To: <DUB113-W1405024A1BD2BE5FF28CE14B74E0@phx.gbl>
References: <DUB113-W1405024A1BD2BE5FF28CE14B74E0@phx.gbl>
Message-ID: <A6ECCF8A-A40D-40CA-B560-578267AEABFC@donders.ru.nl>

Hi Fred,

I am not aware of any example code on the FT-website, but I would do something like this:

mri = ft_read_mri('...');
seg = ft_volumesegment([],mri);

cfg = [];
cfg.parameter = 'gray';
cfg.smooth = 10; % or some other value
cfg.downsample = 5; % downsample with a factor of 5
seg = ft_volumedownsample(cfg, seg);

% create a dipole grid
[X,Y,Z] = ndgrid(1:seg.dim(1), 1:seg.dim(2), 1:seg.dim(3));

grid = [];
grid.pos = warp_apply(seg.transform, [X(:) Y(:) Z(:)]); clear X Y Z
grid.dim = seg.dim;
grid.inside = find(seg.gray>0.5); % the threshold value needs to be verified, you can play with the value
grid.outside = find(seg.gray<=0.5);

grid = ft_convert_units(grid, 'cm'); % I assume that the sensors are defined in cm.

Just give it a shot. I would appreciate it very much if you could try this code and maybe optimize it. When you have done that, we could make a piece of documentation on the FT-website, i.e. I will create a page (because I don't think you could do that), and you'll write the documentation ;-). Sounds like a win-win situation to me. How does it sound to you?

Best wishes,

Jan-Mathijs


On Mar 31, 2012, at 1:10 PM, Frederic Roux wrote:

> 
> Dear all,
> 
> I read that it is possible to restrict source reconstruction to gray matter.
> Can anyone give me a hint on where can I find example code on how to do it?
> 
> I was searching for it on the fieldtrip-webstite but couldn't find anything.
> 
> Any help would as always be highly appreciated.
> 
> Fred
> 
> 
> 
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 
> _______________________________________________
> 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

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From litvak.vladimir at gmail.com  Thu Mar  1 16:02:28 2012
From: litvak.vladimir at gmail.com (Vladimir Litvak)
Date: Thu, 1 Mar 2012 15:02:28 +0000
Subject: [FieldTrip] Missing triggers with Biosemi EEG data
In-Reply-To: <f0f5f26cc301f41af598ca01ebe2a853.squirrel@www.drcmr.dk>
References: <f0f5f26cc301f41af598ca01ebe2a853.squirrel@www.drcmr.dk>
Message-ID: <CACq1BhKUJwiXMGEWM-OeD2tzbKOaQo=iR15VJ6qFr4HOMMcJ_A@mail.gmail.com>

Dear Mark,

I'm not sure what the reason is for not supporting downgoing triggers
in Biosemi, but there probably is one. I'm CCing your message to
Fieldtrip mailing list where it might be better answered. Are you sure
that the missing triggers are recorded correctly? Can you see them
with any other software you have? Sometimes there is a problem with
connectors which leads to incorrect assignments of trigger codes.

Vladimir

On Thu, Mar 1, 2012 at 2:54 PM, Mark Schram Christensen <markc at drcmr.dk> wrote:
> Dear Vladimir Litvak
> I am currently analysing some EEG data with SPM8 obtained with the biosemi
> system, and I am missing quite a lot of my triggers. I get the warning
> that only upcoing flanks are supported for biosemi, and I suspect that
> that is the reason. I can see that the status channel changes when ever I
> should have had the trigger.
> I guess it is related to the field trip file ft_read_event.m, which seems
> to have this biosemi exception, that even though it should look for both
> up and down flanks it only finds up with biosemi.
> Do you know if there is a possibility of also getting downflank triggers?
> Looking forward to hear from you.
> Best wishes
> Mark Schram Christensen
>
>
> _______________________________________________
> Mark Schram Christensen, MSc, PhD
> Copenhagen Neural Control of Movement &
> Danish Research Centre for Magnetic Resonance
> Department of Exercise and Sport Sciences
> Copenhagen University Hospital Hvidovre
> Kettegård Allé 30
> DK-2650 Hvidovre
> Phone: +45 3862 3407
> E-mail: markc at drcmr.dk
> http://www.ifi.ku.dk/
> http://www.cph-ncm.ku.dk/
> http://www.drcmr.dk/markc
>
>
>
>



From ghahremani.aida at gmail.com  Fri Mar  2 00:56:57 2012
From: ghahremani.aida at gmail.com (aida ghahremani)
Date: Thu, 1 Mar 2012 18:56:57 -0500
Subject: [FieldTrip] fieldtrip Digest, Vol 16, Issue 1
In-Reply-To: <mailman.1.1330599616.2810.fieldtrip@donders.ru.nl>
References: <mailman.1.1330599616.2810.fieldtrip@donders.ru.nl>
Message-ID: <CAM50FKDcYrPq2oSYnLkFHFNrX5ALT9Q2jVc9vU9PMxUc0tEYTQ@mail.gmail.com>

Dear Fieldtrip group

I have got a problem with a very simple program to solve a forward problem.
I used the below program to compute leadfield from a source in the origin
for two electrodes in different locations. I noticed that when I change the
position of one of the electrodes, it affects on the leadfield of the
other. I know it should not be like that, since electrodes do not affect
each other. Would you please help me?


elec.pnt=[4.6*cos(pi/3) 4.6*sin(pi/3) 7.96;4.6*cos(pi/6) 4.6*sin(pi/6)
7.96];
for i=1:2
   elec.label{i} = sprintf('%03d', i);
end

% create a concentric 3-sphere volume conductor, the radius is the same as
for the electrodes
vol = [];
vol.r = [8 8.1 8.6 9.2]; % radii of spheres
vol.c = [1 1 1/80 1];       % conductivity
vol.o = [0 0 0];          % center of sphere

% compute the leadfield for a dipole at position [0 0 0]
pos = [0 0 0];
lf = ft_compute_leadfield(pos, elec, vol);

% compute the potential distribution for a dipole with z-orientation
mom = [0 0 1]';
pot = lf * mom;
end

Best
Ayda

On Thu, Mar 1, 2012 at 6:00 AM, <fieldtrip-request at donders.ru.nl> wrote:

> Send fieldtrip mailing list submissions to
>        fieldtrip at donders.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>        fieldtrip-request at donders.ru.nl
>
> You can reach the person managing the list at
>        fieldtrip-owner at donders.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>   1. question about MNI alignment (Ali Bahramisharif)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 29 Feb 2012 21:10:54 +0100
> From: "Ali Bahramisharif" <ali at cs.ru.nl>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] question about MNI alignment
> Message-ID:
>        <fac73988589583150fc4a6a7a958a215.squirrel at squirrel.science.ru.nl>
> Content-Type: text/plain;charset=iso-8859-1
>
> Dear Fieldtrip users,
>
> I want to create MNI-aligned grids in individual head-space, and I follow
> the guidelines in :
>
>
> http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s[]=template&s[]=grid
>
>
> I do not know how old this page is, but I noticed that for example in the
> current version "cfg.coordinates" should be "cfg.coordsys". I have the
> following problems:
>
> 1- When I run "ft_plot_mesh(template_grid);", I get a cubic grid which is
> apparently different from the one shown in the page.
>
> 2- When I run, ft_plot_vol(hdm), it does not seem to be aligned to
> "ft_plot_sens(ft_read_sens(dataset{i}));"
>
> I checked my segmented volumes, and they seem to be fine, and I did not
> need to run flipdim. I am wondering whether my segmented data is correct
> or it should be flipped somewhere. Please let me know if anybody knows how
> to resolve this problem.
>
> Cheers,
> Ali
>
>
>
>
> ------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> End of fieldtrip Digest, Vol 16, Issue 1
> ****************************************
>
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From r.oostenveld at donders.ru.nl  Mon Mar  5 12:27:53 2012
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Mon, 5 Mar 2012 12:27:53 +0100
Subject: [FieldTrip] FieldTrip course at the Donders in Nijmegen: 7-10 May
Message-ID: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>

Dear FieldTrip users,

The registration for our yearly toolkit course on "MEG and EEG data analysis" at the Donders Institute has opened. This year's MEG/EEG toolkit will take place from 7-10 May 2012. 

This 4-day toolkit course will teach you advanced MEG and EEG data analysis skills. Preprocessing, frequency analysis, source reconstruction and various statistical methods will be covered. The toolkit will consist of a number of lectures, followed by hands-on sessions in which you will be tutored through the complete analysis of a MEG data set using the FieldTrip toolbox. The fee for senior participants is € 400. The (PhD) student fee is € 200. Registration fee includes coffee/tea, Dutch sandwich lunches and one dinner.

Have a look at http://www.ru.nl/donders/agenda-news/courses/toolkits-2012/ for the preliminary programme and to register. Please do note that the number of seats is limited and that in the previous years the course was oversubscribed. We therefore expect to have to select participants; this is done on the basis of the information that you provide on your background, skills and research interest. Note that the registration closes 31 March. You will be informed about whether you can participate before mid-April.

Best wishes,

Robert Oostenveld & Jan-Mathijs Schoffelen

-----------------------------------------------------------
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
tel.: +31 (0)24 3619695
e-mail: r.oostenveld at donders.ru.nl
web: http://www.ru.nl/neuroimaging
skype: r.oostenveld
-----------------------------------------------------------



From ugabrewer at gmail.com  Mon Mar  5 18:58:33 2012
From: ugabrewer at gmail.com (Gene Brewer)
Date: Mon, 5 Mar 2012 10:58:33 -0700
Subject: [FieldTrip] Postdoctoral Fellowship at Arizona State University
In-Reply-To: <CADo-6W+m9eKFykATMtJhHEgEvZuA5xY09y3Y1s-bNwZgf573=Q@mail.gmail.com>
References: <CADo-6W+m9eKFykATMtJhHEgEvZuA5xY09y3Y1s-bNwZgf573=Q@mail.gmail.com>
Message-ID: <CADo-6WJRiPNv+KyL9cSAnbHonaGWX5=tV=KDMOcNmsz_njzmXg@mail.gmail.com>

List Members,

*Arizona State University Postdoctoral Fellowship in Neuropsychology of
Strategic Communication*

The Center for Strategic Communication (CSC) and the Department of
Psychology at Arizona State University are pleased to announce a new
Postdoctoral Fellowship program beginning May 2012.

*Postdoctoral Fellowship*

A postdoctoral fellowship will be awarded beginning in the May/June 2012
time frame. The appointment is for full time employment (40 hours per week)
for 18 months.  Renewal for up to two additional 18 month periods is
possible, contingent on additional funding by the sponsor and satisfactory
job performance. Salary is $60,000 and the University offers subsidized
health insurance. Support for travel to conferences will be available.
Fellows are responsible for relocation and housing expenses.  Fellows will
support a research project sponsored by the Defense Advanced Research
Projects Agency (DARPA) involving multi-modal neuroimaging (fMRI + EEG) of
narrative comprehension and persuasion.

For additional information regarding postdoctoral fellowships at ASU,
please see: http://provost.asu.edu/postdoc.

*Eligibility*

Applicants must have an earned or pending doctoral degree in Neuroscience,
Statistics, Social Psychology, Cognitive Psychology, or a related
field/discipline. The degree must have been earned no earlier than 2010.
Candidates with pending degrees who will have successfully defended their
dissertations by May 1, 2012 will also be considered. Applicants must have
no more than two years of formal postdoctoral experience.

*Required Expertise*

Applicants must have relevant expertise in fMRI data acquisition and
analysis and/or EEG data acquisition and analysis, as applied to the study
of cognitive or social psychological processes.

*Desired Expertise*

Relevant expertise or experience in multi-modal mapping (fMRI + EEG) of
cognitive and social psychological processes and/or neuropsychology of
narrative or persuasion is desirable.

*Responsibilities*

Postdoctoral scholars are expected to carry out the research plan and
fulfill the goals established with the supervising faculty members, Drs.
Gene Brewer and Leslie Baxter; to assist the supervising faculty members
and other Principal Investigators in fulfilling the requirements of the
grant in a timely manner; to communicate regularly with the supervising
faculty member and other members of the research team; and to notify the
faculty member of any change in research plans.

Beyond grant-related activities, our facilities will help create valuable
opportunities for the postdoctoral scholar to continue their fMRI and EEG
research agenda, develop new multi-modal techniques, teach, and get
training experience.

For further information about the position contact Prof. Gene Brewer,
gene.brewer at asu.edu

*Application*

Submit application materials electronically with all documents included in
a single PDF file, to include the following:

1. A cover letter stating your interest in the Postdoctoral Fellowship.
Provide details on

a. how your research and expertise relates to neuroimaging, especially with
regard to combining data from fMRI and EEG.

b. how your research and expertise relates to the project described above,
and

c. your long-term professional goals.

2. An up to date curriculum vitae.

3. Names and contact information for two references who agree to be
contacted.

4. Copies of up to three published papers/scholarly work.

5. Scanned copies of current academic transcript from all degree awarding
institutions. Official transcripts will be requested from those who
received formal offers.

The search will initially close with applications received by* April 15,
2012*.  If the position is not filled, then applications will be accepted
every subsequent Friday until search is closed.

Send materials to:

Josephine Wong, Program Manager

Center for Strategic Communication

jody at asu.edu

ASU is an equal opportunity/affirmative action employer committed to
excellence through diversity.  Women and minorities are encouraged to apply.
ASU’s complete non-discrimination statement can be found at:
http://www.asu.edu/titleIX/

-- 
Gene A. Brewer Jr.
Arizona State University
Department of Psychology
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From alotof_xd at yahoo.com  Tue Mar  6 21:52:37 2012
From: alotof_xd at yahoo.com (alotof eve)
Date: Tue, 6 Mar 2012 12:52:37 -0800 (PST)
Subject: [FieldTrip] error message in databrowser
In-Reply-To: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
References: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
Message-ID: <1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>

Hello, experts,

I am using ICA following the tutirial steps. 
I got IC dataset "comp" with the command: comp = ft_componentanalysis (cfg, data);
and ft_topoplotIC(cfg, comp) works.

However, then I used ft_databrowser(cfg, comp), I got an error message:
Operands to the || and && operators must be
convertible to logical scalar values.

Error in ft_databrowser (line 135)
if hasdata && isfield(data, 'topo') &&
strmatch (cfg.viewmode, 'component')

Can anyone know the way to settle this? 
Thanks in advance.

Eve
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From alotof_xd at yahoo.com  Wed Mar  7 09:01:59 2012
From: alotof_xd at yahoo.com (alotof eve)
Date: Wed, 7 Mar 2012 00:01:59 -0800 (PST)
Subject: [FieldTrip] error message in databrowser
In-Reply-To: <1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>
References: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
	<1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>
Message-ID: <1331107319.55433.YahooMailNeo@web125502.mail.ne1.yahoo.com>

Updated: I changed "&&" to "&", it worked but later a new error happened:

Reference to non-existent field 'hlim'.

Error in ft_databrowser>redraw_cb (line 1015)
             eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - opt.hlim(1)); 

 
Error in ft_databrowser (line 434)
redraw_cb(h);
_____
Thanks,
Eve



________________________________
 From: alotof eve <alotof_xd at yahoo.com>
To: Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
Sent: Tuesday, March 6, 2012 12:52 PM
Subject: [FieldTrip] error message in databrowser
 

Hello, experts,

I am using ICA following the tutirial steps. 
I got IC dataset "comp" with the command: comp = ft_componentanalysis (cfg, data);
and ft_topoplotIC(cfg, comp) works.

However, then I used ft_databrowser(cfg, comp), I got an error message:
Operands to the || and && operators must be
convertible to logical scalar values.

Error in ft_databrowser (line 135)
if hasdata && isfield(data, 'topo') &&
strmatch (cfg.viewmode, 'component')

Can anyone know the way to settle this? 
Thanks in advance.

Eve


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From mcoskun at mail.uh.edu  Wed Mar  7 14:26:04 2012
From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun)
Date: Wed, 07 Mar 2012 07:26:04 -0600
Subject: [FieldTrip] error message in databrowser
In-Reply-To: <1331107319.55433.YahooMailNeo@web125502.mail.ne1.yahoo.com>
References: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
	<1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>
	<1331107319.55433.YahooMailNeo@web125502.mail.ne1.yahoo.com>
Message-ID: <7050dbcfcd6be.4f570d8c@mail.uh.edu>

Hi Eve,


I have posted same error earlier but got no suggestions. In my case, the error started popping up after i tried using parallel processing, but i don't know if this has anything to do with the error. I tried many things but no result.


finally, i simply uninstalled and re-installed matlab and everything worked perfectly there after. You may want to try this as a final option if you don't hear any other solution.


Mehmet

----- Original Message -----
From: alotof eve <alotof_xd at yahoo.com>
Date: Wednesday, March 7, 2012 2:03 am
Subject: Re: [FieldTrip] error message in databrowser
To: alotof eve <alotof_xd at yahoo.com>, Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl>



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



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



> Updated: I changed "&&" to "&", it worked but later a new error happened:

> 

> Reference to non-existent field 'hlim'.
> 

> Error in ft_databrowser>redraw_cb (line 1015)
>              eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - opt.hlim(1)); 

>  
> Error in ft_databrowser (line 434)
> redraw_cb(h);
> _____
> Thanks,
> Eve

> 
>
-----------------------------------------------------------
From: alotof eve <alotof_xd at yahoo.com>
> To: Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
> Sent: Tuesday, March 6, 2012 12:52 PM
> Subject: [FieldTrip] error message in databrowser
>
> 

> Hello, experts,
> 
> I am using ICA following the tutirial steps. 
> I got IC dataset "comp" with the command: comp = ft_componentanalysis (cfg, data);
> and ft_topoplotIC(cfg, comp) works.
> 
> However, then I used ft_databrowser(cfg, comp), I got an error message:
> Operands to the || and && operators must be
> convertible to logical scalar values.
> 
> Error in ft_databrowser (line 135)
> if hasdata && isfield(data, 'topo') &&
> strmatch (cfg.viewmode, 'component')
> 
> Can anyone know the way to settle this? 
> Thanks in advance.
> 
> Eve
>

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



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From MEpstein at NKI.RFMH.ORG  Wed Mar  7 18:28:48 2012
From: MEpstein at NKI.RFMH.ORG (Epstein, Michael)
Date: Wed, 7 Mar 2012 12:28:48 -0500
Subject: [FieldTrip] Error -> ft_databrowser
Message-ID: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>

Hi - I am actually encountering the same error with databrowser, and was
wondering if you ever came up with a solution to this problem - or if
anyone else has a solution - I didn't find a response on the mailing
list.

 

-Michael

 

 

 

________________________________

Dear Fieldtrippers,

 

 

I am encountering a strange error while i try to use ft_databrowser. The
error code is as below. I have never seen this error earlier. I used
ft_databrowser many times and its only last 2 days that i am getting the
error. I downloaded a newer version of fieldtrip (fieldtrip-20120130)
and used the newer version but still the same error. Strangely, i dont
get this error when i tried with other computers (same matlab version
(R2010a), same operating system (windows 7) on both computers. Has
anyone got this error before? what may cause this error?

 

 

fieldtrip version 20120130, matlab version R2010a, operating system
windows 7.

 

 

Thanks in advance for any suggestions.

 

 

 

??? Error using ==> ft_fetch_data at 57

data does not contain a consistent trial definition, fetching data is
not

possible

 

 

Error in ==> ft_databrowser>redraw_cb at 1159

art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample',
endsample);

 

 

Error in ==> ft_databrowser at 535

redraw_cb(h);

 



Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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From max-philipp.stenner at med.ovgu.de  Wed Mar  7 18:46:06 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Wed, 07 Mar 2012 17:46:06 +0000
Subject: [FieldTrip] ft_sourcestatistics
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830C999B@ESEN4.imed.uni-magdeburg.de>

Dear fieldtrip users,



I am encountering a problem with ft_sourcestatistics when using output from ft_sourcegrandaverage. My parameter of interest is a logratio: log(mean(moments(time of interest))/mean(moments(baseline))) which I simply named 'pow' to be compatible with ft functions. Apart from this, nothing else deviates from how fieldtrip handles the data/nothing else was changed 'manually'.



The problem arises from the fact that the existence of 10 different subjects in the grandaverage (in the usual 1x10 struct field 'trial') isn't represented in the 'powdimord' field of the data after ft_checkdata(varargin{i}, 'datatype', {'source', 'volume'}, 'feedback', 'no', 'inside', 'index', 'sourcerepresentation', 'new'); in the new implementation of ft_sourcestatistics:



varargin{1}

ans =



(before ft_checkdata:)



        pos: [8196x3 double]
        var: [1x1 struct]
     dimord: 'voxel'
      trial: [1x10 struct]
     inside: [8196x1 double]
    outside: [0x1 double]
         df: [8196x1 double]
        cfg: [1x1 struct]



(after ft_checkdata:)



          pos: [8196x3 double]
          var: [1x1 struct]
       dimord: 'pos'
       inside: [8196x1 double]
      outside: [0x1 double]
           df: [8196x1 double]
          cfg: [1x1 struct]
          pow: [8196x10 double]
    powdimord: 'pos'



This leads to a (wrong) transpose of the design (originally row1 = uvar, row2 = ivar [with two conditions for a depsamples T test]) and ultimately to the message

'The data must contain at least two units (usually subjects).'



Any help would be much appreciated, thanks very much!

Max

(fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)


From mcoskun at mail.uh.edu  Wed Mar  7 18:55:38 2012
From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun)
Date: Wed, 07 Mar 2012 11:55:38 -0600
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
Message-ID: <7270aa3bcbfd9.4f574cba@mail.uh.edu>

Hi Michael,


I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. 


just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution.


But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution.


Mehmet





----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
Date: Wednesday, March 7, 2012 11:29 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: fieldtrip at donders.ru.nl



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



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


> Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list.
>  
> -Michael
>  
>  
>  
-----------------------------------------------------------
> Dear Fieldtrippers,
>  
>  
> I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error?
>  
>  
> fieldtrip version 20120130, matlab version R2010a, operating system windows 7.
>  
>  
> Thanks in advance for any suggestions.
>  
>  
>  
> ??? Error using ==> ft_fetch_data at 57
> data does not contain a consistent trial definition, fetching data is not
> possible
>  
>  
> Error in ==> ft_databrowser>redraw_cb at 1159
> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample);
>  
>  
> Error in ==> ft_databrowser at 535
> redraw_cb(h);
>  



-----------------------------------------------------------
> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. 

|-----------------------------------------------------------



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From MEpstein at NKI.RFMH.ORG  Wed Mar  7 18:57:25 2012
From: MEpstein at NKI.RFMH.ORG (Epstein, Michael)
Date: Wed, 7 Mar 2012 12:57:25 -0500
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <7270aa3bcbfd9.4f574cba@mail.uh.edu>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
	<7270aa3bcbfd9.4f574cba@mail.uh.edu>
Message-ID: <2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>

Interesting... can I ask what version of matlab you were running? and
was it 64 bit?

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Mehmet-Akif Coskun
Sent: Wednesday, March 07, 2012 12:56 PM
To: Email discussion list for the FieldTrip project
Cc: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Michael,


I have posted the question actually but I didn't hear any suggestions
about it. The same error was posted yesterday by someone else. 


just to repeat what i have replied in the other post, i tried many
things to solve it (changed the code, run the databrowser code line by
line, updated fieldtrip version at etc.), but none of them solved the
problem. I started getting the error after I tried using parallel
processing scripts in matlab. But as i said, i have no basis to say that
this caused the problem. So basically, i do not know any scientific
solution.


But an old school method solved the problem in my case. Simply i
uninstalled and re-installed matlab. Never got the error again. You may
want to try this. I have no other solution.


Mehmet





----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
Date: Wednesday, March 7, 2012 11:29 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: fieldtrip at donders.ru.nl

> Hi - I am actually encountering the same error with databrowser, and
was wondering if you ever came up with a solution to this problem - or
if anyone else has a solution - I didn't find a response on the mailing
list.

>  

> -Michael

>  

>  

>  

________________________________

> Dear Fieldtrippers,

>  

>  

> I am encountering a strange error while i try to use ft_databrowser.
The error code is as below. I have never seen this error earlier. I used
ft_databrowser many times and its only last 2 days that i am getting the
error. I downloaded a newer version of fieldtrip (fieldtrip-20120130)
and used the newer version but still the same error. Strangely, i dont
get this error when i tried with other computers (same matlab version
(R2010a), same operating system (windows 7) on both computers. Has
anyone got this error before? what may cause this error?

>  

>  

> fieldtrip version 20120130, matlab version R2010a, operating system
windows 7.

>  

>  

> Thanks in advance for any suggestions.

>  

>  

>  

> ??? Error using ==> ft_fetch_data at 57

> data does not contain a consistent trial definition, fetching data is
not

> possible

>  

>  

> Error in ==> ft_databrowser>redraw_cb at 1159

> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample',
endsample);

>  

>  

> Error in ==> ft_databrowser at 535

> redraw_cb(h);

>  

 

________________________________

> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the
intended recipient. It may contain confidential information which is
legally privilegedor otherwise protected by law. If you received this
e-mail in error or from someone who is not authorized to send it to you,
you are strictly prohibited from reviewing, using, disseminating,
distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE
ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank
you for your cooperation. 

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



Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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From jnortonf at uci.edu  Wed Mar  7 19:05:43 2012
From: jnortonf at uci.edu (Jessamy Norton-Ford)
Date: Wed, 7 Mar 2012 10:05:43 -0800
Subject: [FieldTrip] EEG layout help
Message-ID: <CACvc6xQXFTQ+wnLafdrx7nFnjwZNF6GMOPMYOh2BvjasELDdpw@mail.gmail.com>

Hello,

I am trying to use the plotting functions with my 34-channel data (32
standard EEG channels + VEOG and HEOG).  In EEGLAB, I use the
'standard-10-5-cap385.elp' file for the locations, however I get the
following error in Fieldtrip (v. 20120220).

cfg = [];
cfg.baseline         = [-0.5 -0.1];
cfg.baselinetype     = 'absolute';
cfg.zlim             = [-3e-25 3e-25];
cfg.showlabels       = 'yes';
cfg.layout           = 'standard-10-5-cap385.elp';
figure
ft_multiplotTFR(cfg, TFRwave)
creating layout from electrode file standard-10-5-cap385.elp
??? Error using ==> ft_read_sens at 84
unknown fileformat for electrodes or gradiometers

Error in ==> ft_prepare_layout at 253
  lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
  cfg.style);

Error in ==> ft_multiplotTFR at 241
lay = ft_prepare_layout(cfg, data);

In ft_read_sens, it appears as though fieldtrip cannot yet deal with such
.elp files?  I wonder if (1) I am making an easy mistake as I am still new
to Fieldtrip, or (2) if there is perhaps an easy workaround for this .elp
incompatibility?

In case it is useful, here are the channels that I am using:

1 Fp1  2 Fpz  3 Fp2  4 F7  5 F3  6 Fz  7 F4  8 F8  9 FC5  10 FC1  11 FC2  12
FC6  13 M1  14 T7  15 C3  16 Cz  17 C4  18 T8  19 M2  20 CP5  21 CP1
22 CP2  23
CP6  24 P7  25 P3  26 Pz  27 P4  28 P8  29 POz  30 O1  31 Oz  32 O2
33 VEOG  34
HEOG

Thanks very much,

Jessamy Norton-Ford








-- 
Jessamy Norton-Ford
Doctoral Student, Department of Cognitive Sciences
University of California, Irvine
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From mcoskun at mail.uh.edu  Wed Mar  7 19:17:33 2012
From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun)
Date: Wed, 07 Mar 2012 12:17:33 -0600
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
	<7270aa3bcbfd9.4f574cba@mail.uh.edu>
	<2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
Message-ID: <72b0dfc7cc8ec.4f5751dd@mail.uh.edu>

Matlab R2010a 64-bit under windows 7. I did not update matlab version. just uninstalled and re-installed the same version. 


Mehmet

----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
Date: Wednesday, March 7, 2012 11:58 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl>



| 


> Interesting... can I ask what version of matlab you were running? and was it 64 bit?
>  
> -Michael
>  
> From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Mehmet-Akif Coskun
> Sent: Wednesday, March 07, 2012 12:56 PM
> To: Email discussion list for the FieldTrip project
> Cc: fieldtrip at donders.ru.nl
> Subject: Re: [FieldTrip] Error -> ft_databrowser
>  
> Hi Michael,
> 
> 
> I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. 
> 
> 
> just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution.
> 
> 
> But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution.
> 
> 
> Mehmet
> 
> 
> 
> 
> 
> ----- Original Message -----
> From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
> Date: Wednesday, March 7, 2012 11:29 am
> Subject: Re: [FieldTrip] Error -> ft_databrowser
> To: fieldtrip at donders.ru.nl

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

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



-----------------------------------------------------------
> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. 

|-----------------------------------------------------------


> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
-----------------------------------------------------------
|
> > Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list.
>  
> -Michael
>  
>  
>  
-----------------------------------------------------------
> > Dear Fieldtrippers,
> >  
> >  
> > I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error?
> >  
> >  
> > fieldtrip version 20120130, matlab version R2010a, operating system windows 7.
> >  
> >  
> > Thanks in advance for any suggestions.
> >  
> >  
> >  
> > ??? Error using ==> ft_fetch_data at 57
> > data does not contain a consistent trial definition, fetching data is not
> > possible
> >  
> >  
> > Error in ==> ft_databrowser>redraw_cb at 1159
> > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample);
> >  
> >  
> > Error in ==> ft_databrowser at 535
> > redraw_cb(h);
> >  
>  
-----------------------------------------------------------
> > Conserve Resources. Print only when necessary.
> > 
> > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. 
| -----------------------------------------------------------



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From alotof_xd at yahoo.com  Thu Mar  8 08:04:14 2012
From: alotof_xd at yahoo.com (alotof eve)
Date: Wed, 7 Mar 2012 23:04:14 -0800 (PST)
Subject: [FieldTrip] error message in databrowser
In-Reply-To: <7050dbcfcd6be.4f570d8c@mail.uh.edu>
References: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
	<1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>
	<1331107319.55433.YahooMailNeo@web125502.mail.ne1.yahoo.com>
	<7050dbcfcd6be.4f570d8c@mail.uh.edu>
Message-ID: <1331190254.90650.YahooMailNeo@web125502.mail.ne1.yahoo.com>

Hi, Mehmet,

Thank you so much for the suggestion. I will try this and will report the result.

Thanks,
Eve



________________________________
 From: Mehmet-Akif Coskun <mcoskun at mail.uh.edu>
To: alotof eve <alotof_xd at yahoo.com>; Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
Cc: alotof eve <alotof_xd at yahoo.com>; Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
Sent: Wednesday, March 7, 2012 5:26 AM
Subject: Re: [FieldTrip] error message in databrowser
 

Hi Eve,


I have posted same error earlier but got no suggestions. In my case, the error started popping up after i tried using parallel processing, but i don't know if this has anything to do with the error. I tried many things but no result.


finally, i simply uninstalled and re-installed matlab and everything worked perfectly there after. You may want to try this as a final option if you don't hear any other solution.


Mehmet

----- Original Message -----
From: alotof eve <alotof_xd at yahoo.com>
Date: Wednesday, March 7, 2012 2:03 am
Subject: Re: [FieldTrip] error message in databrowser
To: alotof eve <alotof_xd at yahoo.com>, Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl>


> Updated: I changed "&&" to "&", it worked but later a new error happened:
> 

> Reference to non-existent field 'hlim'.
> 

> Error in ft_databrowser>redraw_cb (line 1015)
>              eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - opt.hlim(1)); 

>  
> Error in ft_databrowser (line 434)
> redraw_cb(h);
> _____
> Thanks,
> Eve

> 
>  

________________________________
 From: alotof eve <alotof_xd at yahoo.com>
>  To: Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
>  Sent: Tuesday, March 6, 2012 12:52 PM
>  Subject: [FieldTrip] error message in databrowser
>   >  



> Hello, experts,
> 
> I am using ICA following the tutirial steps. 
> I got IC dataset "comp" with the command: comp = ft_componentanalysis (cfg, data);
> and ft_topoplotIC(cfg, comp) works.
> 
> However, then I used ft_databrowser(cfg, comp), I got an error message:
> Operands to the || and && operators must be
> convertible to logical scalar values.
> 
> Error in ft_databrowser (line 135)
> if hasdata && isfield(data, 'topo') &&
> strmatch (cfg.viewmode, 'component')
> 
> Can anyone know the way to settle this? 
> Thanks in advance.
> 
> Eve
>  

>  >  > 
> _______________________________________________
> 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 h.morgan at bangor.ac.uk  Thu Mar  8 10:49:59 2012
From: h.morgan at bangor.ac.uk (Helen Morgan)
Date: Thu, 08 Mar 2012 09:49:59 +0000
Subject: [FieldTrip] Call for abstracts - HIVE workshop - Berlin,
	April 27-28th, 2012
Message-ID: <4F5880C7.7020608@bangor.ac.uk>

Call for abstracts

HIVE WORKSHOP - Berlin, April 27-28th, 2012.

Could computers someday interact directly with the human brain? The 
vision of HIVE is that in the next 50 years we will witness the coming 
of age of technologies for fluent brain-computer and computer-mediated 
brain-to-brain interaction. While recent research has delivered 
important breakthroughs in brain-to-computer transmission, little has 
been achieved in the other direction––computer-controlled brain 
stimulation. The goal of the workshop is to present research toward 
developing a new generation of powerful and controllable non-invasive 
brain stimulation technologies.

State-of-the-art presentations on current distribution models and 
multi-scale neuron current interaction modeling will be presented. 
Results from stimulation experiments using tDCS, TMS, EEG and fMRI in 
different scenarios are given in overview and original presentations. 
Discussions during the workshop will lead to the design of multisite 
transcranial current stimulation technologies using real time EEG 
monitoring and feedback.

Keynote speakers:

Dr. Michael Nitsche
Dr. Klaus-Robert Müller
Dr. Lisa Marshall
Dr. Fabio Babiloni

The HIVE project has opened this workshop to all researchers from in 
this new multi-disciplinary field, based on acceptance of an abstract. 
You can find the Call for Abstracts here.

http://hive-eu.org/hive2012/call_for_papers

Best abstracts and presentations will be selected for publication in a 
Special Issue of the journal "Physiological Measurement".

Download the flyer here 
http://hive-eu.org/sites/hive-eu.org/files/Hive%20workshop%202012_final.pdf

-- 
Dr. Helen M. Morgan
Research Officer
Wolfson Centre for Clinical and Cognitive Neuroscience
School of Psychology
Bangor University
tel: 01248 388172
email: h.morgan at bangor.ac.uk

-- 
Rhif Elusen Gofrestredig / Registered Charity No. 1141565

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From max-philipp.stenner at med.ovgu.de  Thu Mar  8 13:26:13 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Thu, 08 Mar 2012 12:26:13 +0000
Subject: [FieldTrip] monte-carlo on LCMV moments
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830C9AB1@ESEN4.imed.uni-magdeburg.de>

Dear fieldtrip users, 

in addition to the question on the new implementation of ft_sourcestatistics for sourcegrandaveraged data which I sent yesterday, I have a second question regarding sourcestatistics on grandaveraged data obtained from LCMV beamforming of ERF. 

I would like to perfrom cluster corrected monte-carlo statistics on subj_voxel_time dipole moments, comparable (in its dimensions) to the sensor-level ERF cluster permutation test on subj_channel_time data that is described in the respective tutorial and that worked well. 

However, ft_sourcegrandaverage doesn't seem to permit "averaging" (with keepindividual = yes) of parameters that have more than one value per gridpoint (i.e. other than pow, nai etc.). 

In addition, the get_source_lcmv_mom subfunction in statistics_wrapper requires 4 rather than 3 dimensions. 

Is there any way that subj_voxel_time dipole moment data can be used for monte-carlo statistics comparable to the respective sensor-level ERF test?

Thanks very much, 

best wishes
Max
(fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)






________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]&quot; im Auftrag von &quot;Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de]
Gesendet: Mittwoch, 7. März 2012 18:46
Bis: Email discussion list for the FieldTrip project
Betreff: [FieldTrip] ft_sourcestatistics

Dear fieldtrip users,



I am encountering a problem with ft_sourcestatistics when using output from ft_sourcegrandaverage. My parameter of interest is a logratio: log(mean(moments(time of interest))/mean(moments(baseline))) which I simply named 'pow' to be compatible with ft functions. Apart from this, nothing else deviates from how fieldtrip handles the data/nothing else was changed 'manually'.



The problem arises from the fact that the existence of 10 different subjects in the grandaverage (in the usual 1x10 struct field 'trial') isn't represented in the 'powdimord' field of the data after ft_checkdata(varargin{i}, 'datatype', {'source', 'volume'}, 'feedback', 'no', 'inside', 'index', 'sourcerepresentation', 'new'); in the new implementation of ft_sourcestatistics:



varargin{1}

ans =



(before ft_checkdata:)



        pos: [8196x3 double]
        var: [1x1 struct]
     dimord: 'voxel'
      trial: [1x10 struct]
     inside: [8196x1 double]
    outside: [0x1 double]
         df: [8196x1 double]
        cfg: [1x1 struct]



(after ft_checkdata:)



          pos: [8196x3 double]
          var: [1x1 struct]
       dimord: 'pos'
       inside: [8196x1 double]
      outside: [0x1 double]
           df: [8196x1 double]
          cfg: [1x1 struct]
          pow: [8196x10 double]
    powdimord: 'pos'



This leads to a (wrong) transpose of the design (originally row1 = uvar, row2 = ivar [with two conditions for a depsamples T test]) and ultimately to the message

'The data must contain at least two units (usually subjects).'



Any help would be much appreciated, thanks very much!

Max

(fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From jan.schoffelen at donders.ru.nl  Thu Mar  8 13:38:46 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 8 Mar 2012 13:38:46 +0100
Subject: [FieldTrip] ft_sourcestatistics
In-Reply-To: <FBEFFA1F493D8944969D2F5AE78E58830C999B@ESEN4.imed.uni-magdeburg.de>
References: <FBEFFA1F493D8944969D2F5AE78E58830C999B@ESEN4.imed.uni-magdeburg.de>
Message-ID: <23891D6F-057F-4DBE-8C52-C43DAB74608E@donders.ru.nl>

Hi Max,

At the moment we are designing some major code changes to deal with source level data, and we need to ask you for some patience in this regard.
For now, you could try to move the call to ft_checkdata to outside ft_sourcestatistics, and change the powdimord into 'pos_rpt'; 
Does it work if you subsequently call ft_sourcestatistics (with cfg.implementation = 'new')? This new implementation has never fully matured and may be instable. It has been found to work in certain situations, but it has never been fully tested on all possible processing histories that users may throw at it. Hence the urgent need to clean up the code. 

Best,

Jan-Mathijs



On Mar 7, 2012, at 6:46 PM, Stenner, Max-Philipp wrote:

> Dear fieldtrip users,
> 
> 
> 
> I am encountering a problem with ft_sourcestatistics when using output from ft_sourcegrandaverage. My parameter of interest is a logratio: log(mean(moments(time of interest))/mean(moments(baseline))) which I simply named 'pow' to be compatible with ft functions. Apart from this, nothing else deviates from how fieldtrip handles the data/nothing else was changed 'manually'.
> 
> 
> 
> The problem arises from the fact that the existence of 10 different subjects in the grandaverage (in the usual 1x10 struct field 'trial') isn't represented in the 'powdimord' field of the data after ft_checkdata(varargin{i}, 'datatype', {'source', 'volume'}, 'feedback', 'no', 'inside', 'index', 'sourcerepresentation', 'new'); in the new implementation of ft_sourcestatistics:
> 
> 
> 
> varargin{1}
> 
> ans =
> 
> 
> 
> (before ft_checkdata:)
> 
> 
> 
>        pos: [8196x3 double]
>        var: [1x1 struct]
>     dimord: 'voxel'
>      trial: [1x10 struct]
>     inside: [8196x1 double]
>    outside: [0x1 double]
>         df: [8196x1 double]
>        cfg: [1x1 struct]
> 
> 
> 
> (after ft_checkdata:)
> 
> 
> 
>          pos: [8196x3 double]
>          var: [1x1 struct]
>       dimord: 'pos'
>       inside: [8196x1 double]
>      outside: [0x1 double]
>           df: [8196x1 double]
>          cfg: [1x1 struct]
>          pow: [8196x10 double]
>    powdimord: 'pos'
> 
> 
> 
> This leads to a (wrong) transpose of the design (originally row1 = uvar, row2 = ivar [with two conditions for a depsamples T test]) and ultimately to the message
> 
> 'The data must contain at least two units (usually subjects).'
> 
> 
> 
> Any help would be much appreciated, thanks very much!
> 
> Max
> 
> (fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)
> _______________________________________________
> 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

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From r.vandermeij at donders.ru.nl  Thu Mar  8 13:59:07 2012
From: r.vandermeij at donders.ru.nl (Roemer van der Meij)
Date: Thu, 08 Mar 2012 13:59:07 +0100
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
	<7270aa3bcbfd9.4f574cba@mail.uh.edu>
	<2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
Message-ID: <4F58AD1B.906@donders.ru.nl>

Hi Eve, Hi Michael,

I cannot find the specific line of code in the latest version, so I 
assume you are using an old version? If you update to the latest 
version, the problem should be solved.

Just for your curiosity, the bug was most likely caused by using the 
ancient strmatch (deprecated in later version of matlab). Changing it 
strcmp would have most likely fixed the problem.

Cheers,
Roemer




On 07-03-12 18:57, Epstein, Michael wrote:
>
> Interesting... can I ask what version of matlab you were running? and 
> was it 64 bit?
>
> -Michael
>
> *From:*fieldtrip-bounces at donders.ru.nl 
> [mailto:fieldtrip-bounces at donders.ru.nl] *On Behalf Of *Mehmet-Akif Coskun
> *Sent:* Wednesday, March 07, 2012 12:56 PM
> *To:* Email discussion list for the FieldTrip project
> *Cc:* fieldtrip at donders.ru.nl
> *Subject:* Re: [FieldTrip] Error -> ft_databrowser
>
> Hi Michael,
>
>
> I have posted the question actually but I didn't hear any suggestions 
> about it. The same error was posted yesterday by someone else.
>
>
> just to repeat what i have replied in the other post, i tried many 
> things to solve it (changed the code, run the databrowser code line by 
> line, updated fieldtrip version at etc.), but none of them solved the 
> problem. I started getting the error after I tried using parallel 
> processing scripts in matlab. But as i said, i have no basis to say 
> that this caused the problem. So basically, i do not know any 
> scientific solution.
>
>
> But an old school method solved the problem in my case. Simply i 
> uninstalled and re-installed matlab. Never got the error again. You 
> may want to try this. I have no other solution.
>
>
> Mehmet
>
>
>
>
>
> ----- Original Message -----
> From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
> Date: Wednesday, March 7, 2012 11:29 am
> Subject: Re: [FieldTrip] Error -> ft_databrowser
> To: fieldtrip at donders.ru.nl
>
> > Hi - I am actually encountering the same error with databrowser, and 
> was wondering if you ever came up with a solution to this problem - or 
> if anyone else has a solution - I didn't find a response on the 
> mailing list.
>
> >
>
> > -Michael
>
> >
>
> >
>
> >
>
> ------------------------------------------------------------------------
>
> > Dear Fieldtrippers,
>
> >
>
> >
>
> > I am encountering a strange error while i try to use ft_databrowser. 
> The error code is as below. I have never seen this error earlier. I 
> used ft_databrowser many times and its only last 2 days that i am 
> getting the error. I downloaded a newer version of fieldtrip 
> (fieldtrip-20120130) and used the newer version but still the same 
> error. Strangely, i dont get this error when i tried with other 
> computers (same matlab version (R2010a), same operating system 
> (windows 7) on both computers. Has anyone got this error before? what 
> may cause this error?
>
> >
>
> >
>
> > fieldtrip version 20120130, matlab version R2010a, operating system 
> windows 7.
>
> >
>
> >
>
> > Thanks in advance for any suggestions.
>
> >
>
> >
>
> >
>
> > ??? Error using ==> ft_fetch_data at 57
>
> > data does not contain a consistent trial definition, fetching data is not
>
> > possible
>
> >
>
> >
>
> > Error in ==> ft_databrowser>redraw_cb at 1159
>
> > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', 
> endsample);
>
> >
>
> >
>
> > Error in ==> ft_databrowser at 535
>
> > redraw_cb(h);
>
> >
>
> ------------------------------------------------------------------------
>
> > Conserve Resources. Print only when necessary.
> >
> > IMPORTANT NOTICE: This e-mail is meant only for the use of the 
> intended recipient. It may contain confidential information which is 
> legally privilegedor otherwise protected by law. If you received this 
> e-mail in error or from someone who is not authorized to send it to 
> you, you are strictly prohibited from reviewing, using, disseminating, 
> distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF 
> THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. 
> Thank you for your cooperation.
>
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> ------------------------------------------------------------------------
> Conserve Resources. Print only when necessary.
>
> IMPORTANT NOTICE: This e-mail is meant only for the use of the 
> intended recipient. It may contain confidential information which is 
> legally privilegedor otherwise protected by law. If you received this 
> e-mail in error or from someone who is not authorized to send it to 
> you, you are strictly prohibited from reviewing, using, disseminating, 
> distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF 
> THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. 
> Thank you for your cooperation.
>
>
> _______________________________________________
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> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

-- 
Roemer van der Meij M.Sc.
PhD student
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 max-philipp.stenner at med.ovgu.de  Thu Mar  8 14:36:16 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Thu, 08 Mar 2012 13:36:16 +0000
Subject: [FieldTrip] ft_sourcestatistics
In-Reply-To: <23891D6F-057F-4DBE-8C52-C43DAB74608E@donders.ru.nl>
References: <FBEFFA1F493D8944969D2F5AE78E58830C999B@ESEN4.imed.uni-magdeburg.de>
	<23891D6F-057F-4DBE-8C52-C43DAB74608E@donders.ru.nl>
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830C9AD3@ESEN4.imed.uni-magdeburg.de>

Hi Jan-Mathijs,



thank you for your response, since it worked for cfg.implementation = 'old' I haven't tried your suggestion of calling ft_checkdata outside of ft_sourcestatistics so far but will later during the day,



thanks again,

best

Max



________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von "jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl]
Gesendet: Donnerstag, 8. März 2012 13:38
Bis: Email discussion list for the FieldTrip project
Betreff: Re: [FieldTrip] ft_sourcestatistics

Hi Max,

At the moment we are designing some major code changes to deal with source level data, and we need to ask you for some patience in this regard.
For now, you could try to move the call to ft_checkdata to outside ft_sourcestatistics, and change the powdimord into 'pos_rpt';
Does it work if you subsequently call ft_sourcestatistics (with cfg.implementation = 'new')? This new implementation has never fully matured and may be instable. It has been found to work in certain situations, but it has never been fully tested on all possible processing histories that users may throw at it. Hence the urgent need to clean up the code.

Best,

Jan-Mathijs



On Mar 7, 2012, at 6:46 PM, Stenner, Max-Philipp wrote:

Dear fieldtrip users,



I am encountering a problem with ft_sourcestatistics when using output from ft_sourcegrandaverage. My parameter of interest is a logratio: log(mean(moments(time of interest))/mean(moments(baseline))) which I simply named 'pow' to be compatible with ft functions. Apart from this, nothing else deviates from how fieldtrip handles the data/nothing else was changed 'manually'.



The problem arises from the fact that the existence of 10 different subjects in the grandaverage (in the usual 1x10 struct field 'trial') isn't represented in the 'powdimord' field of the data after ft_checkdata(varargin{i}, 'datatype', {'source', 'volume'}, 'feedback', 'no', 'inside', 'index', 'sourcerepresentation', 'new'); in the new implementation of ft_sourcestatistics:



varargin{1}

ans =



(before ft_checkdata:)



       pos: [8196x3 double]
       var: [1x1 struct]
    dimord: 'voxel'
     trial: [1x10 struct]
    inside: [8196x1 double]
   outside: [0x1 double]
        df: [8196x1 double]
       cfg: [1x1 struct]



(after ft_checkdata:)



         pos: [8196x3 double]
         var: [1x1 struct]
      dimord: 'pos'
      inside: [8196x1 double]
     outside: [0x1 double]
          df: [8196x1 double]
         cfg: [1x1 struct]
         pow: [8196x10 double]
   powdimord: 'pos'



This leads to a (wrong) transpose of the design (originally row1 = uvar, row2 = ivar [with two conditions for a depsamples T test]) and ultimately to the message

'The data must contain at least two units (usually subjects).'



Any help would be much appreciated, thanks very much!

Max

(fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto: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<mailto:J.Schoffelen at donders.ru.nl>
Telephone: +31-24-3614793




From MEpstein at NKI.RFMH.ORG  Thu Mar  8 16:17:56 2012
From: MEpstein at NKI.RFMH.ORG (Epstein, Michael)
Date: Thu, 8 Mar 2012 10:17:56 -0500
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <4F58AD1B.906@donders.ru.nl>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org><7270aa3bcbfd9.4f574cba@mail.uh.edu><2586A1048152BE4D
	861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
	<4F58AD1B.906@donders.ru.nl>
Message-ID: <2586A1048152BE4D861E64A98700AD420A999DCD@nki-mail.NKI.rfmh.org>

Interesting... I'll look into that if I ever have the issue again.
However following Mehmet's advice and simply reinstalling the same
version of MATLAB seems to have fixed the problem anyway - not exactly
sure how that happened, but at least it worked. 

 

Thanks for the advice anyway though,

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Roemer van der
Meij
Sent: Thursday, March 08, 2012 7:59 AM
To: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Eve, Hi Michael,

I cannot find the specific line of code in the latest version, so I
assume you are using an old version? If you update to the latest
version, the problem should be solved.

Just for your curiosity, the bug was most likely caused by using the
ancient strmatch (deprecated in later version of matlab). Changing it
strcmp would have most likely fixed the problem.

Cheers,
Roemer




On 07-03-12 18:57, Epstein, Michael wrote: 

Interesting... can I ask what version of matlab you were running? and
was it 64 bit?

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Mehmet-Akif Coskun
Sent: Wednesday, March 07, 2012 12:56 PM
To: Email discussion list for the FieldTrip project
Cc: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Michael,


I have posted the question actually but I didn't hear any suggestions
about it. The same error was posted yesterday by someone else. 


just to repeat what i have replied in the other post, i tried many
things to solve it (changed the code, run the databrowser code line by
line, updated fieldtrip version at etc.), but none of them solved the
problem. I started getting the error after I tried using parallel
processing scripts in matlab. But as i said, i have no basis to say that
this caused the problem. So basically, i do not know any scientific
solution.


But an old school method solved the problem in my case. Simply i
uninstalled and re-installed matlab. Never got the error again. You may
want to try this. I have no other solution.


Mehmet





----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
<mailto:MEpstein at NKI.RFMH.ORG> 
Date: Wednesday, March 7, 2012 11:29 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: fieldtrip at donders.ru.nl

> Hi - I am actually encountering the same error with databrowser, and
was wondering if you ever came up with a solution to this problem - or
if anyone else has a solution - I didn't find a response on the mailing
list.

>  

> -Michael

>  

>  

>  

________________________________

> Dear Fieldtrippers,

>  

>  

> I am encountering a strange error while i try to use ft_databrowser.
The error code is as below. I have never seen this error earlier. I used
ft_databrowser many times and its only last 2 days that i am getting the
error. I downloaded a newer version of fieldtrip (fieldtrip-20120130)
and used the newer version but still the same error. Strangely, i dont
get this error when i tried with other computers (same matlab version
(R2010a), same operating system (windows 7) on both computers. Has
anyone got this error before? what may cause this error?

>  

>  

> fieldtrip version 20120130, matlab version R2010a, operating system
windows 7.

>  

>  

> Thanks in advance for any suggestions.

>  

>  

>  

> ??? Error using ==> ft_fetch_data at 57

> data does not contain a consistent trial definition, fetching data is
not

> possible

>  

>  

> Error in ==> ft_databrowser>redraw_cb at 1159

> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample',
endsample);

>  

>  

> Error in ==> ft_databrowser at 535

> redraw_cb(h);

>  

 

________________________________

> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the
intended recipient. It may contain confidential information which is
legally privilegedor otherwise protected by law. If you received this
e-mail in error or from someone who is not authorized to send it to you,
you are strictly prohibited from reviewing, using, disseminating,
distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE
ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank
you for your cooperation. 

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

________________________________

Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally
privilegedor otherwise protected by law. If you received this e-mail in
error or from someone who is not authorized to send it to you, you are
strictly prohibited from reviewing, using, disseminating, distributing
or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY
RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for
your cooperation. 






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

 

-- 
Roemer van der Meij M.Sc.
PhD student
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



Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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From MEpstein at NKI.RFMH.ORG  Thu Mar  8 16:27:03 2012
From: MEpstein at NKI.RFMH.ORG (Epstein, Michael)
Date: Thu, 8 Mar 2012 10:27:03 -0500
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <2586A1048152BE4D861E64A98700AD420A999DCD@nki-mail.NKI.rfmh.org>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org><7270aa3bcbfd9.4f574cba@mail.uh.edu><2586A1048152BE4D
	861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org><4F58AD1B.906@donders.ru.nl>
	<2586A1048152BE4D861E64A98700AD420A999DCD@nki-mail.NKI.rfmh.org>
Message-ID: <2586A1048152BE4D861E64A98700AD420A999DE5@nki-mail.NKI.rfmh.org>

Stephan said David is a 'guru' so that sounds good. He actually said
that he uses EEGLAB for ICA too, so I guess that really is the way to
go.

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Epstein, Michael
Sent: Thursday, March 08, 2012 10:18 AM
To: r.vandermeij at donders.ru.nl; Email discussion list for the FieldTrip
project
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Interesting... I'll look into that if I ever have the issue again.
However following Mehmet's advice and simply reinstalling the same
version of MATLAB seems to have fixed the problem anyway - not exactly
sure how that happened, but at least it worked. 

 

Thanks for the advice anyway though,

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Roemer van der
Meij
Sent: Thursday, March 08, 2012 7:59 AM
To: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Eve, Hi Michael,

I cannot find the specific line of code in the latest version, so I
assume you are using an old version? If you update to the latest
version, the problem should be solved.

Just for your curiosity, the bug was most likely caused by using the
ancient strmatch (deprecated in later version of matlab). Changing it
strcmp would have most likely fixed the problem.

Cheers,
Roemer




On 07-03-12 18:57, Epstein, Michael wrote: 

Interesting... can I ask what version of matlab you were running? and
was it 64 bit?

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Mehmet-Akif Coskun
Sent: Wednesday, March 07, 2012 12:56 PM
To: Email discussion list for the FieldTrip project
Cc: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Michael,


I have posted the question actually but I didn't hear any suggestions
about it. The same error was posted yesterday by someone else. 


just to repeat what i have replied in the other post, i tried many
things to solve it (changed the code, run the databrowser code line by
line, updated fieldtrip version at etc.), but none of them solved the
problem. I started getting the error after I tried using parallel
processing scripts in matlab. But as i said, i have no basis to say that
this caused the problem. So basically, i do not know any scientific
solution.


But an old school method solved the problem in my case. Simply i
uninstalled and re-installed matlab. Never got the error again. You may
want to try this. I have no other solution.


Mehmet





----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
<mailto:MEpstein at NKI.RFMH.ORG> 
Date: Wednesday, March 7, 2012 11:29 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: fieldtrip at donders.ru.nl

> Hi - I am actually encountering the same error with databrowser, and
was wondering if you ever came up with a solution to this problem - or
if anyone else has a solution - I didn't find a response on the mailing
list.

>  

> -Michael

>  

>  

>  

________________________________

> Dear Fieldtrippers,

>  

>  

> I am encountering a strange error while i try to use ft_databrowser.
The error code is as below. I have never seen this error earlier. I used
ft_databrowser many times and its only last 2 days that i am getting the
error. I downloaded a newer version of fieldtrip (fieldtrip-20120130)
and used the newer version but still the same error. Strangely, i dont
get this error when i tried with other computers (same matlab version
(R2010a), same operating system (windows 7) on both computers. Has
anyone got this error before? what may cause this error?

>  

>  

> fieldtrip version 20120130, matlab version R2010a, operating system
windows 7.

>  

>  

> Thanks in advance for any suggestions.

>  

>  

>  

> ??? Error using ==> ft_fetch_data at 57

> data does not contain a consistent trial definition, fetching data is
not

> possible

>  

>  

> Error in ==> ft_databrowser>redraw_cb at 1159

> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample',
endsample);

>  

>  

> Error in ==> ft_databrowser at 535

> redraw_cb(h);

>  

 

________________________________

> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the
intended recipient. It may contain confidential information which is
legally privilegedor otherwise protected by law. If you received this
e-mail in error or from someone who is not authorized to send it to you,
you are strictly prohibited from reviewing, using, disseminating,
distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE
ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank
you for your cooperation. 

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

________________________________

Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally
privilegedor otherwise protected by law. If you received this e-mail in
error or from someone who is not authorized to send it to you, you are
strictly prohibited from reviewing, using, disseminating, distributing
or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY
RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for
your cooperation. 





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

 

-- 
Roemer van der Meij M.Sc.
PhD student
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

________________________________

Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally
privilegedor otherwise protected by law. If you received this e-mail in
error or from someone who is not authorized to send it to you, you are
strictly prohibited from reviewing, using, disseminating, distributing
or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY
RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for
your cooperation. 



Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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From frerap at gist.ac.kr  Fri Mar  9 12:56:13 2012
From: frerap at gist.ac.kr (MinKyu Ahn)
Date: Fri, 9 Mar 2012 20:56:13 +0900 (KST)
Subject: [FieldTrip] question for ft_freqanalysis()
Message-ID: <1182294678.1331294173648.JavaMail.root@eunhasu>

I am new fieldtrip and wavelet analysis.



Fortunately, fieldtrip webpage has some examples for that.



While I follow it, I found that the scale between the resuts of fixed hann method and wavelet method in http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis.



When it plots results, the zlimt is used  as cfg.zlim         = [-3e-27 3e-27] while  it is used as [-3e-25 3e-25]    for wavelet.



The scale difference is about 10^2, why this happen?





Please let me know about it.







Thank you.






============================================================ MinKyu Ahn, Ph.D. Student, Member of BioComputing Lab. School of Information and Communications Gwangju Institute of Science and Technology (GIST)  261 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, Korea  Tel : +82-62-715-3126/2266  Cell : +82-10-7360-8232  E-mail : frerap at gist.ac.kr  URL : http://biocomput.gist.ac.kr ============================================================

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From matt.mollison at gmail.com  Fri Mar  9 20:16:42 2012
From: matt.mollison at gmail.com (Matt Mollison)
Date: Fri, 9 Mar 2012 12:16:42 -0700
Subject: [FieldTrip] Oscillatory power normalization
Message-ID: <CAJB8axm9J3=ktKM16bVhjFiToBOcD1RrVbn+1xxD4HiiqP1_WA@mail.gmail.com>

My questions essentially boil down to: what do people do for power
normalization when assessing statistical differences?

It gets more detailed below regarding examining event-related power changes
relative to a baseline (within-subjects, comparing two conditions, stimulus
onset = 0 ms). I didn't find much discussion of this on the list or the
wiki. Any references for these issues would also be appreciated.

(1) Does power data need to be baseline normalized for statistical tests
comparing conditions? Normalization would put power on equal footing across
all subjects, conditions, sensors, times, frequencies, etc., but it will
surely affect power during the stimulus period in a particular way. If so,
do the two (or more) conditions need to use the same baseline condition, or
can each trial be normalized to its own pre-stim baseline period (a la
ft_freqbaseline)? For either, it seems like you'd always need
keeptrials='yes' in ft_freqanalysis. However, it does not seem to get
normalized in the cluster_permutation_freq tutorial (within-subjects)---am
I missing something?

If we should normalize:
(2) I've read a number of papers that Z-transform stimulus period power
relative to pre-stim activity (subtract mean, divide by std) before doing
statistics. I've also read a lot that don't mention baselines, or e.g. do a
decibel [dB] transform. ft_freqbaseline does not have a Z-transform option.
There is ft_preproc_standardize, but this seems to operate at a lower level
than is usually recommended. Z-transforming seems like a good option, but
how can I use it in the FT pipeline for within-subjects analyses
(especially with keeptrials='no')? Alternatively, when should one use
'absolute', 'relative', or 'relchange'?

Regarding choosing the baseline period:
(3) It seems that the baseline period needs to precede stimulus onset by a
sufficient amount of time so that the stimulus period doesn't bleed into
the baseline; this time would be specific to both the frequency and either
wavelet width or taper window length. For example, at 4 Hz with wavelet
width=6 or a taper with 6 cycles per time window (t_ftimwin) the
wavelet/window would be 1500 ms long, and the end of the baseline must
precede stimulus onset by at least half this to keep them separate. At
lower frequencies this could get quite unruly (e.g., 1 Hz would require
ending 3000 ms before stimulus). Is this correct? Maybe that's why it's
better to have a single separate baseline condition. Anyway, the
timefrequencyanalysis tutorial seems to disregard this separation of
baseline and stimulus activity (as have many papers I've read), so maybe
I'm wrong about this being necessary.

Thanks for your time,
Matt Mollison

--
Univ. of Colorado at Boulder
Dept. of Psychology and Neuroscience
matthew.mollison at colorado.edu
http://psych.colorado.edu/~mollison/
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From cas243 at georgetown.edu  Sun Mar 11 22:52:15 2012
From: cas243 at georgetown.edu (Clara A. Scholl)
Date: Sun, 11 Mar 2012 17:52:15 -0400
Subject: [FieldTrip] clustering, spatial neighbors and minnbchan
In-Reply-To: <CAAHOyr7pc8qkmeJ4X9NOsGQAmEUsg3viPPYo5v+4d5rE3bQ-Mw@mail.gmail.com>
References: <CAAHOyr7pc8qkmeJ4X9NOsGQAmEUsg3viPPYo5v+4d5rE3bQ-Mw@mail.gmail.com>
Message-ID: <CAAHOyr6APDwrRwfONA0xuYXNJbhYKtNrpd0QuVxcKcAXTUL5Yg@mail.gmail.com>

Hi,

I have a question about how to identify appropriate parameters for
neighbor distance in ft_neighbourselection and how to set minnbchan
for space-time cluster analysis.

I identified a neighbor distance based on our sensor layout, so that
spatially adjacent channels were defined as neighbors, and spatially
non-adjacent channels were not defined as neighbors.  I then ran
space-time cluster analysis and identified a cluster with a large
spatial and temporal extent which appears to be the continuation of
several effects lumped together.  I subsequently increased minnbchan,
so that this cluster gets separated into separate clusters following
the logic in this discussion thread:
http://mailman.science.ru.nl/pipermail/fieldtrip/2011-February/003501.html

However now a new problem appears: it seems that channels near the
periphery of the sensor layout, which have few adjacent spatial
neighbors, are not included in the clusters when minnbchan has a value
greater than the number of neighbors the channels have according to
the neighbor distance used in ft_neighbourselection.  Is this correct?
 Put differently, increasing minnbchan appears to bias clusters toward
including only channels at the center of the sensor layout, with many
adjacent other channels (and channels at the periphery of the layout,
which have fewer spatial neighbors, are excluded from the identified
clusters).

Obviously I want a principled, data-independent selection of cluster
identification parameters so I want to ask what the "correct" way to
identify these parameters (neighbor distance, and minnbchan) is.
Should minnbchan be used differently for channel-time cluster analysis
(what I'm doing) compared to channel-time-frequency cluster analysis?

Thanks,
Clara



From jm.horschig at donders.ru.nl  Mon Mar 12 09:48:53 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 12 Mar 2012 09:48:53 +0100
Subject: [FieldTrip] clustering, spatial neighbors and minnbchan
In-Reply-To: <CAAHOyr6APDwrRwfONA0xuYXNJbhYKtNrpd0QuVxcKcAXTUL5Yg@mail.gmail.com>
References: <CAAHOyr7pc8qkmeJ4X9NOsGQAmEUsg3viPPYo5v+4d5rE3bQ-Mw@mail.gmail.com>
	<CAAHOyr6APDwrRwfONA0xuYXNJbhYKtNrpd0QuVxcKcAXTUL5Yg@mail.gmail.com>
Message-ID: <4F5DB875.9080501@donders.ru.nl>

Dear Clara,

First of all, defining neighbours based on a sensor layout may not be 
the best approach. If you have 3D positions of your sensors available, I 
would suggest that you use these for neighbour selection (note that for 
EEG sensors, this is much less an issue than for MEG sensors, but you 
didn't mention what system you are using)

Second, for minnbchan, I think you are right. Of course sensors at the 
outer rim have, by definition, less neighbouring sensors than other 
sensors. As far as I know, minnbchan is defined as the number of 
neighbouring significant sensors. So, if you specify it to be e.g. 10, 
than of course all sensors with less than 10 neighbours can never be 
part of a cluster. Those with more than 10 need to have also at least 10 
neighbouring sensors that are significant as well. Of course, sensors in 
the center have more neighbouring sensors, thus higher minnbchan will 
have a less tremendous effect there. So as far as I can see, there are 
four ways out for you:

1) If you didn't do so already, you can choose a finer time-scale, 
hoping that this will separate the different neural effects (if they are 
different)

2) Do the same on source level - maybe this will reduce spatial leakage.

3) Define a wider range of neighbours for sensors at the outer rim, 
thereby forcing a minimum number of neighbouring sensors. Instead (or 
additionally), you could try to use cfg.method = 'triangulation' or 
'template' for neighbour selection. For more information, see here: 
http://fieldtrip.fcdonders.nl/faq/how_does_ft_prepare_neighbours_work
I would suggest that you use cfg.feedback = 'yes' and choose the 
method/parameters that seem most optimal to you (there is not *the* best 
way, unfortunately)

4) Live with it, as there are technical limitations with our recording 
equipment, and of course physiological limitations. As Eric pointed out 
in the old mails you referred to:
"

In fact, it is looking for isolated blobs that one would like to interpret as separate physiological entities.
This contrast with the nature of the EEG/MEG data, which has poor spatial resolution (due to volume conduction and common pick-up),
often poor spectral resolution (due to the short time windows of our time-resolved spectral analysis), and often poor time resolution
(due to latency jitter over trials).
"



Hope this helps.
Best,
Jörn



On 3/11/2012 10:52 PM, Clara A. Scholl wrote:
> Hi,
>
> I have a question about how to identify appropriate parameters for
> neighbor distance in ft_neighbourselection and how to set minnbchan
> for space-time cluster analysis.
>
> I identified a neighbor distance based on our sensor layout, so that
> spatially adjacent channels were defined as neighbors, and spatially
> non-adjacent channels were not defined as neighbors.  I then ran
> space-time cluster analysis and identified a cluster with a large
> spatial and temporal extent which appears to be the continuation of
> several effects lumped together.  I subsequently increased minnbchan,
> so that this cluster gets separated into separate clusters following
> the logic in this discussion thread:
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-February/003501.html
>
> However now a new problem appears: it seems that channels near the
> periphery of the sensor layout, which have few adjacent spatial
> neighbors, are not included in the clusters when minnbchan has a value
> greater than the number of neighbors the channels have according to
> the neighbor distance used in ft_neighbourselection.  Is this correct?
>   Put differently, increasing minnbchan appears to bias clusters toward
> including only channels at the center of the sensor layout, with many
> adjacent other channels (and channels at the periphery of the layout,
> which have fewer spatial neighbors, are excluded from the identified
> clusters).
>
> Obviously I want a principled, data-independent selection of cluster
> identification parameters so I want to ask what the "correct" way to
> identify these parameters (neighbor distance, and minnbchan) is.
> Should minnbchan be used differently for channel-time cluster analysis
> (what I'm doing) compared to channel-time-frequency cluster analysis?
>
> Thanks,
> Clara
>
> _______________________________________________
> 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

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 vitoria.piai at gmail.com  Mon Mar 12 11:06:19 2012
From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=)
Date: Mon, 12 Mar 2012 11:06:19 +0100
Subject: [FieldTrip] bug in new ft_checkdata?
Message-ID: <4F5DCA9B.5030208@gmail.com>

Hi everyone,

I've just got an error when running ft_megplanar and ft_multiplotER that 
I had never had before when running the exact same scripts on exact same 
data:

"Undefined function or method 'fixname' for input arguments of type 'char'.
The chain of errors makes reference to warning_once at 66, fixsampleinfo 
at 66/68, and ft_checkdata at 604.

I'm using the most up-to-date fieldtrip version since I'm working within 
the Donders.
Is this a bug or should I re-structure my data?

Thanks a lot, Vitória

-- 
** Please consider the environment - do you really need to print? **	



From ali at cs.ru.nl  Mon Mar 12 11:32:53 2012
From: ali at cs.ru.nl (Ali Bahramisharif)
Date: Mon, 12 Mar 2012 11:32:53 +0100
Subject: [FieldTrip] bug in new ft_checkdata?
In-Reply-To: <4F5DCA9B.5030208@gmail.com>
References: <4F5DCA9B.5030208@gmail.com>
Message-ID: <8590fee73375ab9349c94481d6a98ebf.squirrel@squirrel.science.ru.nl>

Hi Vitória,

Just be sure that you have removed SPM from your path. SPM has an old
version of fieldtrip and if you have it in your path, it causes a lot of
troubles.

Cheers,
Ali

> Hi everyone,
>
> I've just got an error when running ft_megplanar and ft_multiplotER that
> I had never had before when running the exact same scripts on exact same
> data:
>
> "Undefined function or method 'fixname' for input arguments of type
> 'char'.
> The chain of errors makes reference to warning_once at 66, fixsampleinfo
> at 66/68, and ft_checkdata at 604.
>
> I'm using the most up-to-date fieldtrip version since I'm working within
> the Donders.
> Is this a bug or should I re-structure my data?
>
> Thanks a lot, Vitória
>
> --
> ** Please consider the environment - do you really need to print? **
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>


-- 
Address:
        HG02.517
        Intelligent Systems
        Radboud University Nijmegen
        Heyendaalseweg 135
        6525 AJ Nijmegen
        The Netherlands

http://www.cs.ru.nl/~ali
Tel.:   +31 (0)24 36 52634



From bibi.raquel at gmail.com  Mon Mar 12 13:03:33 2012
From: bibi.raquel at gmail.com (Raquel Bibi)
Date: Mon, 12 Mar 2012 08:03:33 -0400
Subject: [FieldTrip] bug in new ft_checkdata?
In-Reply-To: <4F5DCA9B.5030208@gmail.com>
References: <4F5DCA9B.5030208@gmail.com>
Message-ID: <D550BDC5-8AED-45A9-A8F9-DBEDB52BDB82@gmail.com>

I had the had same error running ft_redefinetrial. As a quick fix I put fixname.m (in private folder) into fieldtrip folder. 

Best,

Raquel

Sent from my iPhone

On Mar 12, 2012, at 6:06 AM, Vitória Magalhães Piai <vitoria.piai at gmail.com> wrote:

> Hi everyone,
> 
> I've just got an error when running ft_megplanar and ft_multiplotER that I had never had before when running the exact same scripts on exact same data:
> 
> "Undefined function or method 'fixname' for input arguments of type 'char'.
> The chain of errors makes reference to warning_once at 66, fixsampleinfo at 66/68, and ft_checkdata at 604.
> 
> I'm using the most up-to-date fieldtrip version since I'm working within the Donders.
> Is this a bug or should I re-structure my data?
> 
> Thanks a lot, Vitória
> 
> -- 
> ** Please consider the environment - do you really need to print? **    
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From g.piantoni at nin.knaw.nl  Mon Mar 12 14:22:39 2012
From: g.piantoni at nin.knaw.nl (Gio Piantoni)
Date: Mon, 12 Mar 2012 14:22:39 +0100
Subject: [FieldTrip] bug in new ft_checkdata?
In-Reply-To: <D550BDC5-8AED-45A9-A8F9-DBEDB52BDB82@gmail.com>
References: <4F5DCA9B.5030208@gmail.com>
	<D550BDC5-8AED-45A9-A8F9-DBEDB52BDB82@gmail.com>
Message-ID: <CAHeOcrtUjpEaVA_bnkWFCHUe3H5P1a6oDJ-fB9HwdRk2VuU2ag@mail.gmail.com>

Hi all,

Raquel is correct. fixname.m was missing from utilities/private

I added it to the dev version, should be fixed now and available on FTP tonight.

Gio

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

+31 20 5665492
gio at gpiantoni.com
www.gpiantoni.com

On Mon, Mar 12, 2012 at 13:03, Raquel Bibi <bibi.raquel at gmail.com> wrote:
> I had the had same error running ft_redefinetrial. As a quick fix I put fixname.m (in private folder) into fieldtrip folder.
>
> Best,
>
> Raquel
>
> Sent from my iPhone
>
> On Mar 12, 2012, at 6:06 AM, Vitória Magalhães Piai <vitoria.piai at gmail.com> wrote:
>
>> Hi everyone,
>>
>> I've just got an error when running ft_megplanar and ft_multiplotER that I had never had before when running the exact same scripts on exact same data:
>>
>> "Undefined function or method 'fixname' for input arguments of type 'char'.
>> The chain of errors makes reference to warning_once at 66, fixsampleinfo at 66/68, and ft_checkdata at 604.
>>
>> I'm using the most up-to-date fieldtrip version since I'm working within the Donders.
>> Is this a bug or should I re-structure my data?
>>
>> Thanks a lot, Vitória
>>
>> --
>> ** Please consider the environment - do you really need to print? **
>>
>> _______________________________________________
>> 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 fredericroux at hotmail.de  Mon Mar 12 15:11:07 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Mon, 12 Mar 2012 15:11:07 +0100
Subject: [FieldTrip] read_fcdc_mri error
Message-ID: <DUB113-W99483229B6AF1ABB816C85B75B0@phx.gbl>


Dear all,

I am getting an error when trying to read CTF-V2 formatted
MRI data using the read_fcdc_mri function.

??? Error using ==> reshape
To RESHAPE the number of elements must not change.

Error in ==> fieldtrip-20081208/private/read_ctf_mri at 113
mri = reshape(mri, [256 256 256]);

Error in ==> read_fcdc_mri at 95
 [img,hdr] = read_ctf_mri(filename);

Error in ==> warpMRI_DEV at 18
 mri = read_fcdc_mri([path2files,mrifiles(sujIt).name]);

The error results because at line 105 of the read_fcfc_mri.m function

mri = unint16(fread(fid,256*256*256,'uint16'));

returns a vector of  length = 16777215 when in fact it should be of
lentgh = 16777216. This means that 1 single value is missing.

The ackward thing is that I can open the MR-file without problem
in the MRIViewer and that there it appears to have 256 values
in the x,y and z dimension. Also this error appears only in 
a subset of files. 

I suspect that there is an error somewhere maybe in the data
acquisition or conversion pipeline.
Any suggestions or help would be highly appreciated.

Have a nice day!

Fred


-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From fredericroux at hotmail.de  Mon Mar 12 17:15:58 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Mon, 12 Mar 2012 17:15:58 +0100
Subject: [FieldTrip] how to set lambda for resting state lcmv-beamformer
Message-ID: <DUB113-W27C7B2A586CF97AE4D0EC8B75B0@phx.gbl>


Dear fieldtrip users,

I am trying to compute a spatial filter
to localize alpha-band activity in an
eyes closed resting state meg recording
using the LCMV-method.

The condition of my covariance matrix is > 1*10e6
so I set lambda = 0.01. When I then plot the NAI
I find two clusters of activity: 
one in the center of the head,
one in the occipital cortex.

In Exercise 5 of the tutorial, it is 
mentioned to set lambda to 1e-29 in order 
to suppresses the center of head artifact.

I wanted to ask if anybody could tell me what the
rationale was to set lambda = 1e-29? 
Is there a standardized way to compute lambda?

Best regards,

Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225

 		 	   		  
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From ali at cs.ru.nl  Mon Mar 12 18:30:52 2012
From: ali at cs.ru.nl (Ali Bahramisharif)
Date: Mon, 12 Mar 2012 18:30:52 +0100
Subject: [FieldTrip] how to set lambda for resting state lcmv-beamformer
In-Reply-To: <DUB113-W27C7B2A586CF97AE4D0EC8B75B0@phx.gbl>
References: <DUB113-W27C7B2A586CF97AE4D0EC8B75B0@phx.gbl>
Message-ID: <b81684b6e207fbd7cbfccb066a4fa413.squirrel@squirrel.science.ru.nl>

Hi Fred,

As far as I remember, lambda is used to regularize the covariance matrix.
I mean: regularized_covariance= XX'+lambda*Identity. To set it properly,
you need to look at the eigen-values of XX'. Normally you want to get rid
of the small eigen values. One way is to choose lambda to be 1/1000 of the
largest eigen-value.

Hope this helps.
Ali

>
> Dear fieldtrip users,
>
> I am trying to compute a spatial filter
> to localize alpha-band activity in an
> eyes closed resting state meg recording
> using the LCMV-method.
>
> The condition of my covariance matrix is > 1*10e6
> so I set lambda = 0.01. When I then plot the NAI
> I find two clusters of activity:
> one in the center of the head,
> one in the occipital cortex.
>
> In Exercise 5 of the tutorial, it is
> mentioned to set lambda to 1e-29 in order
> to suppresses the center of head artifact.
>
> I wanted to ask if anybody could tell me what the
> rationale was to set lambda = 1e-29?
> Is there a standardized way to compute lambda?
>
> Best regards,
>
> Fred
>
> --
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
>
>  		 	   		  _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Address:
        HG02.517
        Intelligent Systems
        Radboud University Nijmegen
        Heyendaalseweg 135
        6525 AJ Nijmegen
        The Netherlands

http://www.cs.ru.nl/~ali
Tel.:   +31 (0)24 36 52634



From nathanweisz at mac.com  Mon Mar 12 20:59:42 2012
From: nathanweisz at mac.com (Nathan Weisz)
Date: Mon, 12 Mar 2012 20:59:42 +0100
Subject: [FieldTrip] Master Cognitive Science Trento
Message-ID: <5BE61BE0-E292-4EF6-B6DD-82814DD0F62A@mac.com>

Dear all,

sorry for (mis-)using this mailing list as advertisement platform. 
http://international.unitn.it/sites/international.unitn.it/files/439_11_MCS_Cop_web.pdf


best,
n

International Masters in Cognitive Science, University of Trento, Italy:

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The Master’s course in Cognitive Neuroscience at the University of Trento provides research-focused training with a diverse, international group of faculty and researchers. The two year program combines courses in neuroscience, cognition, statistics, advanced signal and data analysis with hands-on training in cutting-edge research techniques. These include functional magnetic resonance imaging (fMRI), transcranial magnetic stimulation (TMS), magnetic encephalography (MEG), computational modelling, comparative cognition (animal models), EEG, eye tracking, cinematic motion tracking and psychophysics.

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The two-year program combines a solid foundation in scientific and cognitive methods - modules in mathematics, language science, neuroscience, and psychology, including an introduction to advanced methods such as eye tracking, EEG, and fMRI – with an extensive training in computational methods for the statistical analysis of large amounts of language and perceptual data, and in interface design. Theoretical knowledge will be supplemented by the experience acquired in substantial practical projects carried out in research and industry labs.

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fax + 39 0464 808415
www.cogsci.unitn.it
mcs at unitn.it
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From cas243 at georgetown.edu  Tue Mar 13 02:29:39 2012
From: cas243 at georgetown.edu (Clara A. Scholl)
Date: Mon, 12 Mar 2012 21:29:39 -0400
Subject: [FieldTrip] clustering, spatial neighbors and minnbchan
In-Reply-To: <4F5DB875.9080501@donders.ru.nl>
References: <CAAHOyr7pc8qkmeJ4X9NOsGQAmEUsg3viPPYo5v+4d5rE3bQ-Mw@mail.gmail.com>
	<CAAHOyr6APDwrRwfONA0xuYXNJbhYKtNrpd0QuVxcKcAXTUL5Yg@mail.gmail.com>
	<4F5DB875.9080501@donders.ru.nl>
Message-ID: <CAAHOyr5S+U6ZRtBZ77hjQx9EPe0qcq3O8tL++mAkNeZ5aj2HtQ@mail.gmail.com>

Dear Jörn,

Thank you for directing me to ft_prepare_neighbours instead of
ft_neighbourselection, the triangulation method is excellent and I'll
be sure to stick to the most recent version of fieldtrip from now on.

I really like the spirit of the minnbchan parameter for tightening
cluster extent, but as long as different channels have different
numbers of neighbors (which seems both inevitable and sensible), I
find it problematic that for example, for minnbchan=2, a channel with
5 neighbors will be rejected at a given timepoint if fewer than 40% of
its neighbors belong to a cluster, while a channel with 10 neighbors
will be rejected only when fewer than 20% of its neighbors belong to
the cluster (if I understand what's going on correctly -- and I use 5
and 10 as examples because this is the range of neighbors I get using
triangulation for an EGI 128 channel EEG sensor layout).  I have two
questions about a possible modification to this parameter that I've
implemented:

1) Instead of setting minnbchan to a fixed number of channels, would
it make sense to use a percentage of neighbors so that, for the
example above, instead of using minnbchan=2, use
minnbchan=0.4*numneighbours (at each channel), so that a channel with
5 neighbors would need 2 neighboring channels in the cluster to
remain, while a channel with 10 neighbors would need 4 neighboring
channels in the cluster to remain?  Would this introduce problems I'm
not considering?

2) I implemented it by modifying beginning at line 83 of
findcluster.m, so that instead of looking for
remove=(onoff.*nsigneighb)<minnbchan;

I'm now adding an additional line for the number of neighbors at each
channel (in addition to nsigneighb, the number of significant
neighbors), followed by remove:

nneighb=reshape(selectmat*reshape(single(ones(size(onoff))),[spatdimlength
(nfreq*ntime)]),[spatdimlength nfreq ntime]);
remove=(onoff.*nsigneighb)<(nneighb.*minnbchan);

Where now the minnbchan input must be between 0 and 1 so that the
channels removed at each timepoint are some fraction of each channels
number of neighbors.  It seems to work but I want to run it by users
who are more familiar with the parameters & code than I am, because
it's very possible that (1) the concept is esoteric and problematic
and (2) my implementation is faulty.

Thanks enormously for any & all feedback,
Clara


On Mon, Mar 12, 2012 at 4:48 AM, "Jörn M. Horschig"
<jm.horschig at donders.ru.nl> wrote:
> Dear Clara,
>
> First of all, defining neighbours based on a sensor layout may not be the
> best approach. If you have 3D positions of your sensors available, I would
> suggest that you use these for neighbour selection (note that for EEG
> sensors, this is much less an issue than for MEG sensors, but you didn't
> mention what system you are using)
>
> Second, for minnbchan, I think you are right. Of course sensors at the outer
> rim have, by definition, less neighbouring sensors than other sensors. As
> far as I know, minnbchan is defined as the number of neighbouring
> significant sensors. So, if you specify it to be e.g. 10, than of course all
> sensors with less than 10 neighbours can never be part of a cluster. Those
> with more than 10 need to have also at least 10 neighbouring sensors that
> are significant as well. Of course, sensors in the center have more
> neighbouring sensors, thus higher minnbchan will have a less tremendous
> effect there. So as far as I can see, there are four ways out for you:
>
> 1) If you didn't do so already, you can choose a finer time-scale, hoping
> that this will separate the different neural effects (if they are different)
>
> 2) Do the same on source level - maybe this will reduce spatial leakage.
>
> 3) Define a wider range of neighbours for sensors at the outer rim, thereby
> forcing a minimum number of neighbouring sensors. Instead (or additionally),
> you could try to use cfg.method = 'triangulation' or 'template' for
> neighbour selection. For more information, see here:
> http://fieldtrip.fcdonders.nl/faq/how_does_ft_prepare_neighbours_work
> I would suggest that you use cfg.feedback = 'yes' and choose the
> method/parameters that seem most optimal to you (there is not *the* best
> way, unfortunately)
>
> 4) Live with it, as there are technical limitations with our recording
> equipment, and of course physiological limitations. As Eric pointed out in
> the old mails you referred to:
> "
>
> In fact, it is looking for isolated blobs that one would like to interpret
> as separate physiological entities.
> This contrast with the nature of the EEG/MEG data, which has poor spatial
> resolution (due to volume conduction and common pick-up),
> often poor spectral resolution (due to the short time windows of our
> time-resolved spectral analysis), and often poor time resolution
> (due to latency jitter over trials).
> "
>
>
>
> Hope this helps.
> Best,
> Jörn
>
>
>
>
> On 3/11/2012 10:52 PM, Clara A. Scholl wrote:
>>
>> Hi,
>>
>> I have a question about how to identify appropriate parameters for
>> neighbor distance in ft_neighbourselection and how to set minnbchan
>> for space-time cluster analysis.
>>
>> I identified a neighbor distance based on our sensor layout, so that
>> spatially adjacent channels were defined as neighbors, and spatially
>> non-adjacent channels were not defined as neighbors.  I then ran
>> space-time cluster analysis and identified a cluster with a large
>> spatial and temporal extent which appears to be the continuation of
>> several effects lumped together.  I subsequently increased minnbchan,
>> so that this cluster gets separated into separate clusters following
>> the logic in this discussion thread:
>> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-February/003501.html
>>
>> However now a new problem appears: it seems that channels near the
>> periphery of the sensor layout, which have few adjacent spatial
>> neighbors, are not included in the clusters when minnbchan has a value
>> greater than the number of neighbors the channels have according to
>> the neighbor distance used in ft_neighbourselection.  Is this correct?
>>  Put differently, increasing minnbchan appears to bias clusters toward
>> including only channels at the center of the sensor layout, with many
>> adjacent other channels (and channels at the periphery of the layout,
>> which have fewer spatial neighbors, are excluded from the identified
>> clusters).
>>
>> Obviously I want a principled, data-independent selection of cluster
>> identification parameters so I want to ask what the "correct" way to
>> identify these parameters (neighbor distance, and minnbchan) is.
>> Should minnbchan be used differently for channel-time cluster analysis
>> (what I'm doing) compared to channel-time-frequency cluster analysis?
>>
>> Thanks,
>> Clara
>>
>> _______________________________________________
>> 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
>
> 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



From olivia.mariani at epfl.ch  Tue Mar 13 11:44:53 2012
From: olivia.mariani at epfl.ch (Mariani Olivia)
Date: Tue, 13 Mar 2012 10:44:53 +0000
Subject: [FieldTrip] Mesh intersecting BEM headmodel
Message-ID: <BD7CF73B66D0674980FC749AE22A9BFD2B83B0A0@rexma.intranet.epfl.ch>

Hello,

I am using the "create a BEM headmodel" script but I am getting spikes and unwanted holes in the brain compartment when using the triplot function and don't know how to get rid of it.

I get the following warnings on matlab (R2011a):

%%%%%%%%%%%%%%%%%%%%%
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!! WARNING !!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Mesh is self intersecting !
Mesh Info :
    # points : 1000
    # triangles : 1996
    Euler characteristic : 2
    Min Area : 14
    Max Area : 152.381
Self intersection for mesh number 2
%%%%%%%%%%%%%%%%%%%%%%

I get this self intersecting warning for my three meshes and additional warnings that two meshes are intersecting.
My problem may come from ill-defined boundaries. Would you know how to better define the boundaries between the meshes?

And then I get the following error:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
| ------ om_minverser
| ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin
| ./tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin
| -----------------------
Exception: Unable to open the file ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin for reading Doing my best....
Warning: an error ocurred while running OpenMEEG
> In openmeeg at 127
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Error using ==> fread
Invalid file identifier.  Use fopen to generate a valid file identifier.
Warning: File 'tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin' not found.
> In openmeeg>cleaner at 142
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Warning: File 'tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin' not found.
> In openmeeg>cleaner at 143
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The file om_minverser from openmeeg closes and the figures open.

Thank you,

Olivia


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From lihqih at gmail.com  Tue Mar 13 18:10:16 2012
From: lihqih at gmail.com (qi li)
Date: Tue, 13 Mar 2012 13:10:16 -0400
Subject: [FieldTrip] ICA problem
Message-ID: <CAMWMXsDEoFUpC5JhfLBZgcN7PDEJHtJvA3zgrmYH=a36uV3z=A@mail.gmail.com>

Hi there,

I am having trouble to prepare neighbors of the channels after I do
the ICA with the following commands,

cfg            = [];
cfg.method = 'runica';
cfg.runica.pca=64;
comp           = ft_componentanalysis(cfg, datas)

Then I remove the bad components by

cfg=[];
cfg.component=[2 5];
data_c=ft_rejectcomponent(cfg,comp_o);

now I want to prepare the neighbors
cfg=[];
cfg.neighbours = ft_prepare_neighbours(cfg, data_c);

I have the following error message,

'undoing the invcomp balancing
Index exceeds matrix dimensions.

Error in undobalancing (line 25)
      tra3(iy,iy) = (eye(numel(ix))+tmp(ix,ix))*tra1(iy,iy);

Error in channelposition (line 39)
sens = undobalancing(sens);

Error in ft_datatype_sens (line 95)
        [chanpos, chanori, chanlab] = channelposition(sens, 'channel', 'all');

Error in ft_datatype_raw (line 95)
      data.grad = ft_datatype_sens(data.grad);

Error in ft_checkdata (line 177)
  data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo);

Error in ft_prepare_neighbours (line 84)
if hasdata, data = ft_checkdata(data); end'.


From k.muesch at uke.uni-hamburg.de  Tue Mar 13 19:13:31 2012
From: k.muesch at uke.uni-hamburg.de (=?iso-8859-1?Q?Kathrin_M=FCsch?=)
Date: Tue, 13 Mar 2012 19:13:31 +0100
Subject: [FieldTrip] ICA problem
In-Reply-To: <CAMWMXsDEoFUpC5JhfLBZgcN7PDEJHtJvA3zgrmYH=a36uV3z=A@mail.gmail.com>
References: <CAMWMXsDEoFUpC5JhfLBZgcN7PDEJHtJvA3zgrmYH=a36uV3z=A@mail.gmail.com>
Message-ID: <A1BDA1C1-3106-44E3-A0EA-45D9A92B0524@uke.uni-hamburg.de>

Hi Qi,

This error message pops up recently with many ft_functions after ICA and is due to some updates. I don't know with which FieldTrip version it started. After ICA component rejection, the number of gradiometers seems to change and this error message pops up. As a workaround, you can either remove the grad field if you don't need it for your analysis at hand or you can load the grad structure from a processing step before the ICA.

Hope that helps,
Kathrin

Am 13.03.2012 um 18:10 schrieb qi li:

> Hi there,
> 
> I am having trouble to prepare neighbors of the channels after I do
> the ICA with the following commands,
> 
> cfg            = [];
> cfg.method = 'runica';
> cfg.runica.pca=64;
> comp           = ft_componentanalysis(cfg, datas)
> 
> Then I remove the bad components by
> 
> cfg=[];
> cfg.component=[2 5];
> data_c=ft_rejectcomponent(cfg,comp_o);
> 
> now I want to prepare the neighbors
> cfg=[];
> cfg.neighbours = ft_prepare_neighbours(cfg, data_c);
> 
> I have the following error message,
> 
> 'undoing the invcomp balancing
> Index exceeds matrix dimensions.
> 
> Error in undobalancing (line 25)
>      tra3(iy,iy) = (eye(numel(ix))+tmp(ix,ix))*tra1(iy,iy);
> 
> Error in channelposition (line 39)
> sens = undobalancing(sens);
> 
> Error in ft_datatype_sens (line 95)
>        [chanpos, chanori, chanlab] = channelposition(sens, 'channel', 'all');
> 
> Error in ft_datatype_raw (line 95)
>      data.grad = ft_datatype_sens(data.grad);
> 
> Error in ft_checkdata (line 177)
>  data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo);
> 
> Error in ft_prepare_neighbours (line 84)
> if hasdata, data = ft_checkdata(data); end'.
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg

Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus 

From chan at med.uni-frankfurt.de  Wed Mar 14 17:28:49 2012
From: chan at med.uni-frankfurt.de (Jason Chan)
Date: Wed, 14 Mar 2012 17:28:49 +0100
Subject: [FieldTrip] missing pos in beamforming
Message-ID: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>

Greetings,

I am adapting the beamformer tutorial to my data.  When I sourceinterpolate
the subtracted sourceA from sourceB data, the 'pos'  disappears.  This seems
to be important for the volume normalization and Grand Average.  I am
running Fieldtrip version: 20110917.  I have placed the code below.

 

Many thanks in advance.

Jason

 

 

Young_CombineFilter_sourceDiff_16_3={};

for i=1:length(Young_CombineFilter_beamform_16_3);

    cfg=[];

    Young_CombineFilter_sourceDiff_16_3{i}
=Young_CombineFilter_beamform_16_3{i}.sourceA;

    Young_CombineFilter_sourceDiff_16_3{i}.avg.pow
=(Young_CombineFilter_beamform_16_3{i}.sourceA.avg.pow -
Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow)./Young_CombineFilter_b
eamform_16_3{i}.sourceB.avg.pow;

    

    cfg            = [];

    cfg.downsample = 2;

    cfg.parameter  = 'avg.pow';

    cfg.anatomy    = mri{i};

    cfg.keepfilter='yes';

    cfg.interpmethod='linear';

 
Young_CombineFilter_sourceDiffInt_16_3{i}=ft_sourceinterpolate(cfg,Young_Com
bineFilter_sourceDiff_16_3{i}, mri_young{i});

end;

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From michael.wibral at web.de  Wed Mar 14 20:28:31 2012
From: michael.wibral at web.de (Michael Wibral)
Date: Wed, 14 Mar 2012 20:28:31 +0100 (CET)
Subject: [FieldTrip] missing pos in beamforming
In-Reply-To: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
References: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
Message-ID: <trinity-f95591b5-c49e-407e-9e7e-edbf090da54e-1331753310885@3capp-webde-bs48.dlan.cinetic.de>

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From nathanweisz at mac.com  Wed Mar 14 20:29:56 2012
From: nathanweisz at mac.com (Nathan Weisz)
Date: Wed, 14 Mar 2012 20:29:56 +0100
Subject: [FieldTrip] missing pos in beamforming
In-Reply-To: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
References: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
Message-ID: <5AC98AFE-D119-411D-81A9-FE44B021847D@mac.com>

Hi,

don't have any data at hand right now. but i can't recall that a pos-field should be there after ft_sourceinterpolate (you get your data in 3D corresponding to the dimensions of your MRI). did you actually try ft_volumenormalise? did you run into problems and if yes what does the error look like?

totally unrelated to your problem (if there is any problem), I do not think that cfg.keepfilter is a meaningful input to this function.

best,
n

On 14.03.2012, at 17:28, Jason Chan wrote:

> Greetings,
> I am adapting the beamformer tutorial to my data.  When I sourceinterpolate the subtracted sourceA from sourceB data, the ‘pos’  disappears.  This seems to be important for the volume normalization and Grand Average.  I am running Fieldtrip version: 20110917.  I have placed the code below.
>  
> Many thanks in advance.
> Jason
>  
>  
> Young_CombineFilter_sourceDiff_16_3={};
> for i=1:length(Young_CombineFilter_beamform_16_3);
>     cfg=[];
>     Young_CombineFilter_sourceDiff_16_3{i} =Young_CombineFilter_beamform_16_3{i}.sourceA;
>     Young_CombineFilter_sourceDiff_16_3{i}.avg.pow =(Young_CombineFilter_beamform_16_3{i}.sourceA.avg.pow - Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow)./Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow;
>    
>     cfg            = [];
>     cfg.downsample = 2;
>     cfg.parameter  = 'avg.pow';
>     cfg.anatomy    = mri{i};
>     cfg.keepfilter='yes';
>     cfg.interpmethod='linear';
>     Young_CombineFilter_sourceDiffInt_16_3{i}=ft_sourceinterpolate(cfg,Young_CombineFilter_sourceDiff_16_3{i}, mri_young{i});
> end;
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From jeremiemattout at yahoo.fr  Wed Mar 14 21:22:55 2012
From: jeremiemattout at yahoo.fr (Jeremie MATTOUT)
Date: Wed, 14 Mar 2012 20:22:55 +0000 (GMT)
Subject: [FieldTrip] Post-doctoral Position
Message-ID: <1331756575.90158.YahooMailNeo@web29504.mail.ird.yahoo.com>



Two years Post-doctoral position available
 
Lyon Neuroscience Research Center, Brain Dynamics and Cognition Team, Lyon,
France 
 
----------------------------------------------------------------------------------------------------------------------------------------

Applications are invited for a Post-doctoral position at the Brain Dynamics and
Cognition Team, in the Lyon Neuroscience Research Center, in France. The focus
of the position is on the investigation of the electrophysiological markers of attention,
vigilance and conscious perception, in healthy subjects and non-communicating
and non-responsive patients.
 
The post-doctoral fellow will be part of a three years multi-partner
project. Within the laboratory, she/he will be incorporated in a team of
researchers, engineers, post-doctoral and doctoral fellows who work on various research
and clinical applications of human electrophysiology. Techniques range from
EEG, MEG to SEEG (in collaboration with the Neurological Hospital on site).
In interaction with the team members, the post-doctoral fellow will be in
charge of designing and performing new experiments to test hypothesis about the
functional role of electrophysiological markers.
 
The candidates should have a PhD in Neuroimaging, Human electrophysiology,
Cognitive neuroscience, Biomedical Engineering or a related area. Experience
with high density EEG or MEG in humans is highly desirable (acquisition,
processing, statistics) as well as programming skills (Matlab).  Application from candidates with previous
experience or special interest in related fields such as research in attention,
coma or vegetative state patients, real-time electrophysiology and
brain-computer interfaces are welcome.
 
The Lyon Neuroscience Research Center integrates the multidisciplinary
expertise of 14 teams (about 350 researchers), including university-researchers,
clinician-researchers, technicians and engineers, doctoral and post-doctoral
fellows, making possible a synergistic approach on integrative and cognitive
neurophysiology and its related brain disorders. The neural and molecular
substrates of brain functions, from sensory and motor processes to cognition
and mind, are investigated along two entwined strategic directions: from gene
to behavior, and from bench to patient. Our aim is to bridge the gaps between
the different levels of investigation, and to reinforce a translational
research with reciprocal exchanges between basic conceptual advances and
clinical challenges. The Neuroimaging facilities include an EEG, MEG, TMS, MR and
PET scans as well as access to SEEG recordings in epileptic patients.

Please address questions or send CV, letter of application with research
interests, and two references to Jérémie Mattout (jeremie.mattout at inserm.fr). Applications will be considered until position is
filled. Starting date is negotiable.
 
Jérémie Mattout,
PhD   and   Dominique Morlet, PhD
Lyon Neuroscience
Research Center
Brain Dynamics and
Cognition Team
CHS
Le Vinatier
95
Boulevard Pinel
69500
Bron
France
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From c.micheli at fcdonders.ru.nl  Wed Mar 14 21:48:42 2012
From: c.micheli at fcdonders.ru.nl (Micheli, C.)
Date: Wed, 14 Mar 2012 21:48:42 +0100 (CET)
Subject: [FieldTrip] Mesh intersecting BEM headmodel
In-Reply-To: <BD7CF73B66D0674980FC749AE22A9BFD2B83B0A0@rexma.intranet.epfl.ch>
Message-ID: <767172752.17756.1331758122289.JavaMail.root@draco.zimbra.ru.nl>

Dear Olivia, The documentation you are referring to is not up-to-date and I would not recommend to rely on it. Notwithstanding the old documentation, the problem that you encounter is a known issue with the automatic generation of triangulated surfaces. In fact, the surfaces created from any volumetric data (anatomical MRI or segmentations) should be topologically correct for the BEM to work correctly and at the moment FieldTrip does not check for this (we are working currently on this topic). If you plan to use a head model with 3 compartments I would recommend to start with the function ft_prepare_headmodel, and work with concentric spheres.You can call it like this: cfg=[]; cfg.method = 'concentricspheres'; bnd = ft_prepare_headmodel(cfg,seg) The variable seg is the output of ft_volume_segment containing the skin, skull, brain compartments as and you can refer to the standard documentation for this function: http://fieldtrip.fcdonders.nl/tutorial/headmodel This should automatically solve in most of the cases the problem of intersecting or self-intersecting surfaces. If you want to use the openmeeg toolbox with realistic head models the analysis is complicated by the non-correctness of the surfaces topologies, due probably to the outcome of the segmentation and the successive triangulation step (which happens within the ft_prepare_bemmodel function, now obsolete). The generation of the meshes might work straight away also with the realistic segmented compartments, but it would be difficult to visually check for surface correctness (for example by using the ft_plot_mesh function). When you have the three surfaces you can eventually attach them to your next mail, so that I can verify things with the prototype surface management functions, that we are developing/integrating (see http://code.google.com/p/fieldtrip/source). Let me know if this helps Cristiano ----- Oorspronkelijk bericht -----
> Van: "Mariani Olivia" <olivia.mariani at epfl.ch>
> Aan: fieldtrip at donders.ru.nl
> Verzonden: Dinsdag 13 maart 2012 11:44:53
> Onderwerp: [FieldTrip] Mesh intersecting BEM headmodel
> Hello,
> I am using the "create a BEM headmodel" script but I am getting spikes
> and unwanted holes in the brain compartment when using the triplot
> function and don't know how to get rid of it.
> I get the following warnings on matlab (R2011a):
> %%%%%%%%%%%%%%%%%%%%%
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!! WARNING !!!!!!!!!!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> Mesh is self intersecting !
> Mesh Info :
> # points : 1000
> # triangles : 1996
> Euler characteristic : 2
> Min Area : 14
> Max Area : 152.381
> Self intersection for mesh number 2
> %%%%%%%%%%%%%%%%%%%%%%
> I get this self intersecting warning for my three meshes and
> additional warnings that two meshes are intersecting.
> My problem may come from ill-defined boundaries. Would you know how to
> better define the boundaries between the meshes?
> And then I get the following error:
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> | ------ om_minverser
> | ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin
> | ./tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin
> | -----------------------
> Exception: Unable to open the file
> ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin for reading Doing my
> best....
> Warning: an error ocurred while running OpenMEEG
> > In openmeeg at 127
> In ft_prepare_bemmodel at 232
> In projet_mineur at 106
> Error using ==> fread
> Invalid file identifier. Use fopen to generate a valid file
> identifier.
> Warning: File 'tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin' not found.
> > In openmeeg>cleaner at 142
> In openmeeg at 129
> In ft_prepare_bemmodel at 232
> In projet_mineur at 106
> Warning: File 'tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin' not found.
> > In openmeeg>cleaner at 143
> In openmeeg at 129
> In ft_prepare_bemmodel at 232
> In projet_mineur at 106
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> The file om_minverser from openmeeg closes and the figures open.
> Thank you,
> Olivia
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From olivia.mariani at epfl.ch  Fri Mar 16 09:13:29 2012
From: olivia.mariani at epfl.ch (Mariani Olivia)
Date: Fri, 16 Mar 2012 08:13:29 +0000
Subject: [FieldTrip] RE :  Mesh intersecting BEM headmodel
In-Reply-To: <767172752.17756.1331758122289.JavaMail.root@draco.zimbra.ru.nl>
References: <BD7CF73B66D0674980FC749AE22A9BFD2B83B0A0@rexma.intranet.epfl.ch>,
	<767172752.17756.1331758122289.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <BD7CF73B66D0674980FC749AE22A9BFD2B83B1C3@rexma.intranet.epfl.ch>

Hello Cristiano,

yes it was useful thank you very much, I will use for now the concentric sphere model and will try with the ft_plot_mesh.

I forgot to mention that I am actually using the avg152T1 head model. Does an other method exist to extract the skin from an average? I was thinking of defining the skin and skull as outer and inner skull. Do you think it might solve the triangulation problem?

Thank you very much,

Olivia
________________________________
De : fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] de la part de Micheli, C. [c.micheli at fcdonders.ru.nl]
Date d'envoi : mercredi 14 mars 2012 21:48
À : Email discussion list for the FieldTrip project
Objet : Re: [FieldTrip] Mesh intersecting BEM headmodel

Dear Olivia,
The documentation you are referring to is not up-to-date and I would not recommend to rely on it.
Notwithstanding the old documentation, the problem that you encounter is a known issue with the automatic generation of triangulated surfaces. In fact, the surfaces created from any volumetric data (anatomical MRI or segmentations) should be topologically correct for the BEM to work correctly and at the moment FieldTrip does not check for this (we are working currently on this topic).
If you plan to use a head model with 3 compartments I would recommend to start with the function ft_prepare_headmodel, and work with concentric spheres.You can call it like this:

cfg=[];
cfg.method = 'concentricspheres';
bnd = ft_prepare_headmodel(cfg,seg)

The variable seg is the output of ft_volume_segment containing the skin, skull, brain compartments as
and you can refer to the standard documentation for this function:

http://fieldtrip.fcdonders.nl/tutorial/headmodel

This should automatically solve in most of the cases the problem of intersecting or self-intersecting surfaces.
If you want to use the openmeeg toolbox with realistic head models the analysis is complicated by the non-correctness of the surfaces topologies, due probably to the outcome of the segmentation and the successive triangulation step (which happens within the ft_prepare_bemmodel function, now obsolete).
The generation of the meshes might work straight away also with the realistic segmented compartments, but it would be difficult to visually check for surface correctness (for example by using the ft_plot_mesh function).
When you have the three surfaces you can eventually attach them to your next mail, so that I can verify things with the prototype surface management functions, that we are developing/integrating (see http://code.google.com/p/fieldtrip/source).

Let me know if this helps
Cristiano


________________________________
Van: "Mariani Olivia" <olivia.mariani at epfl.ch>
Aan: fieldtrip at donders.ru.nl
Verzonden: Dinsdag 13 maart 2012 11:44:53
Onderwerp: [FieldTrip] Mesh intersecting BEM headmodel

Hello,

I am using the "create a BEM headmodel" script but I am getting spikes and unwanted holes in the brain compartment when using the triplot function and don't know how to get rid of it.

I get the following warnings on matlab (R2011a):

%%%%%%%%%%%%%%%%%%%%%
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!! WARNING !!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Mesh is self intersecting !
Mesh Info :
    # points : 1000
    # triangles : 1996
    Euler characteristic : 2
    Min Area : 14
    Max Area : 152.381
Self intersection for mesh number 2
%%%%%%%%%%%%%%%%%%%%%%

I get this self intersecting warning for my three meshes and additional warnings that two meshes are intersecting.
My problem may come from ill-defined boundaries. Would you know how to better define the boundaries between the meshes?

And then I get the following error:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
| ------ om_minverser
| ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin
| ./tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin
| -----------------------
Exception: Unable to open the file ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin for reading Doing my best....
Warning: an error ocurred while running OpenMEEG
> In openmeeg at 127
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Error using ==> fread
Invalid file identifier.  Use fopen to generate a valid file identifier.
Warning: File 'tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin' not found.
> In openmeeg>cleaner at 142
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Warning: File 'tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin' not found.
> In openmeeg>cleaner at 143
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The file om_minverser from openmeeg closes and the figures open.

Thank you,

Olivia



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

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From ivano_triggiani at yahoo.it  Fri Mar 16 09:42:10 2012
From: ivano_triggiani at yahoo.it (Ivano Triggiani)
Date: Fri, 16 Mar 2012 08:42:10 +0000 (GMT)
Subject: [FieldTrip] channel type (EEG, EMG,etc.) and when to filter data
Message-ID: <1331887330.12945.YahooMailNeo@web132104.mail.ird.yahoo.com>

Hi everybody,


I'm back to use fieldtrip after a long period, and now everything seems to work (I used .edf file and I had problem with trigger).

Now I have some questions, if someone would be so kind to help me:

1. I'd like to label my channel to select among EEG type, EMG type etc. because my acquire system labeled them all as EEG. When is it specified in cfg ? I can't find it! And if I can't, how can I exclude EMG,TRIGGER and EOG channels from ICA computation? 


2. I have a lot of channel, but ICA gave me back just 33 of them. How can I proceed to obtain a correct ICA from my 56 channels?

3. is it wrong if I filter my data before ICA?


4. If I use ICA probably I can't use other source separation method (like BSS) to analyze my data, am I wrong?


Sorry
 if I post so much questions, but I'm back with fieldtrip and I want to improve my techniques.

Ivano 
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From nathanweisz at mac.com  Fri Mar 16 09:53:20 2012
From: nathanweisz at mac.com (Nathan Weisz)
Date: Fri, 16 Mar 2012 09:53:20 +0100
Subject: [FieldTrip] channel type (EEG, EMG,
	etc.) and when to filter data
In-Reply-To: <1331887330.12945.YahooMailNeo@web132104.mail.ird.yahoo.com>
References: <1331887330.12945.YahooMailNeo@web132104.mail.ird.yahoo.com>
Message-ID: <83DC888D-74CA-467E-90BE-8615B181E8AB@mac.com>

hi,

> I'm back to use fieldtrip after a long period, and now everything seems to work (I used .edf file and I had problem with trigger).

congratulations.

> 1. I'd like to label my channel to select among EEG type, EMG type etc. because my acquire system labeled them all as EEG. When is it specified in cfg ? I can't find it! And if I can't, how can I exclude EMG,TRIGGER and EOG channels from ICA computation? 

you must have had a consitent way of plugging in the channels into your amplifier, haven't you? if yes, then you should find out which channel corresponds to which row in your EEG data and you can relabel them within Matlab.

Your EMG, TRIGGER and EOG channels should also be easy to detect when looking at your data. but you should get back to your recording configurations (also data acquisition software) if you are interested in the positions / labels of the other EEG electrodes. You may want to keep your EOG channels if they have a common reference like the EEG channels.

> 2. I have a lot of channel, but ICA gave me back just 33 of them. How can I proceed to obtain a correct ICA from my 56 channels?

you mean components? 

> 3. is it wrong if I filter my data before ICA?

no.

> 4. If I use ICA probably I can't use other source separation method (like BSS) to analyze my data, am I wrong?

dunno.

good luck,
n

> 
> Sorry if I post so much questions, but I'm back with fieldtrip and I want to improve my techniques.
> 
> Ivano 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From olivia.mariani at epfl.ch  Fri Mar 16 11:16:39 2012
From: olivia.mariani at epfl.ch (Mariani Olivia)
Date: Fri, 16 Mar 2012 10:16:39 +0000
Subject: [FieldTrip] Concentricspheres method
Message-ID: <BD7CF73B66D0674980FC749AE22A9BFD2B83B1EF@rexma.intranet.epfl.ch>

Hello Cristiano,

I am using the concentricsphere but get the following errors:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

??? Error using ==> ft_prepare_headmodel at 233
no input available

Error in ==> Olivia at 29
vol = ft_prepare_headmodel(cfg, seg);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

My code is as follows:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%adds the path toward fieldtrip
addpath_projet;

%récupère les données du fichier mri
mri = ft_read_mri('avg152T1.nii');

%segmentation du volume
cfg = [];
cfg.coordinates = 'spm';

seg = ft_volumesegment(cfg, mri);

seg.anatomy = mri.anatomy;

cfg                = [];
cfg.tissue         = [1 2 3]; % value of each tissue type in the segmentation
cfg.numvertices    = [1000 2000 3000];
cfg.conductivity   = [1 1/80 1];
cfg.isolatedsource = true;
cfg.method         = 'concentricspheres';
cfg.smooth = 'no';

cfg.sourceunits = 'mm';
cfg.mriunits = 'mm';

vol = ft_prepare_headmodel(cfg, seg);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

It seems that I never have the good conditions to put some values in "geometry" but I can't find what I am missing.

Thank you very much,

Olivia
________________________________
De : fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] de la part de Micheli, C. [c.micheli at fcdonders.ru.nl]
Date d'envoi : mercredi 14 mars 2012 21:48
À : Email discussion list for the FieldTrip project
Objet : Re: [FieldTrip] Mesh intersecting BEM headmodel

Dear Olivia,
The documentation you are referring to is not up-to-date and I would not recommend to rely on it.
Notwithstanding the old documentation, the problem that you encounter is a known issue with the automatic generation of triangulated surfaces. In fact, the surfaces created from any volumetric data (anatomical MRI or segmentations) should be topologically correct for the BEM to work correctly and at the moment FieldTrip does not check for this (we are working currently on this topic).
If you plan to use a head model with 3 compartments I would recommend to start with the function ft_prepare_headmodel, and work with concentric spheres.You can call it like this:

cfg=[];
cfg.method = 'concentricspheres';
bnd = ft_prepare_headmodel(cfg,seg)

The variable seg is the output of ft_volume_segment containing the skin, skull, brain compartments as
and you can refer to the standard documentation for this function:

http://fieldtrip.fcdonders.nl/tutorial/headmodel

This should automatically solve in most of the cases the problem of intersecting or self-intersecting surfaces.
If you want to use the openmeeg toolbox with realistic head models the analysis is complicated by the non-correctness of the surfaces topologies, due probably to the outcome of the segmentation and the successive triangulation step (which happens within the ft_prepare_bemmodel function, now obsolete).
The generation of the meshes might work straight away also with the realistic segmented compartments, but it would be difficult to visually check for surface correctness (for example by using the ft_plot_mesh function).
When you have the three surfaces you can eventually attach them to your next mail, so that I can verify things with the prototype surface management functions, that we are developing/integrating (see http://code.google.com/p/fieldtrip/source).

Let me know if this helps
Cristiano


________________________________
Van: "Mariani Olivia" <olivia.mariani at epfl.ch>
Aan: fieldtrip at donders.ru.nl
Verzonden: Dinsdag 13 maart 2012 11:44:53
Onderwerp: [FieldTrip] Mesh intersecting BEM headmodel

Hello,

I am using the "create a BEM headmodel" script but I am getting spikes and unwanted holes in the brain compartment when using the triplot function and don't know how to get rid of it.

I get the following warnings on matlab (R2011a):

%%%%%%%%%%%%%%%%%%%%%
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!! WARNING !!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Mesh is self intersecting !
Mesh Info :
    # points : 1000
    # triangles : 1996
    Euler characteristic : 2
    Min Area : 14
    Max Area : 152.381
Self intersection for mesh number 2
%%%%%%%%%%%%%%%%%%%%%%

I get this self intersecting warning for my three meshes and additional warnings that two meshes are intersecting.
My problem may come from ill-defined boundaries. Would you know how to better define the boundaries between the meshes?

And then I get the following error:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
| ------ om_minverser
| ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin
| ./tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin
| -----------------------
Exception: Unable to open the file ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin for reading Doing my best....
Warning: an error ocurred while running OpenMEEG
> In openmeeg at 127
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Error using ==> fread
Invalid file identifier.  Use fopen to generate a valid file identifier.
Warning: File 'tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin' not found.
> In openmeeg>cleaner at 142
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Warning: File 'tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin' not found.
> In openmeeg>cleaner at 143
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The file om_minverser from openmeeg closes and the figures open.

Thank you,

Olivia



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

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From michael.wibral at web.de  Fri Mar 16 14:32:21 2012
From: michael.wibral at web.de (Michael Wibral)
Date: Fri, 16 Mar 2012 14:32:21 +0100 (CET)
Subject: [FieldTrip] Workshop on Non-linear and model-free Interdependence
 Measures in Neuroscience and TRENTOOL course
Message-ID: <trinity-c81db96e-2921-4177-8653-0919d68bd344-1331904741681@3capp-webde-bs47.dlan.cinetic.de>

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From chan at med.uni-frankfurt.de  Fri Mar 16 15:17:09 2012
From: chan at med.uni-frankfurt.de (Jason Chan)
Date: Fri, 16 Mar 2012 15:17:09 +0100
Subject: [FieldTrip] missing pos in beamforming
In-Reply-To: <trinity-f95591b5-c49e-407e-9e7e-edbf090da54e-1331753310885@3capp-webde-bs48.dlan.cinetic.de>
References: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
	<trinity-f95591b5-c49e-407e-9e7e-edbf090da54e-1331753310885@3capp-webde-bs48.dlan.cinetic.de>
Message-ID: <002601cd037f$793ca580$6bb5f080$@med.uni-frankfurt.de>

Hi Michael,

 

Many thanks for your informative reply.  I was able to use the reverse normalization technique and eliminated the ft_sourceinterpolate and ft_volumenormalise commands.

However, after I subtract ‘sourceA’ from ‘sourceB’ I now get the error “different grid locations in source reconstructions” when I try to do a ft_sourcegrandaverage.  Any suggestions would be very welcome.

 

Thanks in advance.

Jason

 

From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Michael Wibral
Sent: Mittwoch, 14. März 2012 20:29
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] missing pos in beamforming

 

Dear Jason,

the pos indicates where the original sources were (i.e. on a regular grid with a certain spacing or self-defined). After interpolation this information does not reflect the data anymore. I would suggest to use Ingrid nieuwenhuis famous reverse normalization technique to create individual subject grids taht all match in MNI space - the script is found on the ft website. Sourceinterpoltae should really only be used for plotting IMHO.

Michael

Gesendet: Mittwoch, 14. März 2012 um 17:28 Uhr
Von: "Jason Chan" <chan at med.uni-frankfurt.de>
An: fieldtrip at donders.ru.nl
Betreff: [FieldTrip] missing pos in beamforming 

Greetings,

I am adapting the beamformer tutorial to my data.  When I sourceinterpolate the subtracted sourceA from sourceB data, the ‘pos’  disappears.  This seems to be important for the volume normalization and Grand Average.  I am running Fieldtrip version: 20110917.  I have placed the code below.

 

Many thanks in advance.

Jason

 

 

Young_CombineFilter_sourceDiff_16_3={};

for i=1:length(Young_CombineFilter_beamform_16_3);

    cfg=[];

    Young_CombineFilter_sourceDiff_16_3{i} =Young_CombineFilter_beamform_16_3{i}.sourceA;

    Young_CombineFilter_sourceDiff_16_3{i}.avg.pow =(Young_CombineFilter_beamform_16_3{i}.sourceA.avg.pow - Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow)./Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow;

    

    cfg            = [];

    cfg.downsample = 2;

    cfg.parameter  = 'avg.pow';

    cfg.anatomy    = mri{i};

    cfg.keepfilter='yes';

    cfg.interpmethod='linear';

    Young_CombineFilter_sourceDiffInt_16_3{i}=ft_sourceinterpolate(cfg,Young_CombineFilter_sourceDiff_16_3{i}, mri_young{i});

end;

 

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From michael.wibral at web.de  Fri Mar 16 16:21:46 2012
From: michael.wibral at web.de (Michael Wibral)
Date: Fri, 16 Mar 2012 16:21:46 +0100 (CET)
Subject: [FieldTrip] missing pos in beamforming
In-Reply-To: <002601cd037f$793ca580$6bb5f080$@med.uni-frankfurt.de>
References: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
	<trinity-f95591b5-c49e-407e-9e7e-edbf090da54e-1331753310885@3capp-webde-bs48.dlan.cinetic.de>,
	<002601cd037f$793ca580$6bb5f080$@med.uni-frankfurt.de>
Message-ID: <trinity-d7e7ebe6-1de2-434c-a5e2-1f12f9f5681b-1331911306816@3capp-webde-bs47.dlan.cinetic.de>

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From mark.noordenbos at gmail.com  Fri Mar 16 18:05:39 2012
From: mark.noordenbos at gmail.com (Mark Noordenbos)
Date: Fri, 16 Mar 2012 18:05:39 +0100
Subject: [FieldTrip] Combine Grand Average
Message-ID: <CAJSb8nPaJcyFsKU7+nMzPd9r9trs70t=iRWvCgGSxw-k_QFZ0Q@mail.gmail.com>

Hi,

I'm looking for a function that combines two timelocked Grand Averages
(keeping the 'subj_chan_time' dimord).
I have for several conditions seperate Grand Averages, but now I need to
combine some of them into a new Grand Average while keeping the individual
data.

Does Fieldtrip has a buit-in function to do this?

When just calculating the mean, one dimension ('subj' or 'chan' or 'time')
is always lost.

Thanks,
Mark


-- 
Mark Noordenbos, MSc

Radboud University Nijmegen
Behavioural Science Institute

P.O. Box 9104, Room A05.36
6500 HE Nijmegen
The Netherlands

Email: m.noordenbos at bsi.ru.nl
Telephone: +31 24 3612070
Fax:          +31 24 3616211

http://www.ru.nl
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From michael.wibral at web.de  Fri Mar 16 21:51:42 2012
From: michael.wibral at web.de (Michael Wibral)
Date: Fri, 16 Mar 2012 21:51:42 +0100 (CET)
Subject: [FieldTrip] Post-doctoral position available at the Group of
 Michael Wibral, Brain Imaging Center, Frankurt Germany
Message-ID: <trinity-d1f8194a-a8c2-4ba5-b861-c808251892a8-1331931102882@3capp-webde-bs47.dlan.cinetic.de>

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From batrod at gmail.com  Fri Mar 16 18:49:09 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Fri, 16 Mar 2012 12:49:09 -0500
Subject: [FieldTrip] channel type (EEG, EMG,
	etc.) and when to filter data
In-Reply-To: <83DC888D-74CA-467E-90BE-8615B181E8AB@mac.com>
References: <1331887330.12945.YahooMailNeo@web132104.mail.ird.yahoo.com>
	<83DC888D-74CA-467E-90BE-8615B181E8AB@mac.com>
Message-ID: <CAPy7a9B2nCTYXDvr4o86wtxN1na1yAUnystjaMDRTXeWYaxQhA@mail.gmail.com>

Let me add my 2 cents :

I'm back to use fieldtrip after a long period, and now everything seems to
> work (I used .edf file and I had problem with trigger).
>
>
> congratulations.
>

Rodolphe: Congratulations too

>
> 1. I'd like to label my channel to select among EEG type, EMG type etc.
> because my acquire system labeled them all as EEG. When is it specified in
> cfg ? I can't find it! And if I can't, how can I exclude EMG,TRIGGER and
> EOG channels from ICA computation?
>
>
> you must have had a consitent way of plugging in the channels into your
> amplifier, haven't you? if yes, then you should find out which channel
> corresponds to which row in your EEG data and you can relabel them within
> Matlab.
>
> Your EMG, TRIGGER and EOG channels should also be easy to detect when
> looking at your data. but you should get back to your recording
> configurations (also data acquisition software) if you are interested in
> the positions / labels of the other EEG electrodes. You may want to keep
> your EOG channels if they have a common reference like the EEG channels.
>

Rodolphe: Same answer

>
> 2. I have a lot of channel, but ICA gave me back just 33 of them. How can
> I proceed to obtain a correct ICA from my 56 channels?
>
>
> you mean components?
>

Rodolphe: Did you use a PCA to reduce your components first?

>
> 3. is it wrong if I filter my data before ICA?
>
>
> no.
>

Rodolphe: I would tend to say yes. ICA needs a maximum of information to
separate the components,
See for example Snyder and Foxe (2010) where they used ICA to get
components with a dominant of alpha oscillations. They argued that
filtering before is making ICA analysis worse

>
> 4. If I use ICA probably I can't use other source separation method (like
> BSS) to analyze my data, am I wrong?
>
>
> dunno.
>
Rodolphe : as ICA is a BSS, what other method did you have in mind?

>
> good luck,
> n
>
>
> Rodolphe Nenert, PhD.
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From fredericroux at hotmail.de  Sun Mar 18 15:51:21 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Sun, 18 Mar 2012 15:51:21 +0100
Subject: [FieldTrip] indepsamplesF with sourcestatistics
Message-ID: <DUB113-W53D91DAF011D28E811FBE7B75D0@phx.gbl>


Dear all,

I noticed that the result of sourcestatistics can be quite different when using cfg.statistic = 'indepsamplesF'
or also cfg.statistic ='indepsamplesregrT', depending on whether you specify a unit of observations (UO's)
variable in the design matrix or not.

For example when running the code without the UOs-variable as following

cfg.design(1,:) = [ones(1,length(indx1)) 2*ones(1,length(indx1)) 3*ones(1,length(indx1)) 4*ones(1,length(indx1))];
cfg.ivar = 1;

I get a different result than if I run:

cfg.design(1,:) = [ones(1,length(indx1)) 2*ones(1,length(indx2)) 3*ones(1,length(indx3)) 4*ones(1,length(indx4))];
cfg.design(2,:) = [indx1' indx2' indx3' indx4'];
cfg.ivar = 1;

cfg.uvar = 2;

Note that in the second case the indexes in the UOs variable are not sorted.

I guess that you are not supposed to run the code as in the second case,
but I would still like to know why I get different results. Shouldn't it be the same anyways?

It would be great to get an explanation for the discrepancy between both codes.

Best,
Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From eelke.spaak at donders.ru.nl  Mon Mar 19 11:37:47 2012
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Mon, 19 Mar 2012 11:37:47 +0100
Subject: [FieldTrip] Combine Grand Average
In-Reply-To: <CAJSb8nPaJcyFsKU7+nMzPd9r9trs70t=iRWvCgGSxw-k_QFZ0Q@mail.gmail.com>
References: <CAJSb8nPaJcyFsKU7+nMzPd9r9trs70t=iRWvCgGSxw-k_QFZ0Q@mail.gmail.com>
Message-ID: <CABPNLUoTApRzDeyZGvWFfwJjxQcE_QgTwf+pRJcy-jjh+_E7iA@mail.gmail.com>

Hi Mark,

I am not entirely sure, but I think ft_appendtimelock might be what
you are looking for. If not, you could probably also just append the
timelocked information 'by hand':

tl_combined = tl1;
tl_combined.individual = [tl1.individual; tl2.individual];

But be aware that this could get messy, and you then need to make sure
the .avg and other fields are still consistent. So, if at all
possible, stick to ft_appendtimelock :)

Best,
Eelke

On 16 March 2012 18:05, Mark Noordenbos <mark.noordenbos at gmail.com> wrote:
> Hi,
>
> I'm looking for a function that combines two timelocked Grand Averages
> (keeping the 'subj_chan_time' dimord).
> I have for several conditions seperate Grand Averages, but now I need to
> combine some of them into a new Grand Average while keeping the individual
> data.
>
> Does Fieldtrip has a buit-in function to do this?
>
> When just calculating the mean, one dimension ('subj' or 'chan' or 'time')
> is always lost.
>
> Thanks,
> Mark
>
>
> --
> Mark Noordenbos, MSc
>
> Radboud University Nijmegen
> Behavioural Science Institute
>
> P.O. Box 9104, Room A05.36
> 6500 HE Nijmegen
> The Netherlands
>
> Email: m.noordenbos at bsi.ru.nl
> Telephone: +31 24 3612070
> Fax:          +31 24 3616211
>
> http://www.ru.nl
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From politzerahless at gmail.com  Mon Mar 19 12:08:49 2012
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Mon, 19 Mar 2012 06:08:49 -0500
Subject: [FieldTrip] Combine Grand Average
Message-ID: <CAJT2k_80VhT3oBTNCLipJz5J9PDg2y-DjuRecYWdP9ZaP1ZThQ@mail.gmail.com>

Hi Mark,

Do you mean to combine multiple conditions into a single condition? For
that I'm not sure of a built-in function that can do this using grand
averages; you might need to re-do ft_timelockanalysis for the new condition
and then make new grand averages. Since it's possible that a given subject
has more trials contributing to her average for condition A than for
condition B, simply averaging the two condition averages together might not
be accurate.

Best,
Steve Politzer-Ahles

Message: 2
> Date: Mon, 19 Mar 2012 11:37:47 +0100
> From: Eelke Spaak <eelke.spaak at donders.ru.nl>
> To: Email discussion list for the FieldTrip project
>        <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] Combine Grand Average
> Message-ID:
>        <CABPNLUoTApRzDeyZGvWFfwJjxQcE_QgTwf+pRJcy-jjh+_E7iA at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Mark,
>
> I am not entirely sure, but I think ft_appendtimelock might be what
> you are looking for. If not, you could probably also just append the
> timelocked information 'by hand':
>
> tl_combined = tl1;
> tl_combined.individual = [tl1.individual; tl2.individual];
>
> But be aware that this could get messy, and you then need to make sure
> the .avg and other fields are still consistent. So, if at all
> possible, stick to ft_appendtimelock :)
>
> Best,
> Eelke
>
> On 16 March 2012 18:05, Mark Noordenbos <mark.noordenbos at gmail.com> wrote:
> > Hi,
> >
> > I'm looking for a function that combines two timelocked Grand Averages
> > (keeping the 'subj_chan_time' dimord).
> > I have for several conditions seperate Grand Averages, but now I need to
> > combine some of them into a new Grand Average while keeping the
> individual
> > data.
> >
> > Does Fieldtrip has a buit-in function to do this?
> >
> > When just calculating the mean, one dimension ('subj' or 'chan' or
> 'time')
> > is always lost.
> >
> > Thanks,
> > Mark
> >
> >
> > --
> > Mark Noordenbos, MSc
> >
> > Radboud University Nijmegen
> > Behavioural Science Institute
> >
> > P.O. Box 9104, Room A05.36
> > 6500 HE Nijmegen
> > The Netherlands
> >
> > Email: m.noordenbos at bsi.ru.nl
> > Telephone: +31 24 3612070
> > Fax:? ? ? ? ? +31 24 3616211
> >
> > http://www.ru.nl
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
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From jm.horschig at donders.ru.nl  Mon Mar 19 13:35:17 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 19 Mar 2012 13:35:17 +0100
Subject: [FieldTrip] Combine Grand Average
In-Reply-To: <CAJT2k_80VhT3oBTNCLipJz5J9PDg2y-DjuRecYWdP9ZaP1ZThQ@mail.gmail.com>
References: <CAJT2k_80VhT3oBTNCLipJz5J9PDg2y-DjuRecYWdP9ZaP1ZThQ@mail.gmail.com>
Message-ID: <4F672805.5060404@donders.ru.nl>

Hi Mark,

I agree with Steve. Though, in order to not re-compute the averages, you 
could create the weighted average yourself. Just make a weight vector 
like this:

/weights = no_trials_cond_A / (no_trials_cond_A+no_trials_cond_B);/

Where /no_trials_cond_A /and /*_b/ contai  the number of trials in 
condition A and B, respectively.
Then you can take the weighted sum of the two grand-averages you have, 
something like:

/    grandavg.individual = condA.individual * weights + condB.individual 
* (1-weights);/

This is mathematically equivalent to re-computing the average on all 
trials (note that I am not sure whether this holds for spectral denisity 
matrices and stuff like that, but for ERPs and plain powerspectra, does).

Best,
Jörn

On 3/19/2012 12:08 PM, Stephen Politzer-Ahles wrote:
> Hi Mark,
>
> Do you mean to combine multiple conditions into a single condition? 
> For that I'm not sure of a built-in function that can do this using 
> grand averages; you might need to re-do ft_timelockanalysis for the 
> new condition and then make new grand averages. Since it's possible 
> that a given subject has more trials contributing to her average for 
> condition A than for condition B, simply averaging the two condition 
> averages together might not be accurate.
>
> Best,
> Steve Politzer-Ahles
>
>     Message: 2
>     Date: Mon, 19 Mar 2012 11:37:47 +0100
>     From: Eelke Spaak <eelke.spaak at donders.ru.nl
>     <mailto:eelke.spaak at donders.ru.nl>>
>     To: Email discussion list for the FieldTrip project
>     <fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>>
>     Subject: Re: [FieldTrip] Combine Grand Average
>     Message-ID:
>     <CABPNLUoTApRzDeyZGvWFfwJjxQcE_QgTwf+pRJcy-jjh+_E7iA at mail.gmail.com <mailto:CABPNLUoTApRzDeyZGvWFfwJjxQcE_QgTwf%2BpRJcy-jjh%2B_E7iA at mail.gmail.com>>
>     Content-Type: text/plain; charset=ISO-8859-1
>
>     Hi Mark,
>
>     I am not entirely sure, but I think ft_appendtimelock might be what
>     you are looking for. If not, you could probably also just append the
>     timelocked information 'by hand':
>
>     tl_combined = tl1;
>     tl_combined.individual = [tl1.individual; tl2.individual];
>
>     But be aware that this could get messy, and you then need to make sure
>     the .avg and other fields are still consistent. So, if at all
>     possible, stick to ft_appendtimelock :)
>
>     Best,
>     Eelke
>
>     On 16 March 2012 18:05, Mark Noordenbos <mark.noordenbos at gmail.com
>     <mailto:mark.noordenbos at gmail.com>> wrote:
>     > Hi,
>     >
>     > I'm looking for a function that combines two timelocked Grand
>     Averages
>     > (keeping the 'subj_chan_time' dimord).
>     > I have for several conditions seperate Grand Averages, but now I
>     need to
>     > combine some of them into a new Grand Average while keeping the
>     individual
>     > data.
>     >
>     > Does Fieldtrip has a buit-in function to do this?
>     >
>     > When just calculating the mean, one dimension ('subj' or 'chan'
>     or 'time')
>     > is always lost.
>     >
>     > Thanks,
>     > Mark
>     >
>     >
>     > --
>     > Mark Noordenbos, MSc
>     >
>     > Radboud University Nijmegen
>     > Behavioural Science Institute
>     >
>     > P.O. Box 9104, Room A05.36
>     > 6500 HE Nijmegen
>     > The Netherlands
>     >
>     > Email: m.noordenbos at bsi.ru.nl <mailto:m.noordenbos at bsi.ru.nl>
>     > Telephone: +31 24 3612070 <tel:%2B31%2024%203612070>
>     > Fax:? ? ? ? ? +31 24 3616211 <tel:%2B31%2024%203616211>
>     >
>     > http://www.ru.nl
>     >
>     >
>     > _______________________________________________
>     > 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

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 giulia.rizza at tiscali.it  Mon Mar 19 16:25:20 2012
From: giulia.rizza at tiscali.it (Giulia Rizza)
Date: Mon, 19 Mar 2012 16:25:20 +0100 (GMT+01:00)
Subject: [FieldTrip] Neuroscan .cnt files
Message-ID: <7171049.98631332170720589.JavaMail.defaultUser@defaultHost>

Dear Fieldtrippers,
hi to everyone and thanks in advance for your time.
I'm not 
an expert and I'd like to share with you a problem I found in reading cnt files 
acquired with Neuroscan.

I read the data with ft_read_data function and I find 
the attached link Plot1, for instance the first channel. It seems that the 
signal is forced to pass per zero every two samples, so I tried to read them  
excluding the even samples and I find the result in Plot2, while excluding the 
odd values I find the result in Plot3.

http://dl.dropbox.com/u/28258961/Plot01.
rar

Unfortunately there are still some problems since the maximum value that 
can be represented (about 900) is smaller than some values in the data and the 
result is that I find a sharp change of sign. How can I fix it?

Thanks to 
anyone who can help me

Giulia


E' nata indoona: chiama, videochiama e messaggia Gratis. Scarica indoona per iPhone, Android e PC: http://www.indoona.com/ 


From yuvharpaz at gmail.com  Mon Mar 19 16:46:04 2012
From: yuvharpaz at gmail.com (Yuval Harpaz)
Date: Mon, 19 Mar 2012 17:46:04 +0200
Subject: [FieldTrip] rejectcomponent after ica for 20 comps only
Message-ID: <CAGQZS_kvLUWndQijop+pjEwj0r2=k=-Efp+WLRs1VzhuMVj2bQ@mail.gmail.com>

Dear ft_emaillist

I want to reject components obtained with with fastica.

if I only run ft_componentanalysis with cfg.numcomponent=20, creating only
20 components, can I still reject a specific component by
ft_rejectcomponent(cfg,comp,data) or will it only reconstruct the date
based on the 20 components I calculated?

thanks,Yuval

-- 

Y.Harpaz

a link to the BIU MEG lab:
http://faculty.biu.ac.il/~goldsa/index.html
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From enzo.brunetti at gmail.com  Mon Mar 19 18:32:34 2012
From: enzo.brunetti at gmail.com (Enzo Brunetti)
Date: Mon, 19 Mar 2012 13:32:34 -0400
Subject: [FieldTrip] Neuroscan .cnt files
In-Reply-To: <7171049.98631332170720589.JavaMail.defaultUser@defaultHost>
References: <7171049.98631332170720589.JavaMail.defaultUser@defaultHost>
Message-ID: <2CD6708A-A08A-4AF0-92BB-B78029DF2B76@gmail.com>

Dear Giulia,
I could not see your dropbox link showing the plot, but a known reported problem with importing .cnt neuroscan files is that the file header does not specify the actual precision of your data (typically 32 bits with new neuroscan systems, 16 bits previously). If you are importing 32 bits data without explicitly defining it previously, you can obtain the type of signals you are talking about (the default importing option is '16bits'). If this is the case, you must to specify this in the cfg input structure of the reader function, as:

cfg.headerformat         =  'ns_cnt32';
cfg.dataformat              =  'ns_cnt32';
cfg.eventformat            =  'ns_cnt32';

in addition to the other specific fields of the structure.

Also, you can visit this link: http://fieldtrip.fcdonders.nl/faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_this for more information.

I hope this could help you.
Best

Dr. Enzo Brunetti F.
---------------------------
Institute of Biomedical Sciences
Faculty of Medicine
University of Chile


On Mar 19, 2012, at 11:25 AM, Giulia Rizza wrote:

> Dear Fieldtrippers,
> hi to everyone and thanks in advance for your time.
> I'm not 
> an expert and I'd like to share with you a problem I found in reading cnt files 
> acquired with Neuroscan.
> 
> I read the data with ft_read_data function and I find 
> the attached link Plot1, for instance the first channel. It seems that the 
> signal is forced to pass per zero every two samples, so I tried to read them  
> excluding the even samples and I find the result in Plot2, while excluding the 
> odd values I find the result in Plot3.
> 
> http://dl.dropbox.com/u/28258961/Plot01.
> rar
> 
> Unfortunately there are still some problems since the maximum value that 
> can be represented (about 900) is smaller than some values in the data and the 
> result is that I find a sharp change of sign. How can I fix it?
> 
> Thanks to 
> anyone who can help me
> 
> Giulia
> 
> 
> E' nata indoona: chiama, videochiama e messaggia Gratis. Scarica indoona per iPhone, Android e PC: http://www.indoona.com/ 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From g.piantoni at nin.knaw.nl  Mon Mar 19 17:59:50 2012
From: g.piantoni at nin.knaw.nl (Gio Piantoni)
Date: Mon, 19 Mar 2012 17:59:50 +0100
Subject: [FieldTrip] rejectcomponent after ica for 20 comps only
In-Reply-To: <CAGQZS_kvLUWndQijop+pjEwj0r2=k=-Efp+WLRs1VzhuMVj2bQ@mail.gmail.com>
References: <CAGQZS_kvLUWndQijop+pjEwj0r2=k=-Efp+WLRs1VzhuMVj2bQ@mail.gmail.com>
Message-ID: <CAHeOcrv=saYUviSjchVn-mdnv53Y4Ky37LsG-hit+E=2CLSy2g@mail.gmail.com>

Hi Yuval,

If you pass data as third argument, the function will substract the
weights of rejected component(s) from your data. So, your data will
have the initial rank minus the number of rejected component. No
reconstruction occurs.

See line 121 of ft_rejectcomponent or try the code below.

nelec = 50;
fs = 1000;
ntrl = 5;

data = [];
data.label = cellfun(@(x)['E' num2str(x)], num2cell(1:nelec), 'uni', 0);
data.fsample = fs;
for i =1:ntrl
  data.trial{i} = randn(nelec, fs);
  data.time{i} = 1/fs:1/fs:1;
end

cfg = [];
cfg.method = 'fastica';
cfg.numcomponent = 10;
comp = ft_componentanalysis(cfg, data);

cfg = [];
cfg.component = 2;
data2 = ft_rejectcomponent(cfg, comp, data); % subtract comp from data
data3 = ft_rejectcomponent(cfg, comp); % reconstruct from comp

rank(data.trial{1}) % full rank
rank(data2.trial{1}) % full rank - 1 rejected
rank(data3.trial{1})  % rank of 'comp' - 1 rejected

On Mon, Mar 19, 2012 at 16:46, Yuval Harpaz <yuvharpaz at gmail.com> wrote:
> Dear ft_emaillist
>
> I want to reject components obtained with with fastica.
>
> if I only run ft_componentanalysis with cfg.numcomponent=20, creating only
> 20 components, can I still reject a specific component by
> ft_rejectcomponent(cfg,comp,data) or will it only reconstruct the date based
> on the 20 components I calculated?
>
> thanks,Yuval
>
> --
>
> Y.Harpaz
>
> a link to the BIU MEG lab:
> http://faculty.biu.ac.il/~goldsa/index.html
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From politzerahless at gmail.com  Mon Mar 19 18:56:21 2012
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Mon, 19 Mar 2012 12:56:21 -0500
Subject: [FieldTrip] fieldtrip Digest, Vol 16, Issue 25
In-Reply-To: <mailman.142.1332174700.1184.fieldtrip@donders.ru.nl>
References: <mailman.142.1332174700.1184.fieldtrip@donders.ru.nl>
Message-ID: <CAJT2k__WBFwXyOujLbn-vm6OGLmrMEWOHqy4BpYE5xUEwp=+eg@mail.gmail.com>

Hi Giulia,

The data certainly do look a bit weird to me, and as Enzo suggests
specifying 32 or 16 bits may help. Also, have you tried reading the data
using ft_preprocessing()<http://fieldtrip.fcdonders.nl/reference/ft_preprocessing>rather
than ft_read_data()? In my experience the high-level function
(ft_preprocessing) is easier to work with and handles a lot of the
complicated stuff for you, so unless you have a special reason to need to
read your data with the low-level functions then you might have more luck
just using ft_preprocessing.

Best,
Steve Politzer-Ahles

Message: 5
> Date: Mon, 19 Mar 2012 13:32:34 -0400
> From: Enzo Brunetti <enzo.brunetti at gmail.com>
> To: Giulia Rizza <giulia.rizza at tiscali.it>,     Email discussion list for
>        the FieldTrip project <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] Neuroscan .cnt files
> Message-ID: <2CD6708A-A08A-4AF0-92BB-B78029DF2B76 at gmail.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Giulia,
> I could not see your dropbox link showing the plot, but a known reported
> problem with importing .cnt neuroscan files is that the file header does
> not specify the actual precision of your data (typically 32 bits with new
> neuroscan systems, 16 bits previously). If you are importing 32 bits data
> without explicitly defining it previously, you can obtain the type of
> signals you are talking about (the default importing option is '16bits').
> If this is the case, you must to specify this in the cfg input structure of
> the reader function, as:
>
> cfg.headerformat         =  'ns_cnt32';
> cfg.dataformat              =  'ns_cnt32';
> cfg.eventformat            =  'ns_cnt32';
>
> in addition to the other specific fields of the structure.
>
> Also, you can visit this link:
> http://fieldtrip.fcdonders.nl/faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_thisfor more information.
>
> I hope this could help you.
> Best
>
> Dr. Enzo Brunetti F.
> ---------------------------
> Institute of Biomedical Sciences
> Faculty of Medicine
> University of Chile
>
>
> On Mar 19, 2012, at 11:25 AM, Giulia Rizza wrote:
>
> > Dear Fieldtrippers,
> > hi to everyone and thanks in advance for your time.
> > I'm not
> > an expert and I'd like to share with you a problem I found in reading
> cnt files
> > acquired with Neuroscan.
> >
> > I read the data with ft_read_data function and I find
> > the attached link Plot1, for instance the first channel. It seems that
> the
> > signal is forced to pass per zero every two samples, so I tried to read
> them
> > excluding the even samples and I find the result in Plot2, while
> excluding the
> > odd values I find the result in Plot3.
> >
> > http://dl.dropbox.com/u/28258961/Plot01.
> > rar
> >
> > Unfortunately there are still some problems since the maximum value that
> > can be represented (about 900) is smaller than some values in the data
> and the
> > result is that I find a sharp change of sign. How can I fix it?
> >
> > Thanks to
> > anyone who can help me
> >
> > Giulia
> >
> >
> > E' nata indoona: chiama, videochiama e messaggia Gratis. Scarica indoona
> per iPhone, Android e PC: http://www.indoona.com/
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> -------------- next part --------------
>
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From yuvharpaz at gmail.com  Mon Mar 19 20:49:31 2012
From: yuvharpaz at gmail.com (Yuval Harpaz)
Date: Mon, 19 Mar 2012 21:49:31 +0200
Subject: [FieldTrip] rejectcomponent after ica for 20 comps only
In-Reply-To: <CAHeOcrv=saYUviSjchVn-mdnv53Y4Ky37LsG-hit+E=2CLSy2g@mail.gmail.com>
References: <CAGQZS_kvLUWndQijop+pjEwj0r2=k=-Efp+WLRs1VzhuMVj2bQ@mail.gmail.com>
	<CAHeOcrv=saYUviSjchVn-mdnv53Y4Ky37LsG-hit+E=2CLSy2g@mail.gmail.com>
Message-ID: <CAGQZS_=SbL+U2YumY0HyFc4OpJ2j81199Y_8ke8TddoFoC-29w@mail.gmail.com>

thanks a lot. it clears the matter
Yuval

On 19 March 2012 18:59, Gio Piantoni <g.piantoni at nin.knaw.nl> wrote:

> Hi Yuval,
>
> If you pass data as third argument, the function will substract the
> weights of rejected component(s) from your data. So, your data will
> have the initial rank minus the number of rejected component. No
> reconstruction occurs.
>
> See line 121 of ft_rejectcomponent or try the code below.
>
> nelec = 50;
> fs = 1000;
> ntrl = 5;
>
> data = [];
> data.label = cellfun(@(x)['E' num2str(x)], num2cell(1:nelec), 'uni', 0);
> data.fsample = fs;
> for i =1:ntrl
>  data.trial{i} = randn(nelec, fs);
>  data.time{i} = 1/fs:1/fs:1;
> end
>
> cfg = [];
> cfg.method = 'fastica';
> cfg.numcomponent = 10;
> comp = ft_componentanalysis(cfg, data);
>
> cfg = [];
> cfg.component = 2;
> data2 = ft_rejectcomponent(cfg, comp, data); % subtract comp from data
> data3 = ft_rejectcomponent(cfg, comp); % reconstruct from comp
>
> rank(data.trial{1}) % full rank
> rank(data2.trial{1}) % full rank - 1 rejected
> rank(data3.trial{1})  % rank of 'comp' - 1 rejected
>
> On Mon, Mar 19, 2012 at 16:46, Yuval Harpaz <yuvharpaz at gmail.com> wrote:
> > Dear ft_emaillist
> >
> > I want to reject components obtained with with fastica.
> >
> > if I only run ft_componentanalysis with cfg.numcomponent=20, creating
> only
> > 20 components, can I still reject a specific component by
> > ft_rejectcomponent(cfg,comp,data) or will it only reconstruct the date
> based
> > on the 20 components I calculated?
> >
> > thanks,Yuval
> >
> > --
> >
> > Y.Harpaz
> >
> > a link to the BIU MEG lab:
> > http://faculty.biu.ac.il/~goldsa/index.html
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 

Y.Harpaz

a link to the BIU MEG lab:
http://faculty.biu.ac.il/~goldsa/index.html
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From mark.noordenbos at gmail.com  Tue Mar 20 09:37:51 2012
From: mark.noordenbos at gmail.com (Mark Noordenbos)
Date: Tue, 20 Mar 2012 09:37:51 +0100
Subject: [FieldTrip] Combine Grand Average
Message-ID: <CAJSb8nPtg+d6dFPtWLgNXmasLFXHkOFeHEhrw7FNABMA1pE_fg@mail.gmail.com>

Hi Jörn, Steve and Eelke,

Thanks for the suggestions for combining grand averages.
Unfortunately, ft_appendtimelock did not work for the grand averages.

Probably, the only proper way to this is to make completely new grand
averages with all conditions included, instead of a grand average for each
condition and combine them later.

To quickly view the outcome of combining the grand averages of 2 conditions
a calculated the mean by hand:

datatot.individual = (data1.individual + data2.individual)/2;

Kind regards,
Mark


-- 
Mark Noordenbos, MSc

Radboud University Nijmegen
Behavioural Science Institute

P.O. Box 9104, Room A05.36
6500 HE Nijmegen
The Netherlands

Email: m.noordenbos at bsi.ru.nl
Telephone: +31 24 3612070
Fax:          +31 24 3616211

http://www.ru.nl
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From batrod at gmail.com  Tue Mar 20 18:53:03 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Tue, 20 Mar 2012 12:53:03 -0500
Subject: [FieldTrip] Clusterplot scale?
Message-ID: <CAPy7a9CGu275wjBvMJiUsnaHYSpTpWOwMbhrTovMdvGNXGb26A@mail.gmail.com>

dear Fieldtrippers,

Im using the Montecarlo randomization method with cluster correction to
compare 2 conditions with a t-test.
When i plot the significant cluster with the ft_clusterplot function, it
creates a topoplot with highlighted electrodes.
I was just wondering what values were represented in the topoplot, as it
seems to be the difference between my two conditions, but with a higher
scale.

Rodolphe.
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From jm.horschig at donders.ru.nl  Wed Mar 21 09:45:11 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 21 Mar 2012 09:45:11 +0100
Subject: [FieldTrip] Clusterplot scale?
In-Reply-To: <CAPy7a9CGu275wjBvMJiUsnaHYSpTpWOwMbhrTovMdvGNXGb26A@mail.gmail.com>
References: <CAPy7a9CGu275wjBvMJiUsnaHYSpTpWOwMbhrTovMdvGNXGb26A@mail.gmail.com>
Message-ID: <4F699517.6050407@donders.ru.nl>

Dear Rodolphe,

By default, the corresponding values do not reflect power differences 
directly, but the test-statistic, in your case t-values (that's the 
/stat.stat/ field)
You can see on what scale the plot is by typing /colorbar /in the 
command window or by pressing the colorbar button in the icon bar of the 
matlab figure.

Best,
Jörn


On 3/20/2012 6:53 PM, Rodolphe Nenert wrote:
> dear Fieldtrippers,
>
> Im using the Montecarlo randomization method with cluster correction 
> to compare 2 conditions with a t-test.
> When i plot the significant cluster with the ft_clusterplot function, 
> it creates a topoplot with highlighted electrodes.
> I was just wondering what values were represented in the topoplot, as 
> it seems to be the difference between my two conditions, but with a 
> higher scale.
>
> Rodolphe.
>
>
> _______________________________________________
> 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

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 m.leszczynski.m at googlemail.com  Wed Mar 21 10:51:14 2012
From: m.leszczynski.m at googlemail.com (Marcin)
Date: Wed, 21 Mar 2012 10:51:14 +0100
Subject: [FieldTrip] statfun_depsamplesregrT
Message-ID: <CAAVVtzDY5stRD-XE2Pa5TjrO1L8AJXXSZToy7XhA72hK22bu+w@mail.gmail.com>

Dear Fieldtripers,

Could anyone explain me what is being calculated with the
statfun_depsamplesregrT function, please.

David Groppe (thank you David) suggested in a previous thread on the list
that I might calculate permutation test based on rank correlation to
account for monotonic relationships within the permutation framework. I was
wondering if this is the kind of test that statfun_depsamplesregrT function
calculates.
http://mailman.science.ru.nl/pipermail/fieldtrip/2011-December/004578.html

Best,
Marcin
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From ole.jensen at donders.ru.nl  Wed Mar 21 15:28:58 2012
From: ole.jensen at donders.ru.nl (Ole Jensen)
Date: Wed, 21 Mar 2012 15:28:58 +0100
Subject: [FieldTrip] data analysis competition / Biomag2012
Message-ID: <4F69E5AA.5010507@donders.ru.nl>

Dear colleagues,

We would like to announce (2nd announcement) the data analysis 
competition at the Biomag2012 meeting (Paris, Aug 26-30). Please 
encourage students and postdocs to participate. There were some 
technical glitches in the data after the 1st announcement. They are now 
corrected.

With best wishes,

Ole Jensen and Ali Bahramisharif


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

*Biomag2012 analysis competition - distributed representations
*
http://www.biomag2012.org/content/data-analysis-competition

The decoding of mental states and neuronal representations from brain 
imaging data is a research field in rapid development (Spiers HJ, 
Maguire EA. Decoding human brain activity during real-world experiences. 
Trends Cogn Sci. 2007 ; Haynes JD, Rees G. Decoding mental states from 
brain activity in humans. Nat Rev Neurosci. 2006). These decoding 
approaches have a great potential in MEG research where data are 
recorded from hundreds of sensors with a millisecond time resolution. In 
particular cognitive neuroscience could benefit from further development 
of decoding approaches in order to identify representational specific 
brain activity.
The aim of the competition is to:

  * Promote the development and application of new multivariate analysis
    techniques for decoding of brain activity
  * Make the audience aware of novel approaches
  * Elucidate the pros and cons of the different techniques
      o Which assumptions are behind a given approach?
      o What are the limitations?
  * Attract signal-processing experts from outside the MEG field
  * Encourage a discussion on the cognitive insight the techniques can
    bring about

The deadline for submitting results is Aug 17, 2012.

-- 
Ole Jensen
http://www.neuosc.com

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From vitoria.piai at gmail.com  Wed Mar 21 16:17:24 2012
From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=)
Date: Wed, 21 Mar 2012 16:17:24 +0100
Subject: [FieldTrip] a function for averaging over freq x time x channel
Message-ID: <4F69F104.1000406@gmail.com>

Hi there,

Is there an easy way for averaging over frequency x time x channel if my 
data is the output of ft_freqanalysis with keeptrials = 'no' (so 
chan_freq_time)?

ft_redefinetrial requires rpt to be present, so that's not an option. 
ft_selectdata_old is also complaining about the wrong structure for the 
input data and ft_selectdata_new is outputting exactly the same 
chan_freq_time as the input (I'm using the most recent FT version at the 
DCCN).

I may be missing some really obvious function, but so far I've been 
doing it in the hard way by hand.

Any suggestions are very much appreciated.

Thanks, Vitoria


From jm.horschig at donders.ru.nl  Wed Mar 21 16:21:55 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 21 Mar 2012 16:21:55 +0100
Subject: [FieldTrip] a function for averaging over freq x time x channel
In-Reply-To: <4F69F104.1000406@gmail.com>
References: <4F69F104.1000406@gmail.com>
Message-ID: <4F69F213.5040609@donders.ru.nl>

Hi Vitoria,

try ft_freqdescriptives

Best,
Jörn

On 3/21/2012 4:17 PM, Vitória Magalhães Piai wrote:
> Hi there,
>
> Is there an easy way for averaging over frequency x time x channel if 
> my data is the output of ft_freqanalysis with keeptrials = 'no' (so 
> chan_freq_time)?
>
> ft_redefinetrial requires rpt to be present, so that's not an option. 
> ft_selectdata_old is also complaining about the wrong structure for 
> the input data and ft_selectdata_new is outputting exactly the same 
> chan_freq_time as the input (I'm using the most recent FT version at 
> the DCCN).
>
> I may be missing some really obvious function, but so far I've been 
> doing it in the hard way by hand.
>
> Any suggestions are very much appreciated.
>
> Thanks, Vitoria
> _______________________________________________
> 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

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 jm.horschig at donders.ru.nl  Wed Mar 21 16:32:42 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 21 Mar 2012 16:32:42 +0100
Subject: [FieldTrip] a function for averaging over freq x time x channel
In-Reply-To: <4F69F213.5040609@donders.ru.nl>
References: <4F69F104.1000406@gmail.com> <4F69F213.5040609@donders.ru.nl>
Message-ID: <4F69F49A.5080005@donders.ru.nl>

Hey again,

sorry, it doesn't work with ft_freqdescriptives, then you have to do it 
manually:
squeeze(nanmean(nanmean(nanmean(data.powspctrm, 1), 2), 3))

Best,
Jörn

On 3/21/2012 4:21 PM, "Jörn M. Horschig" wrote:
> Hi Vitoria,
>
> try ft_freqdescriptives
>
> Best,
> Jörn
>
> On 3/21/2012 4:17 PM, Vitória Magalhães Piai wrote:
>> Hi there,
>>
>> Is there an easy way for averaging over frequency x time x channel if 
>> my data is the output of ft_freqanalysis with keeptrials = 'no' (so 
>> chan_freq_time)?
>>
>> ft_redefinetrial requires rpt to be present, so that's not an option. 
>> ft_selectdata_old is also complaining about the wrong structure for 
>> the input data and ft_selectdata_new is outputting exactly the same 
>> chan_freq_time as the input (I'm using the most recent FT version at 
>> the DCCN).
>>
>> I may be missing some really obvious function, but so far I've been 
>> doing it in the hard way by hand.
>>
>> Any suggestions are very much appreciated.
>>
>> Thanks, Vitoria
>> _______________________________________________
>> 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

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 Jan.Hirschmann at med.uni-duesseldorf.de  Wed Mar 21 16:36:39 2012
From: Jan.Hirschmann at med.uni-duesseldorf.de (Jan.Hirschmann at med.uni-duesseldorf.de)
Date: Wed, 21 Mar 2012 16:36:39 +0100
Subject: [FieldTrip] error ft_read_mri
Message-ID: <72E993C35FB11743B79FF9286E5B6D8B03ADFF9E@Mail2-UKD.VMED.UKD>

Dear fieldtrip programmers,

 

with the latest version of fieldtrip I am experiencing problems reading
MRs:

 

a=ft_read_mri('/data/apps/spm/spm8/canonical/avg152T1.nii')

Undefined function or variable "out".

 

Error in fixname (line 55)

while(out(1) == '_'),   out = out(2:end); end;   % remove all underscore
at the begin of the

string

 

Error in ft_hastoolbox (line 366)

  previous.(fixname(toolbox)) = status;

 

Error in ft_read_mri (line 45)

hasmri  = ft_hastoolbox('mri');     % from Darren Weber, see
http://eeg.sourceforge.net/

 

Thanks and all the best,

Jan

--

Jan Hirschmann

MSc. Neuroscience

Institute of Clinical Neuroscience and Medical Psychology

Heinrich Heine University Duesseldorf

Universitaetsstr.  1
40225  Duesseldorf

Tel: 0049 - (0)211 - 81 - 18415

 

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From max-philipp.stenner at med.ovgu.de  Wed Mar 21 19:53:28 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Wed, 21 Mar 2012 18:53:28 +0000
Subject: [FieldTrip] (no subject)
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830CB542@ESEN4.imed.uni-magdeburg.de>

Dear fieldtrip users/developers, 

I'd like to perform time-frequency analysis after computing the planar gradiometer representation of multi-session data and I am wondering whether the order in which the analysis steps are performed matters. The sequence I have used is

ft_megplanar
concatenate data across sessions
ft_average_sens, add the averaged (planar) sensor information to the datapool
ft_freqanalysis
ft_combineplanar

Does that make sense?

Thanks very much, 
best
Max
fieldtrip version: fieldtrip-20111130 on a Windows7 PC


From max-philipp.stenner at med.ovgu.de  Wed Mar 21 23:16:55 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Wed, 21 Mar 2012 22:16:55 +0000
Subject: [FieldTrip] (no subject)
In-Reply-To: <FBEFFA1F493D8944969D2F5AE78E58830CB542@ESEN4.imed.uni-magdeburg.de>
References: <FBEFFA1F493D8944969D2F5AE78E58830CB542@ESEN4.imed.uni-magdeburg.de>
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830CB553@ESEN4.imed.uni-magdeburg.de>

...just to specify the question: I am wondering whether ft_average_sens of data in planar sensor gradiometer representation is problematic

________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]&quot; im Auftrag von &quot;Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de]
Gesendet: Mittwoch, 21. März 2012 19:53
Bis: Email discussion list for the FieldTrip project
Betreff: [FieldTrip] (no subject)

Dear fieldtrip users/developers,

I'd like to perform time-frequency analysis after computing the planar gradiometer representation of multi-session data and I am wondering whether the order in which the analysis steps are performed matters. The sequence I have used is

ft_megplanar
concatenate data across sessions
ft_average_sens, add the averaged (planar) sensor information to the datapool
ft_freqanalysis
ft_combineplanar

Does that make sense?

Thanks very much,
best
Max
fieldtrip version: fieldtrip-20111130 on a Windows7 PC
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From max-philipp.stenner at med.ovgu.de  Wed Mar 21 23:41:21 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Wed, 21 Mar 2012 22:41:21 +0000
Subject: [FieldTrip] (no subject)
In-Reply-To: <FBEFFA1F493D8944969D2F5AE78E58830CB553@ESEN4.imed.uni-magdeburg.de>
References: <FBEFFA1F493D8944969D2F5AE78E58830CB542@ESEN4.imed.uni-magdeburg.de>
	<FBEFFA1F493D8944969D2F5AE78E58830CB553@ESEN4.imed.uni-magdeburg.de>
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830CB561@ESEN4.imed.uni-magdeburg.de>

(i.e. before applying ft_combineplanar)
________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]&quot; im Auftrag von &quot;Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de]
Gesendet: Mittwoch, 21. März 2012 23:16
Bis: Email discussion list for the FieldTrip project
Betreff: Re: [FieldTrip] (no subject)

...just to specify the question: I am wondering whether ft_average_sens of data in planar sensor gradiometer representation is problematic

________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]&quot; im Auftrag von &quot;Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de]
Gesendet: Mittwoch, 21. März 2012 19:53
Bis: Email discussion list for the FieldTrip project
Betreff: [FieldTrip] (no subject)

Dear fieldtrip users/developers,

I'd like to perform time-frequency analysis after computing the planar gradiometer representation of multi-session data and I am wondering whether the order in which the analysis steps are performed matters. The sequence I have used is

ft_megplanar
concatenate data across sessions
ft_average_sens, add the averaged (planar) sensor information to the datapool
ft_freqanalysis
ft_combineplanar

Does that make sense?

Thanks very much,
best
Max
fieldtrip version: fieldtrip-20111130 on a Windows7 PC
_______________________________________________
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 bibi.raquel at gmail.com  Thu Mar 22 04:34:36 2012
From: bibi.raquel at gmail.com (Raquel Bibi)
Date: Wed, 21 Mar 2012 23:34:36 -0400
Subject: [FieldTrip] Combine Grand Average
In-Reply-To: <CAJSb8nPtg+d6dFPtWLgNXmasLFXHkOFeHEhrw7FNABMA1pE_fg@mail.gmail.com>
References: <CAJSb8nPtg+d6dFPtWLgNXmasLFXHkOFeHEhrw7FNABMA1pE_fg@mail.gmail.com>
Message-ID: <CA+Gwb028WOLjw9k9c-c3r6NfovKTG=ukuxroRG5mQPoQ+6XasA@mail.gmail.com>

Mark,
Can you calculate the weighted mean by hand?
(Data1.individual*no_of_trials(data1) +
Data2.individual*no_of_trials(data2)) / (no_trials(data1) +
no_of_trials(data2))

If so, no need to redo!



On Tue, Mar 20, 2012 at 4:37 AM, Mark Noordenbos
<mark.noordenbos at gmail.com>wrote:

> Hi Jörn, Steve and Eelke,
>
> Thanks for the suggestions for combining grand averages.
> Unfortunately, ft_appendtimelock did not work for the grand averages.
>
> Probably, the only proper way to this is to make completely new grand
> averages with all conditions included, instead of a grand average for each
> condition and combine them later.
>
> To quickly view the outcome of combining the grand averages of 2
> conditions a calculated the mean by hand:
>
> datatot.individual = (data1.individual + data2.individual)/2;
>
> Kind regards,
>
> Mark
>
>
> --
> Mark Noordenbos, MSc
>
> Radboud University Nijmegen
> Behavioural Science Institute
>
> P.O. Box 9104, Room A05.36
> 6500 HE Nijmegen
> The Netherlands
>
> Email: m.noordenbos at bsi.ru.nl
> Telephone: +31 24 3612070
> Fax:          +31 24 3616211
>
> http://www.ru.nl
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From jan.schoffelen at donders.ru.nl  Thu Mar 22 09:10:57 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 22 Mar 2012 09:10:57 +0100
Subject: [FieldTrip] error ft_read_mri
In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B03ADFF9E@Mail2-UKD.VMED.UKD>
References: <72E993C35FB11743B79FF9286E5B6D8B03ADFF9E@Mail2-UKD.VMED.UKD>
Message-ID: <F5816B77-88CB-4AA2-9B64-49E9BB83D3CB@donders.ru.nl>

Hi Jan

I cannot reproduce your problem. I'd check the following and try again:
-ensure that you have the latest version of FieldTrip
-ensure that there are no pointers to any spm directory on your matlab-path (apart perhaps from those that are distributed within fieldtrip, i.e. fieldtrip/external/spmXXX)

Cheers,

Jan

On Mar 21, 2012, at 4:36 PM, <Jan.Hirschmann at med.uni-duesseldorf.de> <Jan.Hirschmann at med.uni-duesseldorf.de> wrote:

> Dear fieldtrip programmers,
>  
> with the latest version of fieldtrip I am experiencing problems reading MRs:
>  
> a=ft_read_mri('/data/apps/spm/spm8/canonical/avg152T1.nii')
> Undefined function or variable "out".
>  
> Error in fixname (line 55)
> while(out(1) == '_'),   out = out(2:end); end;   % remove all underscore at the begin of the
> string
>  
> Error in ft_hastoolbox (line 366)
>   previous.(fixname(toolbox)) = status;
>  
> Error in ft_read_mri (line 45)
> hasmri  = ft_hastoolbox('mri');     % from Darren Weber, see http://eeg.sourceforge.net/
>  
> Thanks and all the best,
> Jan
> --
> Jan Hirschmann
> MSc. Neuroscience
> Institute of Clinical Neuroscience and Medical Psychology
> Heinrich Heine University Duesseldorf
> Universitaetsstr.  1
> 40225  Duesseldorf
> Tel: 0049 - (0)211 - 81 - 18415
>  
> _______________________________________________
> 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

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From marco.dahmane at gmail.com  Thu Mar 22 13:13:18 2012
From: marco.dahmane at gmail.com (Marco Dahmane)
Date: Thu, 22 Mar 2012 12:13:18 +0000
Subject: [FieldTrip] Trial-dependant baseline correction
Message-ID: <CAPPdCy__G9a7BL4HJsEbG4eVzYpA5k=pqxyXH5Tm-L=-P3uVrQ@mail.gmail.com>

Dear fellow Fieldtrippers,

I was having a small problem regarding baseline correction in FT.

My situation is rather simple : I have two types of trials, trials A and
trials B. Triggers A are always preceding triggers B, but the delay between
the two is NOT fixed.

I use triggers B to define my trials (for instance -0.5s to +0.5s).
Very straightforward.

However, I would like to use triggers A to define my baseline window. Say I
would like to use the one second preceding each trigger A as the baseline
for the following trial.

Until now the way I was going about it was rather tedious :
a) ft_preprocessing data as one big, long trial (filtering)
b) ft_definetrial to define long trials as starting from trigger A (origin)
to following trigger B (end)
*c) ft_preprocessing to baseline correct*
d) ft_redefinetrial with variable cfg.offset to set origin back to trigger B
e) ft_redefinetrial to take only window [ -0.5s ; +0.5s]

But I'm wondering whether that's not an overkill (especially since the
delay between triggers A and B can be quite long and make the preprocessing
really slow on my old machine).

Any advice is appreciated,

Best regards,
Marco
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From lavado at gmail.com  Thu Mar 22 15:24:42 2012
From: lavado at gmail.com (Ion Lavado)
Date: Thu, 22 Mar 2012 15:24:42 +0100
Subject: [FieldTrip] Sourceanalysis understanding problem
Message-ID: <CAMLwyK6Gi7d_EGxvsCfFGeYM_Pz2HQV8t_2sx8iEMRw9aLxSkA@mail.gmail.com>

Hello, I would like to ask you what does the "cfg.frequency" means in
ft_sourceanalysis. I want to plot a frequency range for example [14 30], do
i have to use cfg.frequency=22? why? It would be perfect if someone could
explain how to make the freqanalysis and the sourceanalysis for a frequency
range for example this one[14 30].

This is the code for my frequency analysis:
cfg = [];
cfg.method    = 'mtmfft';
cfg.output    = 'powandcsd';
cfg.channel   = {'MEG'};
cfg.tapsmofrq = 4;
cfg.foilim    = [14 30];
freq_post = ft_freqanalysis(cfg, words_post);

The i do the sourceanalysis:
cfg              = [];
cfg.frequency    = 22;
cfg.lambda=0;
cfg.method       = 'dics';
cfg.coordsys       = 'neuromag';
cfg.projectnoise = 'yes';
cfg.grad            = freq_pre.grad;
cfg.channel   = {'MEG'};
cfg.grid         = grid;
cfg.reducerank      = 2;
cfg.vol          = vol02;
vol02=ft_convert_units(vol02,'cm');
source_post11= ft_sourceanalysis(cfg, freq_post);


What i get i see that depends only in the cfg.frequency=22, if i change the
previous freqanalysis and use the 22 for the cfg.frequency i get the same
result. Hope someone can help me.

Thanks in advance.

Best,

Ion
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From lavado at gmail.com  Thu Mar 22 17:13:34 2012
From: lavado at gmail.com (Ion Lavado)
Date: Thu, 22 Mar 2012 17:13:34 +0100
Subject: [FieldTrip] is beamforming result correct?
Message-ID: <CAMLwyK4gzzrPbW3qGEfSs6sMz-NwxtsuXRE1J6DURM_Zg7pFbg@mail.gmail.com>

I think the result i got doing the beamforming source reconstruction is not
good as there is lot of activation at the bottom where the cerebellum is.
Can anyone confirm me it is incorrect? Possible mistake?

This is the code i used for the headmodel:

mri = ft_read_mri('/home/ilavado/ilavado/mutiT1/T1_02.mgz');
cfg = [];
cfg.interactive    = 'yes';
cfg.coordsys    = 'neuromag';
mri_real           = ft_volumerealign(cfg,mri);
[segmentedmri]   = ft_volumesegment(cfg, mri_real)
cfg = [];
cfg.sourceunits='cm';
cfg.coordsys       = 'neuromag';
vol02 = ft_prepare_singleshell(cfg, segmentedmri);
ft_plot_vol(vol02);
mri_real = rmfield(mri_real, 'pnt');

sourceDiff = source_post;
sourceDiff.avg.pow = (source_post.avg.pow - source_pre.avg.pow) ./
source_pre.avg.pow;
cfg            = []
cfg.downsample = 2;
sourceDiffInt  = ft_sourceinterpolate(cfg, sourceDiff , mri_real);
cfg = [];
cfg.coordsys      = 'ctf';
cfg.nonlinear     = 'no';
sourceDiffIntNorm = ft_volumenormalise(cfg, sourceDiffInt);

Thank you very much.

Best,

Ion
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From Jarmo.Kontinen at ruhr-uni-bochum.de  Thu Mar 22 17:14:46 2012
From: Jarmo.Kontinen at ruhr-uni-bochum.de (Jarmo Kontinen)
Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
Message-ID: <permail-201203221614466509e8c700002494-Jarmo.Kontinen@msgid.mail.ruhr-uni-bochum.de>

Dear all,
I am trying to import EEG subject averages into Field Trip. The files are
exported with the Brainvision Analyzer in binary form
:subject10_konPro2002.dat and subject10_konPro2002.vhdr.
I have a problem with turning the data into the Field Trip data-structure. I
am following instructions given on this forum on one similar post. What I have
tried is the following:

cfg=[];
cfg.trialdef.eventtype='average'
cfg.dataset='subject10_konPro2002.dat'

 cfg=ft_definetrial(cfg);

Warning: no trialfun was specified, using trialfun_general
> In ft_definetrial at 123
evaluating trialfunction 'trialfun_general'
reading the events from 'subject10_konPro2002.vhdr'
??? Error using ==> ft_definetrial at 176
no trials were defined, see FT_DEFINETRIAL for help

I am grateful for all the help.
Thanks,
Jarmo Kontinen


From Don.Rojas at ucdenver.edu  Thu Mar 22 20:22:47 2012
From: Don.Rojas at ucdenver.edu (Rojas, Don)
Date: Thu, 22 Mar 2012 13:22:47 -0600
Subject: [FieldTrip] is beamforming result correct?
In-Reply-To: <CAMLwyK4gzzrPbW3qGEfSs6sMz-NwxtsuXRE1J6DURM_Zg7pFbg@mail.gmail.com>
References: <CAMLwyK4gzzrPbW3qGEfSs6sMz-NwxtsuXRE1J6DURM_Zg7pFbg@mail.gmail.com>
Message-ID: <4C3A9E0C-C8FB-4B28-9563-8A7942C053B7@ucdenver.edu>

Ion,

I do not think we can say definitively if your result is incorrect or not with the information provided. Can you provide a summary of your task, preprocessing and source analysis steps? There are MEG papers using beamformers that reveal cerebellar activity that is task consistent. If you do not have any a priori reason to expect it, however, then perhaps you are correct.

Best,

Don
-----------------------
Don Rojas, Ph.D.
Associate Professor of Psychiatry
U. of Colorado Denver Anschutz Medical Campus
Director, UCD Magnetoencephalography Lab


On Mar 22, 2012, at 10:13 AM, Ion Lavado wrote:

> I think the result i got doing the beamforming source reconstruction is not good as there is lot of activation at the bottom where the cerebellum is. Can anyone confirm me it is incorrect? Possible mistake?
> 
> This is the code i used for the headmodel:
> 
> mri = ft_read_mri('/home/ilavado/ilavado/mutiT1/T1_02.mgz');
> cfg = [];
> cfg.interactive    = 'yes';
> cfg.coordsys    = 'neuromag';
> mri_real           = ft_volumerealign(cfg,mri); 
> [segmentedmri]   = ft_volumesegment(cfg, mri_real)
> cfg = [];
> cfg.sourceunits='cm';
> cfg.coordsys       = 'neuromag';
> vol02 = ft_prepare_singleshell(cfg, segmentedmri);
> ft_plot_vol(vol02);
> mri_real = rmfield(mri_real, 'pnt');
> 
> sourceDiff = source_post;
> sourceDiff.avg.pow = (source_post.avg.pow - source_pre.avg.pow) ./ source_pre.avg.pow;  
> cfg            = []
> cfg.downsample = 2;
> sourceDiffInt  = ft_sourceinterpolate(cfg, sourceDiff , mri_real);
> cfg = [];
> cfg.coordsys      = 'ctf';
> cfg.nonlinear     = 'no';
> sourceDiffIntNorm = ft_volumenormalise(cfg, sourceDiffInt);
> 
> Thank you very much. 
> 
> Best,
> 
> Ion
> <beam_result.jpg>_______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip






From e.maris at psych.ru.nl  Thu Mar 22 21:12:35 2012
From: e.maris at psych.ru.nl (Eric Maris)
Date: Thu, 22 Mar 2012 21:12:35 +0100 (CET)
Subject: [FieldTrip] statfun_depsamplesregrT
In-Reply-To: <CAAVVtzDY5stRD-XE2Pa5TjrO1L8AJXXSZToy7XhA72hK22bu+w@mail.gmail.com>
References: <CAAVVtzDY5stRD-XE2Pa5TjrO1L8AJXXSZToy7XhA72hK22bu+w@mail.gmail.com>
Message-ID: <035401cd0868$20b27640$621762c0$@maris@psych.ru.nl>

Dear Marcin,

 

 

The statfun_depsamplesregrT calculates a T-statistic for regression
coefficients that are calculated within each of the units-of-observation
(typically, participants) obtained by regressing the subject-specific data
(spatiotemporal, spatio-spectral, spatio-spectro-temporal) on some
predictor variable that varies over the different conditions in which this
participant has provided data (e.g., working-memory load, retention
interval, luminance, contrast, etc). If you doubt the assumed linear
relation between predictor variable and biological data, then you could
write your own statfun_depsamplesrankcorr. To use this test statistic for
cluster-based permutation inference, you need a threshold based on some
reference distribution (which can be parametric, but must not be). 

 

To get this statfun_depsamplesrankcorr running, you will probably have to
take a look in the Fieldtrip code to see how the statistics framework is
structured.

 

Best,

 

Eric Maris

 

 

From: Marcin [mailto:m.leszczynski.m at googlemail.com] 
Sent: woensdag 21 maart 2012 10:51
To: Email discussion list for the FieldTrip project
Subject: [FieldTrip] statfun_depsamplesregrT

 

Dear Fieldtripers,

Could anyone explain me what is being calculated with the
statfun_depsamplesregrT function, please.

David Groppe (thank you David) suggested in a previous thread on the list
that I might calculate permutation test based on rank correlation to
account for monotonic relationships within the permutation framework. I
was wondering if this is the kind of test that statfun_depsamplesregrT
function calculates.
http://mailman.science.ru.nl/pipermail/fieldtrip/2011-December/004578.html

Best,
Marcin

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From g.piantoni at nin.knaw.nl  Fri Mar 23 20:35:22 2012
From: g.piantoni at nin.knaw.nl (Gio Piantoni)
Date: Fri, 23 Mar 2012 20:35:22 +0100
Subject: [FieldTrip] Trial-dependant baseline correction
In-Reply-To: <CAPPdCy__G9a7BL4HJsEbG4eVzYpA5k=pqxyXH5Tm-L=-P3uVrQ@mail.gmail.com>
References: <CAPPdCy__G9a7BL4HJsEbG4eVzYpA5k=pqxyXH5Tm-L=-P3uVrQ@mail.gmail.com>
Message-ID: <CAHeOcru5O5O07Re92i3Eexkj++VHmabqqJ1g7_s9Ww0jFiVN0Q@mail.gmail.com>

Hi Marco,

I don't understand very well if the bottleneck is the number of steps
or the memory/time used in preprocessing (a).

I think that the simplest approach is to use:
1) ft_definetrial (as in your (b))
2) ft_preprocessing (read data and apply preproc options)
3) ft_redefinetrial to take the window [-0.5 0.5] and change the
origin (you can do that in one step if you pass cfg.trl with three
columns: [begin_sample end_sample offset] in sample points)

Otherwise, if you're concerned about memory problems, you could do a
ft_definetrial and preprocessing for A events, and the same for B
events. Then, in Matlab, you average A events and subtract the average
from the B trials.

I think preprocessing on your trials should not take too much memory though.

HTH,
Gio

On Thu, Mar 22, 2012 at 13:13, Marco Dahmane <marco.dahmane at gmail.com> wrote:
> Dear fellow Fieldtrippers,
>
> I was having a small problem regarding baseline correction in FT.
>
> My situation is rather simple : I have two types of trials, trials A and
> trials B. Triggers A are always preceding triggers B, but the delay between
> the two is NOT fixed.
>
> I use triggers B to define my trials (for instance -0.5s to +0.5s).
> Very straightforward.
>
> However, I would like to use triggers A to define my baseline window. Say I
> would like to use the one second preceding each trigger A as the baseline
> for the following trial.
>
> Until now the way I was going about it was rather tedious :
> a) ft_preprocessing data as one big, long trial (filtering)
> b) ft_definetrial to define long trials as starting from trigger A (origin)
> to following trigger B (end)
> *c) ft_preprocessing to baseline correct*
> d) ft_redefinetrial with variable cfg.offset to set origin back to trigger B
> e) ft_redefinetrial to take only window [ -0.5s ; +0.5s]
>
> But I'm wondering whether that's not an overkill (especially since the delay
> between triggers A and B can be quite long and make the preprocessing really
> slow on my old machine).
>
> Any advice is appreciated,
>
> Best regards,
> Marco
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From politzerahless at gmail.com  Sun Mar 25 12:11:28 2012
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sun, 25 Mar 2012 12:11:28 +0200
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
Message-ID: <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg@mail.gmail.com>

Hello Jarmo,

I haven't tried importing Brain Vision files into FieldTrip myself, but
based on the code you sent it looks like the problem may be that you're
missing cfg.trialdef.eventvalue (which is used to tell FieldTrip which
triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim . See
the example at
http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials.

If what you are trying to do is import all trials from all triggers in the
file, I think you have to define your own "trialfun" function to do that
(although I haven't tried this myself so I'm not sure).
http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
information.

Best,
Steve Politzer-Ahles
University of Kansas


Message: 1
> Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> Message-ID:
>        <
> permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de
> >
>
> Content-Type: text/plain; charset=us-ascii
>
> Dear all,
> I am trying to import EEG subject averages into Field Trip. The files are
> exported with the Brainvision Analyzer in binary form
> :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> I have a problem with turning the data into the Field Trip data-structure.
> I
> am following instructions given on this forum on one similar post. What I
> have
> tried is the following:
>
> cfg=[];
> cfg.trialdef.eventtype='average'
> cfg.dataset='subject10_konPro2002.dat'
>
>  cfg=ft_definetrial(cfg);
>
> Warning: no trialfun was specified, using trialfun_general
> > In ft_definetrial at 123
> evaluating trialfunction 'trialfun_general'
> reading the events from 'subject10_konPro2002.vhdr'
> ??? Error using ==> ft_definetrial at 176
> no trials were defined, see FT_DEFINETRIAL for help
>
> I am grateful for all the help.
> Thanks,
> Jarmo Kontinen
>
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From fredericroux at hotmail.de  Mon Mar 26 12:23:50 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Mon, 26 Mar 2012 12:23:50 +0200
Subject: [FieldTrip] SPM path and sourceanalysis on template brain
Message-ID: <DUB113-W76F2D058B3132334525D94B7450@phx.gbl>


Dear all,


I am getting the following error message with the fieldtrip-20120105 version,
and wanted to ask if anyone could tell me:

a) how to prevent it
b) what the consequences of ignoring it will be.

Also I wanted to get some feedback on the possibility of
using a template brain for source localization on data for which
MRI data is missing.

I have a recorded MEG data from n = 98 participants but only have
the MRs of 70 of them. Can I use a template MR to perform
source analysis on the missing data sets?

Looking forward to any kind of suggestions.
Have a nice day,

Fred


-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From ivano_triggiani at yahoo.it  Mon Mar 26 14:14:47 2012
From: ivano_triggiani at yahoo.it (Ivano Triggiani)
Date: Mon, 26 Mar 2012 13:14:47 +0100 (BST)
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
In-Reply-To: <mailman.1.1332756017.8892.fieldtrip@donders.ru.nl>
References: <mailman.1.1332756017.8892.fieldtrip@donders.ru.nl>
Message-ID: <1332764087.47250.YahooMailNeo@web132103.mail.ird.yahoo.com>

Dear Jarmo,

Filedtrip needs a definition of segments of interest. For example reading a trigger channel or something else to cut the EEG recording into trials. If I have understood what you want to do is to get an average of general EEG (for example resting state EEG closed eyes). But you have to indicate which average you want to obtain, for example you can tell fieldtrip to divide EEG into epochs of 3 seconds and then to make an average of all of them.
What you wrote is the request of an average, but you are not specifing of what.
Fof example you can write a trial function that provides a trl matrix, i.e.:
0 3 0

3 6 0
6 9 0
9 12 0
12 13 0
...

where first column is the start sample in seconds (you have to multiply it for sample rate), the second column is the end sample and the third is the offset (in this case is always zero), or look at 
http://fieldtrip.fcdonders.nl/tutorial/preprocessing#use_your_own_function_for_trial_selection

best wishes,
Ivano



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




"No man can wear one face to himself 
and another to the multitude,
without finally getting bewildered 
as to which one is true."


Nathaniel Hawthorne


________________________________
 Da: "fieldtrip-request at donders.ru.nl" <fieldtrip-request at donders.ru.nl>
A: fieldtrip at donders.ru.nl 
Inviato: Lunedì 26 Marzo 2012 12:00
Oggetto: fieldtrip Digest, Vol 16, Issue 33
 
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Today's Topics:

   1. Re: Problem with FT_DEFINETRIAL (Stephen Politzer-Ahles)


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

Message: 1
Date: Sun, 25 Mar 2012 12:11:28 +0200
From: Stephen Politzer-Ahles <politzerahless at gmail.com>
To: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL
Message-ID:
    <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello Jarmo,

I haven't tried importing Brain Vision files into FieldTrip myself, but
based on the code you sent it looks like the problem may be that you're
missing cfg.trialdef.eventvalue (which is used to tell FieldTrip which
triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim . See
the example at
http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials.

If what you are trying to do is import all trials from all triggers in the
file, I think you have to define your own "trialfun" function to do that
(although I haven't tried this myself so I'm not sure).
http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
information.

Best,
Steve Politzer-Ahles
University of Kansas


Message: 1
> Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> Message-ID:
>        <
> permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de
> >
>
> Content-Type: text/plain; charset=us-ascii
>
> Dear all,
> I am trying to import EEG subject averages into Field Trip. The files are
> exported with the Brainvision Analyzer in binary form
> :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> I have a problem with turning the data into the Field Trip data-structure.
> I
> am following instructions given on this forum on one similar post. What I
> have
> tried is the following:
>
> cfg=[];
> cfg.trialdef.eventtype='average'
> cfg.dataset='subject10_konPro2002.dat'
>
>  cfg=ft_definetrial(cfg);
>
> Warning: no trialfun was specified, using trialfun_general
> > In ft_definetrial at 123
> evaluating trialfunction 'trialfun_general'
> reading the events from 'subject10_konPro2002.vhdr'
> ??? Error using ==> ft_definetrial at 176
> no trials were defined, see FT_DEFINETRIAL for help
>
> I am grateful for all the help.
> Thanks,
> Jarmo Kontinen
>
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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 16, Issue 33
*****************************************
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From fredericroux at hotmail.de  Mon Mar 26 14:47:22 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Mon, 26 Mar 2012 14:47:22 +0200
Subject: [FieldTrip] beamforming with rank deficient covariance matrix
Message-ID: <DUB113-W8242FDFA7507E17608A292B7450@phx.gbl>



Dear all,

I have a question related to the rank of the covariance matrix
used for the beamformer.

I preprocessed my data using ICA to reject EOG and ECG component (typically
between 2-4 components). This however, leads to a reduction in the rank
of the covariance matrix and I get a warning using ft_sourceanalysis
saying that my covariance matrix is rank deficient because rank(COV) < Nchannels.

I would like to know, how much of a problem and how serious this can be.

The way I understand things, this should only cause trouble if the number
of active sources exceeds the number of linearly independent rows of the covariance matrix?
Is this assumption correct? 

Is there some step in the ft_sourceanalyis pipeline that assumes that the number of
sources is equal to the number of channels, and that could bias the computation
of the beamformer? I mean in that case I would have more sources than channels
and thus the beamformer would fail.

Would be great if someone could help me to figure this out.

Cheers,
Fred




-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From max-philipp.stenner at med.ovgu.de  Mon Mar 26 14:51:08 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Mon, 26 Mar 2012 12:51:08 +0000
Subject: [FieldTrip] ft_sourceanalysis
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830CB840@ESEN4.imed.uni-magdeburg.de>

Dear fieldtrip developers and users, 

I am computing single trial LCMV beamforming moments with ft_sourceanalysis and cfg.rawtrial = 'yes'. I chose cfg.rawtrial because my fieldtrip version (fieldtrip-lite-20111130) reports a bug when using cfg.singletrial.

Am I right that the single-trial covariance matrices will not affect the moments when using precomputed filters (precomputed on the basis of the covariance matrices from "keeptrial = no" timelockdata across all experimental conditions) on "keeptrial = yes" - timelock data (sorted according to conditions) with cfg.rawtrial = 'yes'?
(I am not interested in power (which is changed to NaN by lcmv_beamforming anyways) or noise).

Thanks very much 
Max

fieldtrip-lite-20111130 on a Windows7 PC


From Jarmo.Kontinen at ruhr-uni-bochum.de  Mon Mar 26 15:09:23 2012
From: Jarmo.Kontinen at ruhr-uni-bochum.de (Jarmo Kontinen)
Date: Mon, 26 Mar 2012 15:09:23 +0200 (CEST)
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
In-Reply-To: <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg@mail.gmail.com>
Message-ID: <permail-201203261309236509e8c70000654b-Jarmo.Kontinen@msgid.mail.ruhr-uni-bochum.de>


Dear Stephen,
Thanks for your reply. I  have added the  missing field you sugegsted, but FT
still gives the same error-message.

Maybe I was also unclear what I want to do in the first place. The data we
have is already preprocessed ( filtered, segmented etc.) with the Analyzer.
Also, we have averaged the ERP's for each subject and each experimental
condition over all the trials. I would like to import these averaged ERP's
into FT and do some statisitics on the data. The problem is that I do not know
how to get required data-structure to use the FT-functions.

Best,
Jarmo


Stephen Politzer-Ahles schrieb am 2012-03-25:
> Hello Jarmo,

> I haven't tried importing Brain Vision files into FieldTrip myself,
> but
> based on the code you sent it looks like the problem may be that
> you're
> missing cfg.trialdef.eventvalue (which is used to tell FieldTrip
> which
> triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim
> . See
> the example at
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials.

> If what you are trying to do is import all trials from all triggers
> in the
> file, I think you have to define your own "trialfun" function to do
> that
> (although I haven't tried this myself so I'm not sure).
> http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
> information.

> Best,
> Steve Politzer-Ahles
> University of Kansas


> Message: 1
> > Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> > From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> > To: <fieldtrip at donders.ru.nl>
> > Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> > Message-ID:
> >        <
> > permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de


> > Content-Type: text/plain; charset=us-ascii

> > Dear all,
> > I am trying to import EEG subject averages into Field Trip. The
> > files are
> > exported with the Brainvision Analyzer in binary form
> > :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> > I have a problem with turning the data into the Field Trip
> > data-structure.
> > I
> > am following instructions given on this forum on one similar post.
> > What I
> > have
> > tried is the following:

> > cfg=[];
> > cfg.trialdef.eventtype='average'
> > cfg.dataset='subject10_konPro2002.dat'

> >  cfg=ft_definetrial(cfg);

> > Warning: no trialfun was specified, using trialfun_general
> > > In ft_definetrial at 123
> > evaluating trialfunction 'trialfun_general'
> > reading the events from 'subject10_konPro2002.vhdr'
> > ??? Error using ==> ft_definetrial at 176
> > no trials were defined, see FT_DEFINETRIAL for help

> > I am grateful for all the help.
> > Thanks,
> > Jarmo Kontinen



From Maria.Pefkou at unige.ch  Mon Mar 26 18:01:00 2012
From: Maria.Pefkou at unige.ch (Maria Pefkou)
Date: Mon, 26 Mar 2012 18:01:00 +0200
Subject: [FieldTrip] Create BEM model for EEG source localisation
Message-ID: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>

Dear FieldTrip users,

I started using the toolbox fairly recently to analyse EEG data and I have
huge trouble making a BEM model, which I need for source localisation.
Following the online tutorial, I processed my subjects' individual
structural MRIs in FreeSurfer and MNE and managed to prepare the
triangulated mesh. However, my problem is the volume conduction model. I
can get a singleshell one, using the ft_prepare_singleshell function, but
as far as I understand it is excusively used for MEG data. I came to this
conclusion because when I try to compute the forward model, given that I
provide information about the electrodes position, I always get the
following error:

"unsupported volume conductor model for EEG".
I guess this is because the vol.type is 'nolte' and there is no such case
for EEG data, at least not in the ft_prepare_vol_sens.m function, which is
automatically called.

I have tried to prepare a BEM model using the ft_prepare_headmodel function
with cfg.method='bemcp' or cfg.method='dipoli' but I was unsuccessful.
The problem is that, after having tried various functions/options, I lost
the general picture and I'm running in circles... The question is: I have a
segmented mri, how can I get a BEM model out of this? I must be missing a
fundamental part of the procedure but I can't quite find out what it is.
Any suggestions/help would be very much appreciated.

Thank you in advance,
Maria Pefkou

------------------------------------------
Research Assistant
Functional Brain Mapping Lab
University of Geneva
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From Maria.Pefkou at unige.ch  Mon Mar 26 18:05:36 2012
From: Maria.Pefkou at unige.ch (Maria Pefkou)
Date: Mon, 26 Mar 2012 18:05:36 +0200
Subject: [FieldTrip] Create BEM model for EEG source localisation
In-Reply-To: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>
References: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>
Message-ID: <CAJ5HwaumWvg4CT5-3MPEO5=H=YWK5kkU-wY2xJR8Fithb7dsRA@mail.gmail.com>

I forgot to mention before that right now I'm running fieldtrip-20120325
under Ubuntu 10.04.

On 26 March 2012 18:01, Maria Pefkou <Maria.Pefkou at unige.ch> wrote:

> Dear FieldTrip users,
>
> I started using the toolbox fairly recently to analyse EEG data and I have
> huge trouble making a BEM model, which I need for source localisation.
> Following the online tutorial, I processed my subjects' individual
> structural MRIs in FreeSurfer and MNE and managed to prepare the
> triangulated mesh. However, my problem is the volume conduction model. I
> can get a singleshell one, using the ft_prepare_singleshell function, but
> as far as I understand it is excusively used for MEG data. I came to this
> conclusion because when I try to compute the forward model, given that I
> provide information about the electrodes position, I always get the
> following error:
>
> "unsupported volume conductor model for EEG".
> I guess this is because the vol.type is 'nolte' and there is no such case
> for EEG data, at least not in the ft_prepare_vol_sens.m function, which is
> automatically called.
>
> I have tried to prepare a BEM model using the ft_prepare_headmodel
> function with cfg.method='bemcp' or cfg.method='dipoli' but I was
> unsuccessful.
> The problem is that, after having tried various functions/options, I lost
> the general picture and I'm running in circles... The question is: I have a
> segmented mri, how can I get a BEM model out of this? I must be missing a
> fundamental part of the procedure but I can't quite find out what it is.
> Any suggestions/help would be very much appreciated.
>
> Thank you in advance,
> Maria Pefkou
>
> ------------------------------------------
> Research Assistant
> Functional Brain Mapping Lab
> University of Geneva
>
>
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From k.muesch at uke.uni-hamburg.de  Mon Mar 26 18:45:35 2012
From: k.muesch at uke.uni-hamburg.de (=?iso-8859-1?Q?Kathrin_M=FCsch?=)
Date: Mon, 26 Mar 2012 18:45:35 +0200
Subject: [FieldTrip] inconsistent results from dipolefitting and beamforming
Message-ID: <5D2500F2-F9AB-41B0-8BA1-25B18E08A5A5@uke.uni-hamburg.de>

Hi Fieldtrip users,

I am trying to apply a beamformer to simulated data to check whether my headmodels are correct. While ft_dipolefit localizes the dipole in the original position, the beamformer results in a source at a totally different position (see figure 1). I kept everything as similar as possible to the example scripts (forward simulation & dipole fit, forward simulation & beamformer) but used individual gradiometer positions, grid and volume of a single subject (CTF space) and plotted the source in a template grid (SPM space). If I run the dipolesimulation with the individual gradiometer structure and the template headmodel vol and template grid, the dipole and the source result in the same position, although the grad and vol are not in the same coordinate system (figure 2). And importantly, shouldn't the dipole be in the right hemisphere anyway with the coordinates 5/2/3? I appended the code below.

Could the different coordinate systems lead to the inconsistent results of dipolefitting and beamforming? Will the dipolesimulation be in the same coordinate system as the volume or gradiometer structure I feed in (CTF space, in my case)? How could I use the dipolesimulation, dipolefitting and beamforming to properly check my headmodels?

I tried so many things now but I couldn't find the error. Any help is very appreciated.

Best,
Kathrin



These are the variables I used:

vol = headmodel of individual subject in CTF space (cm)
data.grad = gradiometer structure of individual subject in CTF space (cm)
mnigrid = grid of individual subject in CTF space (cm)
template_grid = grid of template brain in SPM space (cm)
mri = spm8 template brain in SMP space


%% compute forward simulated data + apply diplole fit
cfg     = [];
cfg.vol = vol;
cfg.grad = data.grad;
cfg.channel = 'MEG';
cfg.dip.pos = [5 2 3]; % pos of dipole in cm
cfg.dip.mom = [1 0 0]';
cfg.dip.frequency = 10;
cfg.ntrials = 20;
cfg.relnoise = 10;
raw = ft_dipolesimulation(cfg);
 
% compute the data covariance matrix, which will capture the activity of
% the simulated dipole
cfg = [];
cfg.covariance = 'yes';
avg = ft_timelockanalysis(cfg, raw);
 
% apply dipolefit
cfg = [];
cfg.vol = vol;
cfg.grad = data.grad;
cfg.dip.pos = [0 0 0];
cfg.gridsearch = 'no';
dip = ft_dipolefitting(cfg, avg);
 
cfg = [];
cfg.location = dip.dip.pos *10;
figure, ft_sourceplot(cfg,mri)

 
% do the beamformer source reconstuction on a 1 cm grid
cfg = [];
cfg.channel = 'MEG';
cfg.vol = vol;
cfg.grad = data.grad;
cfg.grid  = mnigrid;
cfg.method = 'lcmv';
cfg.projectnoise = 'yes'; 
source = ft_sourceanalysis(cfg, avg);

% compute the neural activity index, i.e. projected power divided by
% projected noise
cfg = [];
cfg.powmethod = 'none'; % keep the power as estimated from the data covariance, i.e. the induced power
source = ft_sourcedescriptives(cfg, source);
 
interp = ft_sourceinterpolate([], source, mri);
 
cfg = [];
cfg.method = 'ortho';
cfg.interactive = 'yes';
cfg.funparameter = 'nai';
cfg.funcolorlim = [1.5 4];  % the voxel in the center of the volume conductor messes up the autoscaling
figure, ft_sourceplot(cfg, interp);
 






_____________________________________
Kathrin Müsch

Dept. of Neurophysiology and Pathophysiology
University Medical Center Hamburg-Eppendorf
Martinistr. 52
20246 Hamburg
Germany
Phone: +49-40-7410-54680
Fax: +49-40-7410-57752
E-Mail: k.muesch at uke.uni-hamburg.de
_____________________________________


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

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg

Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus 
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From smoratti at psi.ucm.es  Mon Mar 26 16:13:00 2012
From: smoratti at psi.ucm.es (Stephan Moratti)
Date: Mon, 26 Mar 2012 16:13:00 +0200
Subject: [FieldTrip] beamforming with rank deficient covariance matrix
In-Reply-To: <DUB113-W8242FDFA7507E17608A292B7450@phx.gbl>
References: <DUB113-W8242FDFA7507E17608A292B7450@phx.gbl>
Message-ID: <9BF0E297-D3D1-41F4-A2BF-D9940E50E51C@psi.ucm.es>

Dear Fred,

In case of reduced rank people usually do regularization specifying  a lambda value (cfg.lcmv.lambda ='5%').

Best,

Stephan

El 26/03/2012, a las 14:47, Frederic Roux escribió:

> 
> Dear all,
> 
> I have a question related to the rank of the covariance matrix
> used for the beamformer.
> 
> I preprocessed my data using ICA to reject EOG and ECG component (typically
> between 2-4 components). This however, leads to a reduction in the rank
> of the covariance matrix and I get a warning using ft_sourceanalysis
> saying that my covariance matrix is rank deficient because rank(COV) < Nchannels.
> 
> I would like to know, how much of a problem and how serious this can be.
> 
> The way I understand things, this should only cause trouble if the number
> of active sources exceeds the number of linearly independent rows of the covariance matrix?
> Is this assumption correct? 
> 
> Is there some step in the ft_sourceanalyis pipeline that assumes that the number of
> sources is equal to the number of channels, and that could bias the computation
> of the beamformer? I mean in that case I would have more sources than channels
> and thus the beamformer would fail.
> 
> Would be great if someone could help me to figure this out.
> 
> Cheers,
> Fred
> 
> 
> 
> 
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


________________________________________________________
Stephan Moratti, PhD

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

Universidad Complutense de Madrid
Facultad de Psicología
Departamento de Psicología Básica I
Campus de Somosaguas
28223 Pozuelo de Alarcón (Madrid)
Spain

and

Center for Biomedical Technology
Laboratory for Cognitive and Computational Neuroscience
Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)
Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982


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From jan.schoffelen at donders.ru.nl  Mon Mar 26 21:42:19 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Mon, 26 Mar 2012 21:42:19 +0200
Subject: [FieldTrip] Create BEM model for EEG source localisation
In-Reply-To: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>
References: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>
Message-ID: <29B44597-C214-468C-A291-ABCDEEA6E099@donders.ru.nl>

Hi Maria,

You could have a look at:

http://fieldtrip.fcdonders.nl/tutorial/headmodel

and

http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg

Hopefully this will give you some inspiration.

Best,

Jan-Mathijs

On Mar 26, 2012, at 6:01 PM, Maria Pefkou wrote:

> Dear FieldTrip users,
> 
> I started using the toolbox fairly recently to analyse EEG data and I have huge trouble making a BEM model, which I need for source localisation.
> Following the online tutorial, I processed my subjects' individual structural MRIs in FreeSurfer and MNE and managed to prepare the triangulated mesh. However, my problem is the volume conduction model. I can get a singleshell one, using the ft_prepare_singleshell function, but as far as I understand it is excusively used for MEG data. I came to this conclusion because when I try to compute the forward model, given that I provide information about the electrodes position, I always get the following error: 
> 
> "unsupported volume conductor model for EEG".
> I guess this is because the vol.type is 'nolte' and there is no such case for EEG data, at least not in the ft_prepare_vol_sens.m function, which is automatically called.
> 
> I have tried to prepare a BEM model using the ft_prepare_headmodel function with cfg.method='bemcp' or cfg.method='dipoli' but I was unsuccessful.
> The problem is that, after having tried various functions/options, I lost the general picture and I'm running in circles... The question is: I have a segmented mri, how can I get a BEM model out of this? I must be missing a fundamental part of the procedure but I can't quite find out what it is.
> Any suggestions/help would be very much appreciated.
> 
> Thank you in advance,
> Maria Pefkou
> 
> ------------------------------------------
> Research Assistant
> Functional Brain Mapping Lab
> University of Geneva
> 
> _______________________________________________
> 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




From jan.schoffelen at donders.ru.nl  Mon Mar 26 21:52:11 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Mon, 26 Mar 2012 21:52:11 +0200
Subject: [FieldTrip] inconsistent results from dipolefitting and
	beamforming
In-Reply-To: <5D2500F2-F9AB-41B0-8BA1-25B18E08A5A5@uke.uni-hamburg.de>
References: <5D2500F2-F9AB-41B0-8BA1-25B18E08A5A5@uke.uni-hamburg.de>
Message-ID: <E931E86A-3F5A-4998-A098-3DC9091C72CF@donders.ru.nl>

Dear Kathrin,

Note that you cannot just mix geometrical objects which are defined in different coordinate systems within a simulation / source reconstruction.
The code cannot make the distinction about the coordinate systems, and assumes that all geometrical objects that go into a function are defined within the same coordinate system (i.e. x,y,z position mean the same in all objects). This also goes for the mri used for the interpolation. You should use an MRI volume that has a transformation matrix attached to it that transforms from voxel space into CTF coordinate system, rather than into MNI space. The result of a faulty interpolation would lead among others to the x and y axis being exchanged. I think you should look into this direction for a solution. 
By the way, (5,2,3) is indeed in the right hemisphere, but how it shows up on the screen depends on whether the anatomy is shown in radiological or neurological convention.

Best,

Jan-Mathijs

On Mar 26, 2012, at 6:45 PM, Kathrin Müsch wrote:

> Hi Fieldtrip users,
> 
> I am trying to apply a beamformer to simulated data to check whether my headmodels are correct. While ft_dipolefit localizes the dipole in the original position, the beamformer results in a source at a totally different position (see figure 1). I kept everything as similar as possible to the example scripts (forward simulation & dipole fit, forward simulation & beamformer) but used individual gradiometer positions, grid and volume of a single subject (CTF space) and plotted the source in a template grid (SPM space). If I run the dipolesimulation with the individual gradiometer structure and the template headmodel vol and template grid, the dipole and the source result in the same position, although the grad and vol are not in the same coordinate system (figure 2). And importantly, shouldn't the dipole be in the right hemisphere anyway with the coordinates 5/2/3? I appended the code below.
> 
> Could the different coordinate systems lead to the inconsistent results of dipolefitting and beamforming? Will the dipolesimulation be in the same coordinate system as the volume or gradiometer structure I feed in (CTF space, in my case)? How could I use the dipolesimulation, dipolefitting and beamforming to properly check my headmodels?
> 
> I tried so many things now but I couldn't find the error. Any help is very appreciated.
> 
> Best,
> Kathrin
> 
> 
> 
> These are the variables I used:
> 
> vol = headmodel of individual subject in CTF space (cm)
> data.grad = gradiometer structure of individual subject in CTF space (cm)
> mnigrid = grid of individual subject in CTF space (cm)
> template_grid = grid of template brain in SPM space (cm)
> mri = spm8 template brain in SMP space
> 
> 
> %% compute forward simulated data + apply diplole fit
> cfg     = [];
> cfg.vol = vol;
> cfg.grad = data.grad;
> cfg.channel = 'MEG';
> cfg.dip.pos = [5 2 3]; % pos of dipole in cm
> cfg.dip.mom = [1 0 0]';
> cfg.dip.frequency = 10;
> cfg.ntrials = 20;
> cfg.relnoise = 10;
> raw = ft_dipolesimulation(cfg);
>  
> % compute the data covariance matrix, which will capture the activity of
> % the simulated dipole
> cfg = [];
> cfg.covariance = 'yes';
> avg = ft_timelockanalysis(cfg, raw);
>  
> % apply dipolefit
> cfg = [];
> cfg.vol = vol;
> cfg.grad = data.grad;
> cfg.dip.pos = [0 0 0];
> cfg.gridsearch = 'no';
> dip = ft_dipolefitting(cfg, avg);
>  
> cfg = [];
> cfg.location = dip.dip.pos *10;
> figure, ft_sourceplot(cfg,mri)
> 
>  
> % do the beamformer source reconstuction on a 1 cm grid
> cfg = [];
> cfg.channel = 'MEG';
> cfg.vol = vol;
> cfg.grad = data.grad;
> cfg.grid  = mnigrid;
> cfg.method = 'lcmv';
> cfg.projectnoise = 'yes'; 
> source = ft_sourceanalysis(cfg, avg);
> 
> % compute the neural activity index, i.e. projected power divided by
> % projected noise
> cfg = [];
> cfg.powmethod = 'none'; % keep the power as estimated from the data covariance, i.e. the induced power
> source = ft_sourcedescriptives(cfg, source);
>  
> interp = ft_sourceinterpolate([], source, mri);
>  
> cfg = [];
> cfg.method = 'ortho';
> cfg.interactive = 'yes';
> cfg.funparameter = 'nai';
> cfg.funcolorlim = [1.5 4];  % the voxel in the center of the volume conductor messes up the autoscaling
> figure, ft_sourceplot(cfg, interp);
>  
> 
> <individual.png>
> 
> 
> <template.png>
> 
> 
> _____________________________________
> Kathrin Müsch
> 
> Dept. of Neurophysiology and Pathophysiology
> University Medical Center Hamburg-Eppendorf
> Martinistr. 52
> 20246 Hamburg
> Germany
> Phone: +49-40-7410-54680
> Fax: +49-40-7410-57752
> E-Mail: k.muesch at uke.uni-hamburg.de
> _____________________________________
> 
> 
> --
> Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):
> 
> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg
> 
> Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus
> _______________________________________________
> 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

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From wljj09 at gmail.com  Mon Mar 26 22:06:52 2012
From: wljj09 at gmail.com (Jing Wang)
Date: Mon, 26 Mar 2012 22:06:52 +0200
Subject: [FieldTrip] about ft_appendspike
Message-ID: <CABKH8xZdF2QZsL_WXR2iiSw8GjYnjMBLvaeJ5bmD5n=X9Dh7Xw@mail.gmail.com>

Dear fieldtrip developers and users,

I am trying to append spikes to local field potential with ft_appendspike.

The local field potential data have five channels, but the spikes data have
12 channels. They have some trials. According to the ft_appenddata, the
channels will be concatenated within each trial when the input datasets
have different channels.

However, my purpose is to append the first 2 channel of spike data on the
first channel of local field potential data. And to append the third
channel of spike data on the second channel of local field potential data,
and so on. How can I do with ft_appendspike?

Thank you very much! I am grateful for all the help!

Jing
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From lavado at gmail.com  Tue Mar 27 11:19:12 2012
From: lavado at gmail.com (Ion Lavado)
Date: Tue, 27 Mar 2012 11:19:12 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band, concept problem
Message-ID: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>

Hello, i'm having problems trying the beamformer analysis with a frequency
band of interest. I would like to have for example an interval like [8 14]
Hz. My concept problem is about the cfg.frequency and
cfg.tapsmofrq  values. (it must be a escalar, but i want a frequency band).

%FREQ ANALYSIS
cfg = [];
cfg.method    = 'mtmfft';
cfg.output    = 'powandcsd';
cfg.tapsmofrq = 5;
cfg.foilim    = [8 14];
freq_words_alpha = ft_freqanalysis(cfg, words);


%SOURCE ANALYSIS
cfg              = [];
cfg.frequency    = 11;
cfg.lambda=0;
cfg.method       = 'dics';
cfg.coordsys       = 'neuromag';
cfg.projectnoise = 'yes';
cfg.grad            =  freq_words_alpha.grad;
cfg.channel   = {'MEG'};
cfg.grid         = grid;
cfg.reducerank      = 2;
cfg.vol          = vol02;
vol02=ft_convert_units(vol02,'cm');
source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );


I use a cfg.frequency of 11 but i don't have really clear what i'm doing as
a get the same result using cfg.frequency=11 but a freqanalysis in [10 12].
I would be very grateful if someone could solve my doubt.

Best wishes,

Mikel
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From fredericroux at hotmail.de  Tue Mar 27 12:14:45 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Tue, 27 Mar 2012 12:14:45 +0200
Subject: [FieldTrip] question to the fieldtrip developers - multiple spm
 versions in fieldtrip
Message-ID: <DUB113-W12B64F64480B0A75AB493EB74A0@phx.gbl>



Dear all,

I would like to ask again if the fact of getting a warning
that different spm versions will confuse fieldtrip
can have consequences in the ft_sourceanalysis pipeline.

I am using version 2012-01-05 which has SPM2 and SPM8
in the external folder.

It would be great if someone from the development-team could tell me

a) why this is a problem
b) how to circumvent it


I renamed the spm.m file into spm.m.bak in the SPM2 folder so that
only the spm.m file from the SPM8 folder is used. However, it would
be great if someone could tell me if this is a workaround or not.


Best regards,
Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From smoratti at psi.ucm.es  Tue Mar 27 12:38:19 2012
From: smoratti at psi.ucm.es (Stephan Moratti)
Date: Tue, 27 Mar 2012 12:38:19 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band,
	concept problem
In-Reply-To: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
References: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
Message-ID: <EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>

Dear Mikel,

I understand that you should do a mtmfft with a center frequency of interest (in your case cfg.foil = [11 11]) and then you do a frequency smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you need a time window big enough to allow such a smoothing. The CSD should represent a frequency window of 8 to 14 Hz then. Then you put the result of the mtmfft into the dics beamformer.

Best,

Stephan
 
El 27/03/2012, a las 11:19, Ion Lavado escribió:

> Hello, i'm having problems trying the beamformer analysis with a frequency band of interest. I would like to have for example an interval like [8 14] Hz. My concept problem is about the cfg.frequency and cfg.tapsmofrq  values. (it must be a escalar, but i want a frequency band). 
> 
> %FREQ ANALYSIS
> cfg = [];
> cfg.method    = 'mtmfft';
> cfg.output    = 'powandcsd';
> cfg.tapsmofrq = 5;
> cfg.foilim    = [8 14];
> freq_words_alpha = ft_freqanalysis(cfg, words);
> 
> 
> %SOURCE ANALYSIS
> cfg              = []; 
> cfg.frequency    = 11;  
> cfg.lambda=0;
> cfg.method       = 'dics';
> cfg.coordsys       = 'neuromag';
> cfg.projectnoise = 'yes';
> cfg.grad            =  freq_words_alpha.grad;
> cfg.channel   = {'MEG'}; 
> cfg.grid         = grid; 
> cfg.reducerank      = 2;
> cfg.vol          = vol02;
> vol02=ft_convert_units(vol02,'cm');
> source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
> 
> 
> I use a cfg.frequency of 11 but i don't have really clear what i'm doing as a get the same result using cfg.frequency=11 but a freqanalysis in [10 12]. I would be very grateful if someone could solve my doubt.
> 
> Best wishes,
> 
> Mikel
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


________________________________________________________
Stephan Moratti, PhD

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

Universidad Complutense de Madrid
Facultad de Psicología
Departamento de Psicología Básica I
Campus de Somosaguas
28223 Pozuelo de Alarcón (Madrid)
Spain

and

Center for Biomedical Technology
Laboratory for Cognitive and Computational Neuroscience
Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)
Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982


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From lavado at gmail.com  Tue Mar 27 12:46:35 2012
From: lavado at gmail.com (Ion Lavado)
Date: Tue, 27 Mar 2012 12:46:35 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band,
	concept problem
In-Reply-To: <EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>
References: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
	<EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>
Message-ID: <CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>

Thank you Stephan, just one thing, why i need a time window big enough? so
i'm just studying the frequency.

Best,

Mikel

2012/3/27 Stephan Moratti <smoratti at psi.ucm.es>

> Dear Mikel,
>
> I understand that you should do a mtmfft with a center frequency of
> interest (in your case cfg.foil = [11 11]) and then you do a frequency
> smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you need a time window big
> enough to allow such a smoothing. The CSD should represent a frequency
> window of 8 to 14 Hz then. Then you put the result of the mtmfft into the
> dics beamformer.
>
> Best,
>
> Stephan
>
> El 27/03/2012, a las 11:19, Ion Lavado escribió:
>
> Hello, i'm having problems trying the beamformer analysis with a frequency
> band of interest. I would like to have for example an interval like [8 14]
> Hz. My concept problem is about the cfg.frequency and
> cfg.tapsmofrq  values. (it must be a escalar, but i want a frequency band).
>
> %FREQ ANALYSIS
> cfg = [];
> cfg.method    = 'mtmfft';
> cfg.output    = 'powandcsd';
> cfg.tapsmofrq = 5;
> cfg.foilim    = [8 14];
> freq_words_alpha = ft_freqanalysis(cfg, words);
>
>
> %SOURCE ANALYSIS
> cfg              = [];
> cfg.frequency    = 11;
> cfg.lambda=0;
> cfg.method       = 'dics';
> cfg.coordsys       = 'neuromag';
> cfg.projectnoise = 'yes';
> cfg.grad            =  freq_words_alpha.grad;
> cfg.channel   = {'MEG'};
> cfg.grid         = grid;
> cfg.reducerank      = 2;
> cfg.vol          = vol02;
> vol02=ft_convert_units(vol02,'cm');
> source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
>
>
> I use a cfg.frequency of 11 but i don't have really clear what i'm doing
> as a get the same result using cfg.frequency=11 but a freqanalysis in [10
> 12]. I would be very grateful if someone could solve my doubt.
>
> Best wishes,
>
> Mikel
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> ________________________________________________________
> Stephan Moratti, PhD
>
> see also: http://web.me.com/smoratti/
>
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
> and
>
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
>
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
>
>
>
> _______________________________________________
> 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 Mar 27 13:14:56 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 27 Mar 2012 13:14:56 +0200
Subject: [FieldTrip] SPM path and sourceanalysis on template brain
In-Reply-To: <DUB113-W76F2D058B3132334525D94B7450@phx.gbl>
References: <DUB113-W76F2D058B3132334525D94B7450@phx.gbl>
Message-ID: <4F71A130.7070705@donders.ru.nl>

Dear Frederic,

I meant to send this mail already yesterday - but at least you cleared 
up the issue I had with your first mail ;)
Original mail:

Although you forgot to actually paste the error message into the mail 
you sent, I assume that you get a warning that mentions something like 
"Multiple occurences of SPM have been found on your path". If this is 
the error, you are using 
addpath(genpath('WhereeverFieldTripIsStoredOnYourMachine')), but should 
just do addpath('WhereeverFieldTripIsStoredOnYourMachine') and then call 
ft_defaults. Otherwise, your source reconstruction might be a result of 
different version of SPM, which might lead to faulty behaviour, because 
functions of different versions are not designed to be compatible with 
each other.

Best,
Jörn

On 3/26/2012 12:23 PM, Frederic Roux wrote:
> Dear all,
>
>
> I am getting the following error message with the fieldtrip-20120105 
> version,
> and wanted to ask if anyone could tell me:
>
> a) how to prevent it
> b) what the consequences of ignoring it will be.
>
> Also I wanted to get some feedback on the possibility of
> using a template brain for source localization on data for which
> MRI data is missing.
>
> I have a recorded MEG data from n = 98 participants but only have
> the MRs of 70 of them. Can I use a template MR to perform
> source analysis on the missing data sets?
>
> Looking forward to any kind of suggestions.
> Have a nice day,
>
> Fred
>
>
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
>
>
>
>
> _______________________________________________
> 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

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 Jarmo.Kontinen at ruhr-uni-bochum.de  Tue Mar 27 13:24:43 2012
From: Jarmo.Kontinen at ruhr-uni-bochum.de (Jarmo Kontinen)
Date: Tue, 27 Mar 2012 13:24:43 +0200 (CEST)
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
In-Reply-To: <1332764087.47250.YahooMailNeo@web132103.mail.ird.yahoo.com>
Message-ID: <permail-201203271124436509e8c7000033ba-Jarmo.Kontinen@msgid.mail.ruhr-uni-bochum.de>


Dear Ivano,
I had some problem with email, so if I am replying to you twice, I apologize.

 I was maybe a  bit unclear maybe in my first post. My files already contain
 averaged data.
Problem is to get the right data-structure to use the existing FT-functions to
do analysis on the data.

Best,
Jarmo

Ivano Triggiani schrieb am 2012-03-26:
> Dear Jarmo,

> Filedtrip needs a definition of segments of interest. For example
> reading a trigger channel or something else to cut the EEG recording
> into trials. If I have understood what you want to do is to get an
> average of general EEG (for example resting state EEG closed eyes).
> But you have to indicate which average you want to obtain, for
> example you can tell fieldtrip to divide EEG into epochs of 3 seconds
> and then to make an average of all of them.
> What you wrote is the request of an average, but you are not
> specifing of what.
> Fof example you can write a trial function that provides a trl
> matrix, i.e.:
> 0 3 0

> 3 6 0
> 6 9 0
> 9 12 0
> 12 13 0
> ...

> where first column is the start sample in seconds (you have to
> multiply it for sample rate), the second column is the end sample and
> the third is the offset (in this case is always zero), or look at
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#use_your_own_function_for_trial_selection

> best wishes,
> Ivano



> ------------------------------------------------------------------------




> "No man can wear one face to himself
> and another to the multitude,
> without finally getting bewildered
> as to which one is true."


> Nathaniel Hawthorne


> ________________________________
>  Da: "fieldtrip-request at donders.ru.nl"
>  <fieldtrip-request at donders.ru.nl>
> A: fieldtrip at donders.ru.nl
> Inviato: Lunedì 26 Marzo 2012 12:00
> Oggetto: fieldtrip Digest, Vol 16, Issue 33

> Send fieldtrip mailing list submissions to
>     fieldtrip at donders.ru.nl

> To subscribe or unsubscribe via the World Wide Web, visit
>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>     fieldtrip-request at donders.ru.nl

> You can reach the person managing the list at
>     fieldtrip-owner at donders.ru.nl

> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."


> Today's Topics:

>    1. Re: Problem with FT_DEFINETRIAL (Stephen Politzer-Ahles)


> ----------------------------------------------------------------------

> Message: 1
> Date: Sun, 25 Mar 2012 12:11:28 +0200
> From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL
> Message-ID:
>    
> <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"

> Hello Jarmo,

> I haven't tried importing Brain Vision files into FieldTrip myself,
> but
> based on the code you sent it looks like the problem may be that
> you're
> missing cfg.trialdef.eventvalue (which is used to tell FieldTrip
> which
> triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim
> . See
> the example at
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials.

> If what you are trying to do is import all trials from all triggers
> in the
> file, I think you have to define your own "trialfun" function to do
> that
> (although I haven't tried this myself so I'm not sure).
> http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
> information.

> Best,
> Steve Politzer-Ahles
> University of Kansas


> Message: 1
> > Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> > From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> > To: <fieldtrip at donders.ru.nl>
> > Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> > Message-ID:
> >        <
> > permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de


> > Content-Type: text/plain; charset=us-ascii

> > Dear all,
> > I am trying to import EEG subject averages into Field Trip. The
> > files are
> > exported with the Brainvision Analyzer in binary form
> > :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> > I have a problem with turning the data into the Field Trip
> > data-structure.
> > I
> > am following instructions given on this forum on one similar post.
> > What I
> > have
> > tried is the following:

> > cfg=[];
> > cfg.trialdef.eventtype='average'
> > cfg.dataset='subject10_konPro2002.dat'

> >  cfg=ft_definetrial(cfg);

> > Warning: no trialfun was specified, using trialfun_general
> > > In ft_definetrial at 123
> > evaluating trialfunction 'trialfun_general'
> > reading the events from 'subject10_konPro2002.vhdr'
> > ??? Error using ==> ft_definetrial at 176
> > no trials were defined, see FT_DEFINETRIAL for help

> > I am grateful for all the help.
> > Thanks,
> > Jarmo Kontinen

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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 16, Issue 33
> *****************************************



From jm.horschig at donders.ru.nl  Tue Mar 27 13:27:27 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 27 Mar 2012 13:27:27 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band,
	concept problem
In-Reply-To: <CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>
References: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
	<EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>
	<CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>
Message-ID: <4F71A41F.4080807@donders.ru.nl>

Hi Ion,

A frequency is by definition at least a peak and a trough(up flank and 
down flank), making it one cycle (think of sinusoid here). Thus, you 
could say that one needs at least one cycle of a certain frequency such 
that it is eligible to talk about a 'frequency'. Just in case you don't 
know it already, you might want to look things up as Rayleigh frequency, 
Nyquist frequency, and I would suggest that you read (or start reading) 
the digitial signal processing book: http://www.dspguide.com/

Note that a true oscillation is usually considered to last at least 
three cycles (of course, opinions differ her - I go with four). The 
length of the window of interest reflects the number of cycles that can 
be estimated. For source reconstruction, make sure cfg.toilim is as long 
as the number of cycles you want to estimate, e.g. when using cfg.foi = 
10, then cfg.toilim(2)-cfg.toilim(1) should be at least 400ms when you 
want an estimate of 4 cycles.

Hope it helps!
Best,
Jörn



On 3/27/2012 12:46 PM, Ion Lavado wrote:
> Thank you Stephan, just one thing, why i need a time window big 
> enough? so i'm just studying the frequency.
>
> Best,
>
> Mikel
>
> 2012/3/27 Stephan Moratti <smoratti at psi.ucm.es 
> <mailto:smoratti at psi.ucm.es>>
>
>     Dear Mikel,
>
>     I understand that you should do a mtmfft with a center frequency
>     of interest (in your case cfg.foil = [11 11]) and then you do a
>     frequency smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you
>     need a time window big enough to allow such a smoothing. The CSD
>     should represent a frequency window of 8 to 14 Hz then. Then you
>     put the result of the mtmfft into the dics beamformer.
>
>     Best,
>
>     Stephan
>
>     El 27/03/2012, a las 11:19, Ion Lavado escribió:
>
>>     Hello, i'm having problems trying the beamformer analysis with a
>>     frequency band of interest. I would like to have for example an
>>     interval like [8 14] Hz. My concept problem is about the
>>     cfg.frequency and cfg.tapsmofrq  values. (it must be a escalar,
>>     but i want a frequency band).
>>
>>     %FREQ ANALYSIS
>>     cfg = [];
>>     cfg.method    = 'mtmfft';
>>     cfg.output    = 'powandcsd';
>>     cfg.tapsmofrq = 5;
>>     cfg.foilim    = [8 14];
>>     freq_words_alpha = ft_freqanalysis(cfg, words);
>>
>>
>>     %SOURCE ANALYSIS
>>     cfg              = [];
>>     cfg.frequency    = 11;
>>     cfg.lambda=0;
>>     cfg.method       = 'dics';
>>     cfg.coordsys       = 'neuromag';
>>     cfg.projectnoise = 'yes';
>>     cfg.grad            =  freq_words_alpha.grad;
>>     cfg.channel   = {'MEG'};
>>     cfg.grid         = grid;
>>     cfg.reducerank      = 2;
>>     cfg.vol          = vol02;
>>     vol02=ft_convert_units(vol02,'cm');
>>     source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
>>
>>
>>     I use a cfg.frequency of 11 but i don't have really clear what
>>     i'm doing as a get the same result using cfg.frequency=11 but a
>>     freqanalysis in [10 12]. I would be very grateful if someone
>>     could solve my doubt.
>>
>>     Best wishes,
>>
>>     Mikel
>>     _______________________________________________
>>     fieldtrip mailing list
>>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>     ________________________________________________________
>     Stephan Moratti, PhD
>
>     see also: http://web.me.com/smoratti/
>
>     Universidad Complutense de Madrid
>     Facultad de Psicología
>     Departamento de Psicología Básica I
>     Campus de Somosaguas
>     28223 Pozuelo de Alarcón (Madrid)
>     Spain
>
>     and
>
>     Center for Biomedical Technology
>     Laboratory for Cognitive and Computational Neuroscience
>     Parque Científico y Tecnológico de la Universidad Politecnica de
>     Madrid
>     Campus Montegancedo
>     28223 Pozuelo de Alarcón (Madrid)
>     Spain
>
>
>     email: smoratti at psi.ucm.es <mailto:smoratti at psi.ucm.es>
>     Tel.: +34 679219982 <tel:%2B34%20679219982>
>
>
>
>     _______________________________________________
>     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

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 Ulrich.Pomper at charite.de  Tue Mar 27 15:00:32 2012
From: Ulrich.Pomper at charite.de (Pomper, Ulrich)
Date: Tue, 27 Mar 2012 15:00:32 +0200
Subject: [FieldTrip] one-sample cluster test
Message-ID: <4F71B9F0.8080106@charite.de>

Dear list members,

this topic was discussed some time in 2008, but it seems to me no 
conclusion was found.

I would like to find source activity that differs significantly from 
zero. I could run a one sample t-test for every voxel and end up having 
a huge MC problem, or (preferably) use some kind of cluster based 
permutation statistics. However, the option for a one sample cluster 
test is not implemented in FT.

Would it be correct to test the data from my experimental condition 
against a set of data containing all zeros using a cluster based 
permutation test?

Any help is very much appreciated!
Best, Ulrich



From mark.noordenbos at gmail.com  Tue Mar 27 15:35:00 2012
From: mark.noordenbos at gmail.com (Mark Noordenbos)
Date: Tue, 27 Mar 2012 15:35:00 +0200
Subject: [FieldTrip] one-sample cluster test
Message-ID: <CAJSb8nMMcxO0xxW8+6z1rAswYReKKPxq+3Rc0Htaz-dyoXELJA@mail.gmail.com>

Hi Ulrich,

There is a function 'statfun_actvsblT' to test your activity against the
baseline. However, this function only accepts input with dimord
'chan_freq_time'.
Maybe, you can create your own function based on 'statfun_actvsblT' to test
the activity against zero.

Kind regards,
Mark

Op 27 maart 2012 15:00 schreef <fieldtrip-request at donders.ru.nl> het
volgende:

> Send fieldtrip mailing list submissions to
>        fieldtrip at donders.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>        fieldtrip-request at donders.ru.nl
>
> You can reach the person managing the list at
>        fieldtrip-owner at donders.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>   1. Re: Problem with FT_DEFINETRIAL (Jarmo Kontinen)
>   2. Re: Beamforming analysis in frequency band,       concept problem
>      (J?rn M. Horschig)
>   3. one-sample cluster test (Pomper, Ulrich)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 27 Mar 2012 13:24:43 +0200 (CEST)
> From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> To: Ivano Triggiani <ivano_triggiani at yahoo.it>, Email discussion list
>        for the FieldTrip project <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL
> Message-ID:
>        <
> permail-201203271124436509e8c7000033ba-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de
> >
>
> Content-Type: text/plain; charset=iso-8859-1
>
>
> Dear Ivano,
> I had some problem with email, so if I am replying to you twice, I
> apologize.
>
>  I was maybe a  bit unclear maybe in my first post. My files already
> contain
>  averaged data.
> Problem is to get the right data-structure to use the existing
> FT-functions to
> do analysis on the data.
>
> Best,
> Jarmo
>
> Ivano Triggiani schrieb am 2012-03-26:
> > Dear Jarmo,
>
> > Filedtrip needs a definition of segments of interest. For example
> > reading a trigger channel or something else to cut the EEG recording
> > into trials. If I have understood what you want to do is to get an
> > average of general EEG (for example resting state EEG closed eyes).
> > But you have to indicate which average you want to obtain, for
> > example you can tell fieldtrip to divide EEG into epochs of 3 seconds
> > and then to make an average of all of them.
> > What you wrote is the request of an average, but you are not
> > specifing of what.
> > Fof example you can write a trial function that provides a trl
> > matrix, i.e.:
> > 0 3 0
>
> > 3 6 0
> > 6 9 0
> > 9 12 0
> > 12 13 0
> > ...
>
> > where first column is the start sample in seconds (you have to
> > multiply it for sample rate), the second column is the end sample and
> > the third is the offset (in this case is always zero), or look at
> >
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#use_your_own_function_for_trial_selection
>
> > best wishes,
> > Ivano
>
>
>
> > ------------------------------------------------------------------------
>
>
>
>
> > "No man can wear one face to himself
> > and another to the multitude,
> > without finally getting bewildered
> > as to which one is true."
>
>
> > Nathaniel Hawthorne
>
>
> > ________________________________
> >  Da: "fieldtrip-request at donders.ru.nl"
> >  <fieldtrip-request at donders.ru.nl>
> > A: fieldtrip at donders.ru.nl
> > Inviato: Luned? 26 Marzo 2012 12:00
> > Oggetto: fieldtrip Digest, Vol 16, Issue 33
>
> > Send fieldtrip mailing list submissions to
> > ??? fieldtrip at donders.ru.nl
>
> > To subscribe or unsubscribe via the World Wide Web, visit
> > ??? http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > ??? fieldtrip-request at donders.ru.nl
>
> > You can reach the person managing the list at
> > ??? fieldtrip-owner at donders.ru.nl
>
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
>
>
> > Today's Topics:
>
> > ?  1. Re: Problem with FT_DEFINETRIAL (Stephen Politzer-Ahles)
>
>
> > ----------------------------------------------------------------------
>
> > Message: 1
> > Date: Sun, 25 Mar 2012 12:11:28 +0200
> > From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> > To: fieldtrip at donders.ru.nl
> > Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL
> > Message-ID:
> > ???
> > <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
>
> > Hello Jarmo,
>
> > I haven't tried importing Brain Vision files into FieldTrip myself,
> > but
> > based on the code you sent it looks like the problem may be that
> > you're
> > missing cfg.trialdef.eventvalue (which is used to tell FieldTrip
> > which
> > triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim
> > . See
> > the example at
> >
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials
> .
>
> > If what you are trying to do is import all trials from all triggers
> > in the
> > file, I think you have to define your own "trialfun" function to do
> > that
> > (although I haven't tried this myself so I'm not sure).
> > http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
> > information.
>
> > Best,
> > Steve Politzer-Ahles
> > University of Kansas
>
>
> > Message: 1
> > > Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> > > From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> > > To: <fieldtrip at donders.ru.nl>
> > > Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> > > Message-ID:
> > >? ? ? ? <
> > >
> permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de
>
>
> > > Content-Type: text/plain; charset=us-ascii
>
> > > Dear all,
> > > I am trying to import EEG subject averages into Field Trip. The
> > > files are
> > > exported with the Brainvision Analyzer in binary form
> > > :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> > > I have a problem with turning the data into the Field Trip
> > > data-structure.
> > > I
> > > am following instructions given on this forum on one similar post.
> > > What I
> > > have
> > > tried is the following:
>
> > > cfg=[];
> > > cfg.trialdef.eventtype='average'
> > > cfg.dataset='subject10_konPro2002.dat'
>
> > >? cfg=ft_definetrial(cfg);
>
> > > Warning: no trialfun was specified, using trialfun_general
> > > > In ft_definetrial at 123
> > > evaluating trialfunction 'trialfun_general'
> > > reading the events from 'subject10_konPro2002.vhdr'
> > > ??? Error using ==> ft_definetrial at 176
> > > no trials were defined, see FT_DEFINETRIAL for help
>
> > > I am grateful for all the help.
> > > Thanks,
> > > Jarmo Kontinen
>
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >  <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120325/df4ce70a/attachment-0001.html
> >
>
> > ------------------------------
>
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> > End of fieldtrip Digest, Vol 16, Issue 33
> > *****************************************
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 27 Mar 2012 13:27:27 +0200
> From: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> To: fieldtrip at donders.ru.nl
> Subject: Re: [FieldTrip] Beamforming analysis in frequency band,
>        concept problem
> Message-ID: <4F71A41F.4080807 at donders.ru.nl>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Ion,
>
> A frequency is by definition at least a peak and a trough(up flank and
> down flank), making it one cycle (think of sinusoid here). Thus, you
> could say that one needs at least one cycle of a certain frequency such
> that it is eligible to talk about a 'frequency'. Just in case you don't
> know it already, you might want to look things up as Rayleigh frequency,
> Nyquist frequency, and I would suggest that you read (or start reading)
> the digitial signal processing book: http://www.dspguide.com/
>
> Note that a true oscillation is usually considered to last at least
> three cycles (of course, opinions differ her - I go with four). The
> length of the window of interest reflects the number of cycles that can
> be estimated. For source reconstruction, make sure cfg.toilim is as long
> as the number of cycles you want to estimate, e.g. when using cfg.foi =
> 10, then cfg.toilim(2)-cfg.toilim(1) should be at least 400ms when you
> want an estimate of 4 cycles.
>
> Hope it helps!
> Best,
> J?rn
>
>
>
> On 3/27/2012 12:46 PM, Ion Lavado wrote:
> > Thank you Stephan, just one thing, why i need a time window big
> > enough? so i'm just studying the frequency.
> >
> > Best,
> >
> > Mikel
> >
> > 2012/3/27 Stephan Moratti <smoratti at psi.ucm.es
> > <mailto:smoratti at psi.ucm.es>>
> >
> >     Dear Mikel,
> >
> >     I understand that you should do a mtmfft with a center frequency
> >     of interest (in your case cfg.foil = [11 11]) and then you do a
> >     frequency smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you
> >     need a time window big enough to allow such a smoothing. The CSD
> >     should represent a frequency window of 8 to 14 Hz then. Then you
> >     put the result of the mtmfft into the dics beamformer.
> >
> >     Best,
> >
> >     Stephan
> >
> >     El 27/03/2012, a las 11:19, Ion Lavado escribi?:
> >
> >>     Hello, i'm having problems trying the beamformer analysis with a
> >>     frequency band of interest. I would like to have for example an
> >>     interval like [8 14] Hz. My concept problem is about the
> >>     cfg.frequency and cfg.tapsmofrq  values. (it must be a escalar,
> >>     but i want a frequency band).
> >>
> >>     %FREQ ANALYSIS
> >>     cfg = [];
> >>     cfg.method    = 'mtmfft';
> >>     cfg.output    = 'powandcsd';
> >>     cfg.tapsmofrq = 5;
> >>     cfg.foilim    = [8 14];
> >>     freq_words_alpha = ft_freqanalysis(cfg, words);
> >>
> >>
> >>     %SOURCE ANALYSIS
> >>     cfg              = [];
> >>     cfg.frequency    = 11;
> >>     cfg.lambda=0;
> >>     cfg.method       = 'dics';
> >>     cfg.coordsys       = 'neuromag';
> >>     cfg.projectnoise = 'yes';
> >>     cfg.grad            =  freq_words_alpha.grad;
> >>     cfg.channel   = {'MEG'};
> >>     cfg.grid         = grid;
> >>     cfg.reducerank      = 2;
> >>     cfg.vol          = vol02;
> >>     vol02=ft_convert_units(vol02,'cm');
> >>     source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
> >>
> >>
> >>     I use a cfg.frequency of 11 but i don't have really clear what
> >>     i'm doing as a get the same result using cfg.frequency=11 but a
> >>     freqanalysis in [10 12]. I would be very grateful if someone
> >>     could solve my doubt.
> >>
> >>     Best wishes,
> >>
> >>     Mikel
> >>     _______________________________________________
> >>     fieldtrip mailing list
> >>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
> >>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
> >     ________________________________________________________
> >     Stephan Moratti, PhD
> >
> >     see also: http://web.me.com/smoratti/
> >
> >     Universidad Complutense de Madrid
> >     Facultad de Psicolog?a
> >     Departamento de Psicolog?a B?sica I
> >     Campus de Somosaguas
> >     28223 Pozuelo de Alarc?n (Madrid)
> >     Spain
> >
> >     and
> >
> >     Center for Biomedical Technology
> >     Laboratory for Cognitive and Computational Neuroscience
> >     Parque Cient?fico y Tecnol?gico de la Universidad Politecnica de
> >     Madrid
> >     Campus Montegancedo
> >     28223 Pozuelo de Alarc?n (Madrid)
> >     Spain
> >
> >
> >     email: smoratti at psi.ucm.es <mailto:smoratti at psi.ucm.es>
> >     Tel.: +34 679219982 <tel:%2B34%20679219982>
> >
> >
> >
> >     _______________________________________________
> >     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
>
>
> --
> J?rn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
>
> 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
>
> -------------- next part --------------
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> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120327/6c8a4090/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 3
> Date: Tue, 27 Mar 2012 15:00:32 +0200
> From: "Pomper, Ulrich" <Ulrich.Pomper at charite.de>
> To: Email discussion list for the FieldTrip project
>        <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] one-sample cluster test
> Message-ID: <4F71B9F0.8080106 at charite.de>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear list members,
>
> this topic was discussed some time in 2008, but it seems to me no
> conclusion was found.
>
> I would like to find source activity that differs significantly from
> zero. I could run a one sample t-test for every voxel and end up having
> a huge MC problem, or (preferably) use some kind of cluster based
> permutation statistics. However, the option for a one sample cluster
> test is not implemented in FT.
>
> Would it be correct to test the data from my experimental condition
> against a set of data containing all zeros using a cluster based
> permutation test?
>
> Any help is very much appreciated!
> Best, Ulrich
>
>
>
> ------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> End of fieldtrip Digest, Vol 16, Issue 39
> *****************************************
>
>
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From jm.horschig at donders.ru.nl  Tue Mar 27 15:48:07 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 27 Mar 2012 15:48:07 +0200
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <4F71B9F0.8080106@charite.de>
References: <4F71B9F0.8080106@charite.de>
Message-ID: <4F71C517.9010906@donders.ru.nl>

Dear Ulrich,


First of all, you might want to use the Neural Activity Index (NAI), as 
also described in the tutorial:
http://fieldtrip.fcdonders.nl/tutorial/beamformer#source_analysiswithout_contrasting_condition

Then, to answer your question, I am tempted to say that this would be an 
invalid approach when dealing with power, so in frequency-space. Power 
obviously has a lower bound, so that the average of any random 
collection of power values will never be 0. Though, what you are 
suggesting is the same as a regular t-test, isn't it?
In case you are dealing e.g. with am LCMV beamformer, I am not quite 
sure, but the null-hypothesis you suggested (amplitude==0)  sounds fair.

In any case, building a surrogate distribution same mean and variance 
than your data might be a better way to deal with your problem. That 
should be easily doable in Matlab without any need to implement this in 
FieldTrip. And note that the MC problem is always present, but a 
cluster-based correction (similar to Bonferroni, but correcting by the 
number of voxels in the cluster not by the number of all voxels) sounds 
legitimate to me. Afair, that's how it's done in FT.

Best,
Jörn




On 3/27/2012 3:00 PM, Pomper, Ulrich wrote:
> Dear list members,
>
> this topic was discussed some time in 2008, but it seems to me no
> conclusion was found.
>
> I would like to find source activity that differs significantly from
> zero. I could run a one sample t-test for every voxel and end up having
> a huge MC problem, or (preferably) use some kind of cluster based
> permutation statistics. However, the option for a one sample cluster
> test is not implemented in FT.
>
> Would it be correct to test the data from my experimental condition
> against a set of data containing all zeros using a cluster based
> permutation test?
>
> Any help is very much appreciated!
> Best, Ulrich
>
> _______________________________________________
> 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

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 tessa.vanleeuwen at fcdonders.ru.nl  Tue Mar 27 18:27:25 2012
From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen)
Date: Tue, 27 Mar 2012 18:27:25 +0200 (CEST)
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <189719464.70211.1332863376495.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <1710162166.70656.1332865645305.JavaMail.root@draco.zimbra.ru.nl>

Dear Fieldtrip experts,

I have noticed enhanced coherence (sensor level) in my data after applying ICA during preprocessing, removing only 1 EOG component. Of course the (mainly quantitatively) enhanced coherence could be due to the removal of (artifact induced) noise from the data. But this increase also occured when applying ICA to previously cleaned data, implying changes induced by ICA somehow affect coherence.

One of the aims of our project is to compute coherence/connectivity measures at the source level. Since connectivity measures are often difficult to interpret as they are, I would like to ask whether anyone has experience with connectivity analyses after preprocessing that involved ICA. Are people aware of possible influences of ICA on connectivity measures and is there a way to deal with this? Or would it be advisable NOT to use ICA when later looking at coherence/connectivity at the source level? 

We initially aim to compare across conditions (data that have been preprocessed together and from which the same ICA component has been removed). But we also have different experimental groups for which we would like to qualitatively compare active networks during our task.

Thank you in advance for any input, it is highly appreciated.

Best wishes,
Tessa


---

Tessa van Leeuwen, PhD
postdoctoral researcher

Department of Neurophysiology
Max Planck Institute for Brain Research


From toncho11 at gmail.com  Tue Mar 27 19:13:18 2012
From: toncho11 at gmail.com (Anton Andreev)
Date: Tue, 27 Mar 2012 19:13:18 +0200
Subject: [FieldTrip] Time stamp per sample
Message-ID: <CAG3TGCN+1ZV7zaAbGKvm8j3M1arg8pQXRgrfSLaof2hVp7G-vg@mail.gmail.com>

Hi,

I have a question about the fieldtrip buffer.
Does the protocol provides information about the time every sample has been
taken?

I would like to produce a chunk of data for 300ms or 1 second for example.
I can build such chunk if I simply sort out samples that are in the time
range of 1 second starting with the time stamp of the first one. Then again
for 1 second and ....

Thanks,
Anton
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From eelke.spaak at donders.ru.nl  Tue Mar 27 20:20:28 2012
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Tue, 27 Mar 2012 20:20:28 +0200
Subject: [FieldTrip] question regarding FieldTrip
In-Reply-To: <CAGhHk+itOwLA7rv42X1tbLH=-wYBYwincRSRUdHFM+AvaMAiJw@mail.gmail.com>
References: <CAGhHk+itOwLA7rv42X1tbLH=-wYBYwincRSRUdHFM+AvaMAiJw@mail.gmail.com>
Message-ID: <CABPNLUp9EpsGqqv6pgQPnPrjn09FE1oqcwtO2QUVLrVZn4XQ2Q@mail.gmail.com>

Dear Ilya,

You probably intended to post to the FieldTrip mailing list, so I am
also forwarding my reply to the list. If you are not registered on the
list, please do so (http://fieldtrip.fcdonders.nl/discussion_list).

Your question suggests to me that you are not using FieldTrip-style
data structures. All FT functions are designed to work with such
structures, so you should convert your data to an FT data structure
first. You can have a look at these FAQs on the Wiki for suggestions:
http://fieldtrip.fcdonders.nl/faq/how_are_the_various_data_structures_defined
and http://fieldtrip.fcdonders.nl/faq/how_can_i_import_my_own_dataformat
. Also, you should probably have a look at the tutorial documentation
(http://fieldtrip.fcdonders.nl/tutorial), specifically the one on
time-frequency analysis.

Hope this helps,
Best,

Eelke

On 27 March 2012 19:13, ilya monosov <ilya.monosov at gmail.com> wrote:
> Hello,
> i have a quick question. thank you so much in advance. if i have a matrix of
> single trial lfps (10 by 10,000) .. meaning that i have 10 trials that are
> 10,000 msec long,
> and i want to get single trial frequency power matrixes for each trial and
> also the average (and perhaps do stats, but most likely not as i am doing
> this to just get
> a quick impression of LFP frequency behavior in locations where i recorded
> single neurons), what commands would i use for FieldTrip?
>
> i have tried but i am getting strange errors that lead me to believe that my
> input format is wrong.
>
> Thank you very much
> ilya


From batrod at gmail.com  Tue Mar 27 18:36:54 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Tue, 27 Mar 2012 11:36:54 -0500
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <1710162166.70656.1332865645305.JavaMail.root@draco.zimbra.ru.nl>
References: <189719464.70211.1332863376495.JavaMail.root@draco.zimbra.ru.nl>
	<1710162166.70656.1332865645305.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <CAPy7a9C0Av7RaH7QTsvErDBU-rf-Buu2x0EvfF5+mk=wGn=XnA@mail.gmail.com>

Dear Tessa,
would it be possible to give some precision about your analyzes.

1) After your first "cleaning", do you test coherence on particular
components or your entire data minus the "EOG" component?

2) When you say that you redo ICA on cleaned data (of course, an ICA
analysis made on a result of a previous ICA analysis with components
removed is a bad idea), do you remove another component or do you  test
your coherence on particular components?

Rodolphe

On Tue, Mar 27, 2012 at 11:27 AM, Tessa van Leeuwen <
tessa.vanleeuwen at fcdonders.ru.nl> wrote:

> Dear Fieldtrip experts,
>
> I have noticed enhanced coherence (sensor level) in my data after applying
> ICA during preprocessing, removing only 1 EOG component. Of course the
> (mainly quantitatively) enhanced coherence could be due to the removal of
> (artifact induced) noise from the data. But this increase also occured when
> applying ICA to previously cleaned data, implying changes induced by ICA
> somehow affect coherence.
>
> One of the aims of our project is to compute coherence/connectivity
> measures at the source level. Since connectivity measures are often
> difficult to interpret as they are, I would like to ask whether anyone has
> experience with connectivity analyses after preprocessing that involved
> ICA. Are people aware of possible influences of ICA on connectivity
> measures and is there a way to deal with this? Or would it be advisable NOT
> to use ICA when later looking at coherence/connectivity at the source level?
>
> We initially aim to compare across conditions (data that have been
> preprocessed together and from which the same ICA component has been
> removed). But we also have different experimental groups for which we would
> like to qualitatively compare active networks during our task.
>
> Thank you in advance for any input, it is highly appreciated.
>
> Best wishes,
> Tessa
>
>
> ---
>
> Tessa van Leeuwen, PhD
> postdoctoral researcher
>
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From batrod at gmail.com  Tue Mar 27 19:36:36 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Tue, 27 Mar 2012 12:36:36 -0500
Subject: [FieldTrip] optimum number of cycles
Message-ID: <CAPy7a9B64dcStbT9eEOZ4BR-HXq4WbkQ8LmzeqYxKNrnAooQqw@mail.gmail.com>

Dear filedtrippers, i had a question regarding the time-frequency analysis,
such as the one that can be found on the tutorial :
http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis

In the fixed-widow example, using a hanning taper, it is said that a fixed
widow of 500 ms can estimate power of different frequency bands like 2 Hz,
4Hz, etc...
However, for 2 Hz it means only 1 cycle.

In the frequency-dependent window length, 7 cycles per frequency bands are
used.

My questions are, is it ok to estimate a power with one cycle? What could
be the optimum number of cycles? Is ot ok to compare the power of different
frequency bands that have been estimated using a different number of cycles?

Thanks a lot,

Rodolphe.
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From smoratti at psi.ucm.es  Tue Mar 27 22:33:36 2012
From: smoratti at psi.ucm.es (smoratti at psi.ucm.es)
Date: Tue, 27 Mar 2012 22:33:36 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band,
	concept problem
In-Reply-To: <CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>
References: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
	<EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>
	<CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>
Message-ID: <E0D49E5B-2248-466C-A88D-0ECFB2E57851@psi.ucm.es>

Hi Mikel,

I think Jörn gave you already the answer. You need enough time points to accurately estimate the oscillations of a frequency. For example in wavelet analysis (morlet) people use at least 5 cycles.

Best,

Stephan

________________________________________________________
Stephan Moratti, PhD

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

Universidad Complutense de Madrid
Facultad de Psicología
Departamento de Psicología Básica I
Campus de Somosaguas
28223 Pozuelo de Alarcón (Madrid)
Spain

and

Center for Biomedical Technology
Laboratory for Cognitive and Computational Neuroscience
Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)
Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982

El 27/03/2012, a las 12:46, Ion Lavado escribió:

> Thank you Stephan, just one thing, why i need a time window big enough? so i'm just studying the frequency.
> 
> Best,
> 
> Mikel
> 
> 2012/3/27 Stephan Moratti <smoratti at psi.ucm.es>
> Dear Mikel,
> 
> I understand that you should do a mtmfft with a center frequency of interest (in your case cfg.foil = [11 11]) and then you do a frequency smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you need a time window big enough to allow such a smoothing. The CSD should represent a frequency window of 8 to 14 Hz then. Then you put the result of the mtmfft into the dics beamformer.
> 
> Best,
> 
> Stephan
>  
> El 27/03/2012, a las 11:19, Ion Lavado escribió:
> 
>> Hello, i'm having problems trying the beamformer analysis with a frequency band of interest. I would like to have for example an interval like [8 14] Hz. My concept problem is about the cfg.frequency and cfg.tapsmofrq  values. (it must be a escalar, but i want a frequency band). 
>> 
>> %FREQ ANALYSIS
>> cfg = [];
>> cfg.method    = 'mtmfft';
>> cfg.output    = 'powandcsd';
>> cfg.tapsmofrq = 5;
>> cfg.foilim    = [8 14];
>> freq_words_alpha = ft_freqanalysis(cfg, words);
>> 
>> 
>> %SOURCE ANALYSIS
>> cfg              = []; 
>> cfg.frequency    = 11;  
>> cfg.lambda=0;
>> cfg.method       = 'dics';
>> cfg.coordsys       = 'neuromag';
>> cfg.projectnoise = 'yes';
>> cfg.grad            =  freq_words_alpha.grad;
>> cfg.channel   = {'MEG'}; 
>> cfg.grid         = grid; 
>> cfg.reducerank      = 2;
>> cfg.vol          = vol02;
>> vol02=ft_convert_units(vol02,'cm');
>> source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
>> 
>> 
>> I use a cfg.frequency of 11 but i don't have really clear what i'm doing as a get the same result using cfg.frequency=11 but a freqanalysis in [10 12]. I would be very grateful if someone could solve my doubt.
>> 
>> Best wishes,
>> 
>> Mikel
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> ________________________________________________________
> Stephan Moratti, PhD
> 
> see also: http://web.me.com/smoratti/
> 
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> and
> 
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> 
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
> 
> 
> 
> _______________________________________________
> 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 tessa.vanleeuwen at fcdonders.ru.nl  Tue Mar 27 23:34:33 2012
From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen)
Date: Tue, 27 Mar 2012 23:34:33 +0200 (CEST)
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <CAPy7a9C0Av7RaH7QTsvErDBU-rf-Buu2x0EvfF5+mk=wGn=XnA@mail.gmail.com>
Message-ID: <1832235848.73257.1332884073180.JavaMail.root@draco.zimbra.ru.nl>

Dear Rodolphe, Thank you for your response, I tried to clarify below. > 1) After your first "cleaning", do you test coherence on particular
> components or your entire data minus the "EOG" component?
I tested the coherence on the entire dataset after removal of the EOG component. > 2) When you say that you redo ICA on cleaned data (of course, an ICA
> analysis made on a result of a previous ICA analysis with components
> removed is a bad idea), do you remove another component or do you test
> your coherence on particular components?
Sorry, I could have been more clear about this. I initially compared two versions of the same dataset: one in which all trials containing a blink were removed from the dataset after manual inspection; another version in which only trials with a blink during the actual stimulus period were removed manually and the rest of the trials, including trials with blinks outside the stimulus window, were 'cleaned' with ICA, i.e. the EOG component was removed. Eye-balling coherence in occipital channels, this was increased in the ICA-cleaned version. To check whether the increase in coherence could have been explained by an increased number of retained trials in the ICA-cleaned-version, I also applied the unmixing matrix obtained from the ICA to the manually cleaned version of the data, i.e., in which only smaller eye-movements or unidentified EOG artifacts would have been remaining after manual inspection. Now of course I could have been over-removing non-existent noise in this case, but also here the same difference in coherence appeared, now with the same number of trials in both condition. When I look at the time-frequency representations from both versions, these look highly similar, only small intensity differences can be seen. I only used a small amount of data to test this and these results might therefore not be completely reliable. But I know other people have experienced similar problems with altered coherence and I was wondering whether any effect of ICA-preprocessing on coherence/connectivity measures was generally known on the list and in the literature. Perhaps the removal of common noise with ICA can already explain the differences? Best wishes, Tessa > Rodolphe
> On Tue, Mar 27, 2012 at 11:27 AM, Tessa van Leeuwen <
> tessa.vanleeuwen at fcdonders.ru.nl > wrote:
> > Dear Fieldtrip experts,
> > I have noticed enhanced coherence (sensor level) in my data after
> > applying ICA during preprocessing, removing only 1 EOG component. Of
> > course the (mainly quantitatively) enhanced coherence could be due
> > to
> > the removal of (artifact induced) noise from the data. But this
> > increase also occured when applying ICA to previously cleaned data,
> > implying changes induced by ICA somehow affect coherence.
> > One of the aims of our project is to compute coherence/connectivity
> > measures at the source level. Since connectivity measures are often
> > difficult to interpret as they are, I would like to ask whether
> > anyone
> > has experience with connectivity analyses after preprocessing that
> > involved ICA. Are people aware of possible influences of ICA on
> > connectivity measures and is there a way to deal with this? Or would
> > it be advisable NOT to use ICA when later looking at
> > coherence/connectivity at the source level?
> > We initially aim to compare across conditions (data that have been
> > preprocessed together and from which the same ICA component has been
> > removed). But we also have different experimental groups for which
> > we
> > would like to qualitatively compare active networks during our task.
> > Thank you in advance for any input, it is highly appreciated.
> > Best wishes,
> > Tessa
> > ---
> > Tessa van Leeuwen, PhD
> > postdoctoral researcher
> > Department of Neurophysiology
> > Max Planck Institute for Brain Research
> > _______________________________________________
> > 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 yoni.levy at inserm.fr  Wed Mar 28 00:40:25 2012
From: yoni.levy at inserm.fr (yoni.levy at inserm.fr)
Date: Wed, 28 Mar 2012 00:40:25 +0200
Subject: [FieldTrip] actvsblT test statistic when running ft_freqstatistics
Message-ID: <20120328004025.8z450t1fk04wc8gk@imp.inserm.fr>

I am running the ft_freqstatistics using the actvsblT option, so as to  
statistically test activation period with baseline activity. For this,  
I followed the "Within trial experiments" tutorial in fieldtrip  
(http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq#within_trial_experiments).
The tutorial emphasizes that one should select equal length time  
windows. However, the number of trials in both conditions (activation  
and baseline) remains unequal. Therefore, when I run ft_freqstatistics  
with the design mentioned in the tutorial (inserting only the number  
of trials of the activation condition), I receive the following error  
message:
"the number of observations in the design does not match the number of  
observations in the data"

Is there an error in the turorial, or is the script intended to create  
two frequency output-files, with different total number of trials.

Thanks in advance,
Yoni


----------------------------------------------------------------
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From batrod at gmail.com  Wed Mar 28 02:20:42 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Tue, 27 Mar 2012 19:20:42 -0500
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <1832235848.73257.1332884073180.JavaMail.root@draco.zimbra.ru.nl>
References: <CAPy7a9C0Av7RaH7QTsvErDBU-rf-Buu2x0EvfF5+mk=wGn=XnA@mail.gmail.com>
	<1832235848.73257.1332884073180.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <CAPy7a9CkPgza79Tg7fFykksYQhsfgVRkK63Hq4Q=uN+iO6Y4kQ@mail.gmail.com>

Dear Tessa,

ok this is more clear now.
ICA is a wonderful tool which can easily become your worst enemy in data
analyzing.

By removing yourself certains epochs with blinks before doing an ICA, its
is possible that you remove relevant data that can be used by your ICA
algorithm to better separate components.  Certain people would argue that
even filtering your data before ICA can be a bad idea.
Therefore, when you apply the ICA on your "cleaned" data, there is more
chance that the component that will reflect the most what is left from
blinks will also contains more relevant data.
This data removal could potentially decrease your data variability
therefore increase your coherence.
Also, the number of epochs you keep after your cleaning (which should be
different from ICA compared to visual removal) could potentially explain
such a difference.

Hope this helps,

Rodolphe


On Tue, Mar 27, 2012 at 4:34 PM, Tessa van Leeuwen <
tessa.vanleeuwen at fcdonders.ru.nl> wrote:

> Dear Rodolphe,
>
> Thank you for your response, I tried to clarify below.
>
>
> 1) After your first "cleaning", do you test coherence on particular
> components or your entire data minus the "EOG" component?
>
> I tested the coherence on the entire dataset after removal of the EOG
> component.
>
> 2) When you say that you redo ICA on cleaned data (of course, an ICA
> analysis made on a result of a previous ICA analysis with components
> removed is a bad idea), do you remove another component or do you  test
> your coherence on particular components?
>
> Sorry, I could have been more clear about this. I initially compared two
> versions of the same dataset: one in which all trials containing a blink
> were removed from the dataset after manual inspection; another version in
> which only trials with a blink during the actual stimulus period were
> removed manually and the rest of the trials, including trials with blinks
> outside the stimulus window, were 'cleaned' with ICA, i.e. the EOG
> component was removed. Eye-balling coherence in occipital channels, this
> was increased in the ICA-cleaned version.
>
> To check whether the increase in coherence could have been explained by an
> increased number of retained trials in the ICA-cleaned-version, I also
> applied the unmixing matrix obtained from the ICA to the manually cleaned
> version of the data, i.e., in which only smaller eye-movements or
> unidentified EOG artifacts would have been remaining after manual
> inspection. Now of course I could have been over-removing non-existent
> noise in this case, but also here the same difference in coherence
> appeared, now with the same number of trials in both condition. When I look
> at the time-frequency representations from both versions, these look highly
> similar, only small intensity differences can be seen.
>
> I only used a small amount of data to test this and these results might
> therefore not be completely reliable. But I know other people have
> experienced similar problems with altered coherence and I was wondering
> whether any effect of ICA-preprocessing on coherence/connectivity measures
> was generally known on the list and in the literature. Perhaps the removal
> of common noise with ICA can already explain the differences?
>
> Best wishes,
> Tessa
>
>
> Rodolphe
>
> On Tue, Mar 27, 2012 at 11:27 AM, Tessa van Leeuwen <
> tessa.vanleeuwen at fcdonders.ru.nl> wrote:
>
>> Dear Fieldtrip experts,
>>
>> I have noticed enhanced coherence (sensor level) in my data after
>> applying ICA during preprocessing, removing only 1 EOG component. Of course
>> the (mainly quantitatively) enhanced coherence could be due to the removal
>> of (artifact induced) noise from the data. But this increase also occured
>> when applying ICA to previously cleaned data, implying changes induced by
>> ICA somehow affect coherence.
>>
>> One of the aims of our project is to compute coherence/connectivity
>> measures at the source level. Since connectivity measures are often
>> difficult to interpret as they are, I would like to ask whether anyone has
>> experience with connectivity analyses after preprocessing that involved
>> ICA. Are people aware of possible influences of ICA on connectivity
>> measures and is there a way to deal with this? Or would it be advisable NOT
>> to use ICA when later looking at coherence/connectivity at the source level?
>>
>> We initially aim to compare across conditions (data that have been
>> preprocessed together and from which the same ICA component has been
>> removed). But we also have different experimental groups for which we would
>> like to qualitatively compare active networks during our task.
>>
>> Thank you in advance for any input, it is highly appreciated.
>>
>> Best wishes,
>> Tessa
>>
>>
>> ---
>>
>> Tessa van Leeuwen, PhD
>> postdoctoral researcher
>>
>> Department of Neurophysiology
>> Max Planck Institute for Brain Research
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From sysoevao at psychiatry.wustl.edu  Wed Mar 28 04:01:22 2012
From: sysoevao at psychiatry.wustl.edu (Sysoeva, Olga Vladimirovna)
Date: Wed, 28 Mar 2012 02:01:22 +0000
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <CAPy7a9CkPgza79Tg7fFykksYQhsfgVRkK63Hq4Q=uN+iO6Y4kQ@mail.gmail.com>
References: <CAPy7a9C0Av7RaH7QTsvErDBU-rf-Buu2x0EvfF5+mk=wGn=XnA@mail.gmail.com>
	<1832235848.73257.1332884073180.JavaMail.root@draco.zimbra.ru.nl>,
	<CAPy7a9CkPgza79Tg7fFykksYQhsfgVRkK63Hq4Q=uN+iO6Y4kQ@mail.gmail.com>
Message-ID: <41C83D63782BE149B1B984A58E866D8FE82D@CITEMB2D.cits.wustl.edu>

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From politzerahless at gmail.com  Wed Mar 28 06:58:34 2012
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Tue, 27 Mar 2012 23:58:34 -0500
Subject: [FieldTrip] question to the fieldtrip developers - multiple spm
 versions in fieldtrip
Message-ID: <CAJT2k_-jbUesSdb1b3Y6TaTQwx7P8oFw6nMGoVz-Qjw=VAX26Q@mail.gmail.com>

Hi Frederic,

As far as I know, those SPM errors are a consequence of adding all the
subdirectories of FieldTrip to your MATLAB path; see
http://fieldtrip.fcdonders.nl/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path.
If you add just the main Fieldtrip directory instead of all
subdirectories, you shouldn't get the error. I haven't tried
ft_sourceanalysis myself so I'm not sure if this issue has any consequences
when running that.

Best,
Steve

----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 27 Mar 2012 12:14:45 +0200
> From: Frederic Roux <fredericroux at hotmail.de>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] question to the fieldtrip developers - multiple
>        spm versions in fieldtrip
> Message-ID: <DUB113-W12B64F64480B0A75AB493EB74A0 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
> Dear all,
>
> I would like to ask again if the fact of getting a warning
> that different spm versions will confuse fieldtrip
> can have consequences in the ft_sourceanalysis pipeline.
>
> I am using version 2012-01-05 which has SPM2 and SPM8
> in the external folder.
>
> It would be great if someone from the development-team could tell me
>
> a) why this is a problem
> b) how to circumvent it
>
>
> I renamed the spm.m file into spm.m.bak in the SPM2 folder so that
> only the spm.m file from the SPM8 folder is used. However, it would
> be great if someone could tell me if this is a workaround or not.
>
>
> Best regards,
> Fred
>
> --
> Fr?d?ric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
>
>
>
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From m.leszczynski.m at googlemail.com  Wed Mar 28 08:22:23 2012
From: m.leszczynski.m at googlemail.com (Marcin)
Date: Wed, 28 Mar 2012 08:22:23 +0200
Subject: [FieldTrip] statfun_depsamplesregrT
In-Reply-To: <4f6b87bf.86600e0a.3f3a.ffff8106SMTPIN_ADDED@mx.google.com>
References: <CAAVVtzDY5stRD-XE2Pa5TjrO1L8AJXXSZToy7XhA72hK22bu+w@mail.gmail.com>
	<4f6b87bf.86600e0a.3f3a.ffff8106SMTPIN_ADDED@mx.google.com>
Message-ID: <CAAVVtzAJe6zEuu-wR_6MX8c7bSekX+k0v=H43TAnGRMt2yz=2g@mail.gmail.com>

Dear Dr. Maris,

thanks for your reply.
If I get you right you say that whether I use the statfun_depsamplesregrT
or use/write statfun_depsamplesrankcorr depends on assumed (apriori)
relation between the predictor variable (experimental condition) and the
data. If I assume linearity (i.e. in the case of WM load:  ERP/TF(1) <
ERP/TF(2) < ERP/TF(3) < ERP/TF(4)) I might use the statfun_depsamplesregrT.
If I doubt linearity (i.e.WM load ERP/TF(1) < ERP/TF(2) <= ERP/TF(3) <
ERP/TF(4)) I should use the statfun_depsamplesrankcorr. Is this correct?

I am not sure if I underestood your point about reference distribution. Are
you saying that for the cluster-based permutation inference I need to
threshold on a reference distribution which might be either parametric or
non-parametric? If this is the case. What does it depend on whether I use
parametric or non parametric reference distribution?

Thank you again for your time and your help.

Best,
Marcin

W dniu 22 marca 2012 21:12 użytkownik Eric Maris <e.maris at psych.ru.nl>napisał:

> Dear Marcin,****
>
> ** **
>
> ** **
>
> The statfun_depsamplesregrT calculates a T-statistic for regression
> coefficients that are calculated within each of the units-of-observation
> (typically, participants) obtained by regressing the subject-specific data
> (spatiotemporal, spatio-spectral, spatio-spectro-temporal) on some
> predictor variable that varies over the different conditions in which this
> participant has provided data (e.g., working-memory load, retention
> interval, luminance, contrast, etc). If you doubt the assumed linear
> relation between predictor variable and biological data, then you could
> write your own statfun_depsamplesrankcorr. To use this test statistic for
> cluster-based permutation inference, you need a threshold based on some
> reference distribution (which can be parametric, but must not be). ****
>
> ** **
>
> To get this statfun_depsamplesrankcorr running, you will probably have to
> take a look in the Fieldtrip code to see how the statistics framework is
> structured.****
>
> ** **
>
> Best,****
>
> ** **
>
> Eric Maris****
>
> ** **
>
> ** **
>
> *From:* Marcin [mailto:m.leszczynski.m at googlemail.com]
> *Sent:* woensdag 21 maart 2012 10:51
> *To:* Email discussion list for the FieldTrip project
> *Subject:* [FieldTrip] statfun_depsamplesregrT****
>
> ** **
>
> Dear Fieldtripers,
>
> Could anyone explain me what is being calculated with the
> statfun_depsamplesregrT function, please.
>
> David Groppe (thank you David) suggested in a previous thread on the list
> that I might calculate permutation test based on rank correlation to
> account for monotonic relationships within the permutation framework. I was
> wondering if this is the kind of test that statfun_depsamplesregrT function
> calculates.
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-December/004578.html
>
> Best,
> Marcin****
>
> _______________________________________________
> 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  Wed Mar 28 09:32:30 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 28 Mar 2012 09:32:30 +0200
Subject: [FieldTrip] optimum number of cycles
In-Reply-To: <CAPy7a9B64dcStbT9eEOZ4BR-HXq4WbkQ8LmzeqYxKNrnAooQqw@mail.gmail.com>
References: <CAPy7a9B64dcStbT9eEOZ4BR-HXq4WbkQ8LmzeqYxKNrnAooQqw@mail.gmail.com>
Message-ID: <4F72BE8E.7020603@donders.ru.nl>

Hi Rodolphe,

I don't think that your questions have a 'best' answer, but see below 
for my opinion.

> In the fixed-widow example, using a hanning taper, it is said that a 
> fixed widow of 500 ms can estimate power of different frequency bands 
> like 2 Hz, 4Hz, etc...
> However, for 2 Hz it means only 1 cycle.
>
> In the frequency-dependent window length, 7 cycles per frequency bands 
> are used.
>
> My questions are, is it ok to estimate a power with one cycle?

I would say no, but it depends on what trade-off between precision in 
time and frequency space you want to achieve. Of course it can be done, 
but the estimate is much more unreliable than when taking more cycles.

>  What could be the optimum number of cycles?

It depends on your question and frequency band. I would use at least 
three to five cycles for the most prominent frequencies(theta, alpha, 
beta), maybe two for very low frequencies (delta and below) and at least 
six or seven for higher frequencies (>40Hz). Some people use a fixed 
window length for the gamma-range and frequency smoothing around 10Hz, 
independent of the exact frequency (see e.g. the Neuron paper by Siegel 
et al., 2008, they use 250ms and 12Hz smoothing)

> Is ot ok to compare the power of different frequency bands that have 
> been estimated using a different number of cycles?

Yes and no, because different frequency bands have different 
characteristics, and are influenced differently by the 1/f noise. Taking 
more cycles for a higher frequency band and less for lower sounds 
logical, given that a signal low SNR requires more smoothing to reliably 
estimate the frequency content. However, frequencies bands are due to 
this 1/f noise different in power, e.g. alpha band activity will always 
have more power than gamma band activity.

>
> Thanks a lot,

You're welcome.

Best,
Jörn

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

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 jm.horschig at donders.ru.nl  Wed Mar 28 09:41:29 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 28 Mar 2012 09:41:29 +0200
Subject: [FieldTrip] Time stamp per sample
In-Reply-To: <CAG3TGCN+1ZV7zaAbGKvm8j3M1arg8pQXRgrfSLaof2hVp7G-vg@mail.gmail.com>
References: <CAG3TGCN+1ZV7zaAbGKvm8j3M1arg8pQXRgrfSLaof2hVp7G-vg@mail.gmail.com>
Message-ID: <4F72C0A9.7040604@donders.ru.nl>

Hi Anton,

This depends on the decimation rate that you specify, see here:
http://fieldtrip.fcdonders.nl/development/realtime/ctf?s[]=acq2ftx#downsampling_channel_selection_applying_gains

You can use ft_read_header(buffer) to read out the sampling frequency 
and then call ft_read_data to read the data. Here, you can specify a 
begin and an endsample, which define the length of the data the function 
returns. Prior, you can call ft_read_event to get the time stamp of the 
trigger value of interest. If you are interested in continuously reading 
data in without relying on certain events, you can don't need to call 
ft_read_event.

In FieldTrip, there are some example functions that you can look at, 
/e.g. //ft_realtime_asynchronous/ or/ft_realtime_synchronous/, see also 
here:
http://fieldtrip.fcdonders.nl/tutorial/realtime

 From what you wrote I get that the asynchronous type is what you aim for.

Best,
Jörn



On 3/27/2012 7:13 PM, Anton Andreev wrote:
> Hi,
>
> I have a question about the fieldtrip buffer.
> Does the protocol provides information about the time every sample has 
> been taken?
>
> I would like to produce a chunk of data for 300ms or 1 second for 
> example.
> I can build such chunk if I simply sort out samples that are in the 
> time range of 1 second starting with the time stamp of the first one. 
> Then again for 1 second and ....
>
> Thanks,
> Anton
>
>
> _______________________________________________
> 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

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 tessa.vanleeuwen at fcdonders.ru.nl  Wed Mar 28 10:59:58 2012
From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen)
Date: Wed, 28 Mar 2012 10:59:58 +0200 (CEST)
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <41C83D63782BE149B1B984A58E866D8FE82D@CITEMB2D.cits.wustl.edu>
Message-ID: <2130657903.77844.1332925198031.JavaMail.root@draco.zimbra.ru.nl>

Dear Olga, Thank you very much for your reply, this is very useful information! Because my trials are short I do not have sufficient data to let ICA compute all 275 possible components from my 275 channels - I use component reduction and estimate 80 components. This could then very well be the reason why coherence is altered after ICA. It makes sense that the interpolation would destroy any original phase relationships that are there. Thanks! Best wishes, Tessa ----- Original Message -----
> From: "Olga Vladimirovna Sysoeva" <sysoevao at psychiatry.wustl.edu>
> To: "Email discussion list for the FieldTrip project"
> <fieldtrip at donders.ru.nl>
> Sent: Wednesday, March 28, 2012 4:01:22 AM
> Subject: Re: [FieldTrip] coherence/connectivity measures after
> applying ICA
> Hi, Tessa,
> I do not have much experience for myself with coherence, but I'm very
> interested in the question you raised. Here is what I've seen in
> R.Thatcher's tutorial on Adulteration of Phase Relations when using
> Independent Components Analysis/Blind Identification and other
> Regression Methods to “Correct for Artifact
> http://www.appliedneuroscience.com/Tutorial%20on%20ICA%20Phase%20Adulteration.pdf
> .
> "Let us consider the rejection of eye movement artifact (EOG) using
> the ICA method which is the mathematical basis for Blind Source
> analysis. The ICA method decomposes a time series into a set of
> globally independent time series. Mathematically ICA can invert the
> equation and exactly reproduce the original time series based on the
> mathematical components. In this case the originally measured time or
> phase differences between each electrode are preserved and the
> cross-spectrum is unaltered.
> However, everything changes when the ICA or PCA or Blind Source, etc.
> methods are used to remove artifact by reconstructing 19 channels
> based on a smaller set of components, e.g., 17 or 18 channels and then
> deleting or omitting the EOG “components” to reconstruct 19 channels.
> This is because a regression process (interpolation) is used to
> minimize the deviation of the original 19 channel time series from the
> 17 or 18 “components” by which the remainder is used as weights to
> produce a second time series that has altered all of the phase
> relations in the original time series. The regression uses the average
> of the entire time series and therefore “smoothes” time or phase at
> each time point. Averaging a time series and computing deviations
> (whether information min-max, equimax, or simple linear regression)
> and then using the result to weight each time point by averages
> thereby smoothes each data point’s phase relations at each moment of
> time, distorting coherence, and destroys the time and phase relations
> present in the original time series."
> Hope it can help...
> Best Regards,
> Olga
> Olga Sysoeva,
> Research Associate, PhD
> Washington University School of Medicine
> Campus Box 8134
> 660 South Euclid Ave
> Saint Louis, MO 63110-9909
> From: fieldtrip-bounces at donders.ru.nl
> [fieldtrip-bounces at donders.ru.nl] on behalf of Rodolphe Nenert
> [batrod at gmail.com]
> Sent: Tuesday, March 27, 2012 7:20 PM
> To: Email discussion list for the FieldTrip project
> Subject: Re: [FieldTrip] coherence/connectivity measures after
> applying ICA
> Dear Tessa,
> ok this is more clear now.
> ICA is a wonderful tool which can easily become your worst enemy in
> data analyzing.
> By removing yourself certains epochs with blinks before doing an ICA,
> its is possible that you remove relevant data that can be used by your
> ICA algorithm to better separate components. Certain people would
> argue that even filtering your data before ICA can be a bad idea.
> Therefore, when you apply the ICA on your "cleaned" data, there is
> more chance that the component that will reflect the most what is left
> from blinks will also contains more relevant data.
> This data removal could potentially decrease your data variability
> therefore increase your coherence.
> Also, the number of epochs you keep after your cleaning (which should
> be different from ICA compared to visual removal) could potentially
> explain such a difference.
> Hope this helps,
> Rodolphe
> On Tue, Mar 27, 2012 at 4:34 PM, Tessa van Leeuwen <
> tessa.vanleeuwen at fcdonders.ru.nl > wrote:
> > Dear Rodolphe,
> > Thank you for your response, I tried to clarify below.
> > > 1) After your first "cleaning", do you test coherence on
> > > particular
> > > components or your entire data minus the "EOG" component?
> > I tested the coherence on the entire dataset after removal of the
> > EOG
> > component.
> > > 2) When you say that you redo ICA on cleaned data (of course, an
> > > ICA
> > > analysis made on a result of a previous ICA analysis with
> > > components
> > > removed is a bad idea), do you remove another component or do you
> > > test
> > > your coherence on particular components?
> > Sorry, I could have been more clear about this. I initially compared
> > two versions of the same dataset: one in which all trials containing
> > a
> > blink were removed from the dataset after manual inspection; another
> > version in which only trials with a blink during the actual stimulus
> > period were removed manually and the rest of the trials, including
> > trials with blinks outside the stimulus window, were 'cleaned' with
> > ICA, i.e. the EOG component was removed. Eye-balling coherence in
> > occipital channels, this was increased in the ICA-cleaned version.
> > To check whether the increase in coherence could have been explained
> > by an increased number of retained trials in the
> > ICA-cleaned-version,
> > I also applied the unmixing matrix obtained from the ICA to the
> > manually cleaned version of the data, i.e., in which only smaller
> > eye-movements or unidentified EOG artifacts would have been
> > remaining
> > after manual inspection. Now of course I could have been
> > over-removing
> > non-existent noise in this case, but also here the same difference
> > in
> > coherence appeared, now with the same number of trials in both
> > condition. When I look at the time-frequency representations from
> > both
> > versions, these look highly similar, only small intensity
> > differences
> > can be seen.
> > I only used a small amount of data to test this and these results
> > might therefore not be completely reliable. But I know other people
> > have experienced similar problems with altered coherence and I was
> > wondering whether any effect of ICA-preprocessing on
> > coherence/connectivity measures was generally known on the list and
> > in
> > the literature. Perhaps the removal of common noise with ICA can
> > already explain the differences?
> > Best wishes,
> > Tessa
> > > Rodolphe
> > > On Tue, Mar 27, 2012 at 11:27 AM, Tessa van Leeuwen <
> > > tessa.vanleeuwen at fcdonders.ru.nl > wrote:
> > > > Dear Fieldtrip experts,
> > > > I have noticed enhanced coherence (sensor level) in my data
> > > > after
> > > > applying ICA during preprocessing, removing only 1 EOG
> > > > component.
> > > > Of
> > > > course the (mainly quantitatively) enhanced coherence could be
> > > > due
> > > > to
> > > > the removal of (artifact induced) noise from the data. But this
> > > > increase also occured when applying ICA to previously cleaned
> > > > data,
> > > > implying changes induced by ICA somehow affect coherence.
> > > > One of the aims of our project is to compute
> > > > coherence/connectivity
> > > > measures at the source level. Since connectivity measures are
> > > > often
> > > > difficult to interpret as they are, I would like to ask whether
> > > > anyone
> > > > has experience with connectivity analyses after preprocessing
> > > > that
> > > > involved ICA. Are people aware of possible influences of ICA on
> > > > connectivity measures and is there a way to deal with this? Or
> > > > would
> > > > it be advisable NOT to use ICA when later looking at
> > > > coherence/connectivity at the source level?
> > > > We initially aim to compare across conditions (data that have
> > > > been
> > > > preprocessed together and from which the same ICA component has
> > > > been
> > > > removed). But we also have different experimental groups for
> > > > which
> > > > we
> > > > would like to qualitatively compare active networks during our
> > > > task.
> > > > Thank you in advance for any input, it is highly appreciated.
> > > > Best wishes,
> > > > Tessa
> > > > ---
> > > > Tessa van Leeuwen, PhD
> > > > postdoctoral researcher
> > > > Department of Neurophysiology
> > > > Max Planck Institute for Brain Research
> > > > _______________________________________________
> > > > 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
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If
> you are not the intended recipient, be advised that any unauthorized
> use, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If
> you are not the intended recipient, be advised that any unauthorized
> use, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
> _______________________________________________
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> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From dieter.devlaminck at inria.fr  Wed Mar 28 11:26:15 2012
From: dieter.devlaminck at inria.fr (Dieter Devlaminck)
Date: Wed, 28 Mar 2012 11:26:15 +0200 (CEST)
Subject: [FieldTrip] warning: the trial definition in the configuration is
 inconsistent with the actual data
In-Reply-To: <763718776.653827.1332926546901.JavaMail.root@zmbs2.inria.fr>
Message-ID: <1286872503.653958.1332926775888.JavaMail.root@zmbs2.inria.fr>


Dear All, 

When I try to invoke the 'ft_topoplotER(cfg,GA_FC)' command, I get the following warning 

Warning: the trial definition in the configuration is inconsistent with the actual data 

This happens both with the tutorial data as with my own data and is apparently caused by the fact that in the data structure there is a field 'previous' which in turn contains a field 'trl' which contains information on all triggers found in my original data. As I only take the average of the trials corresponding to certain target stimuli with ft_timelockanalysis (using 'cfg.trials = find(data.cfg.trl(:,end));') and then try to make a plot of that, fieldtrip finds an inconsistency in the dimensions and then does some kind of reconstruction, stating the following 

Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording 

This worries me a bit as I do not know exactly what it is doing although the tutorial plot seemed to be the same as the one on the website. What can I do to avoid this warning? 

I use fieldtrip version 20120308 and matlab R2010b on fedora 14. 

Thanks in advance, 
Best regards, 
Dieter Devlaminck 
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From eelke.spaak at donders.ru.nl  Wed Mar 28 11:39:05 2012
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Wed, 28 Mar 2012 11:39:05 +0200
Subject: [FieldTrip] warning: the trial definition in the configuration
 is inconsistent with the actual data
In-Reply-To: <1286872503.653958.1332926775888.JavaMail.root@zmbs2.inria.fr>
References: <763718776.653827.1332926546901.JavaMail.root@zmbs2.inria.fr>
	<1286872503.653958.1332926775888.JavaMail.root@zmbs2.inria.fr>
Message-ID: <CABPNLUozQGCeGXm3DkH5eVrG5155RsBncFpjCfTwfTbPnSSmOg@mail.gmail.com>

Dear Dieter,

You have correctly tracked down the cause of the warning: the actual
data is inconsistent with a trl-matrix found somewhere in your
data.cfg (.previous) tree.

The reason you are getting these warnings is that certain FieldTrip
functions (apparently including ft_topoplotER and/or some of its
dependencies) require a data.sampleinfo field in your data structure
that is consistent with the actual data. In general, data.sampleinfo
is an Nx2 matrix containing, for each trial in the data, the indices
of the begin and end sample of that trial, with respect to the
original data set (on disk). If such a consistent data.sampleinfo does
not exist, as is the case with your data, fieldtrip will simply
reconstruct this sampleinfo by using 1 as the begin sample of trial 1,
and k as its end sample, where k is the number of samples in trial 1.
Trial 2 will be numbered from k+1 to k+n, where n is trial 2's length,
etc. This allows all FT functions depending on sampleinfo to function
adequately. Thus, given that you understand where the warning comes
from (as is the case), you should not worry about it and can safely
ignore it.

Do keep in mind, though (also for other people on the list, who might
find this post in the future), that you cannot interpret the
reconstructed sampleinfo in terms of the original recording anymore.
This is not an issue with the plotting functions (since you do not
directly use the manipulated data anyway), but might become relevant
when you e.g. use ft_databrowser or ft_artifact_zvalue, which can
return segments of interest in your data, specified in begin and end
samples.

Best,
Eelke

On 28 March 2012 11:26, Dieter Devlaminck <dieter.devlaminck at inria.fr> wrote:
> Dear All,
>
> When I try to invoke the 'ft_topoplotER(cfg,GA_FC)' command, I get the
> following warning
>
> Warning: the trial definition in the configuration is inconsistent with the
> actual data
>
> This happens both with the tutorial data as with my own data and is
> apparently caused by the fact that in the data structure there is a field
> 'previous' which in turn contains a field 'trl' which contains information
> on all triggers found in my original data. As I only take the average of the
> trials corresponding to certain target stimuli with ft_timelockanalysis
> (using 'cfg.trials = find(data.cfg.trl(:,end));') and then try to make a
> plot of that, fieldtrip finds an inconsistency in the dimensions and then
> does some kind of reconstruction, stating the following
>
> Warning: reconstructing sampleinfo by assuming that the trials are
> consecutive segments of a continuous recording
>
> This worries me a bit as I do not know exactly what it is doing although the
> tutorial plot seemed to be the same as the one on the website. What can I do
> to avoid this warning?
>
> I use fieldtrip version 20120308 and matlab R2010b on fedora 14.
>
> Thanks in advance,
> Best regards,
> Dieter Devlaminck
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From dieter.devlaminck at inria.fr  Wed Mar 28 13:07:34 2012
From: dieter.devlaminck at inria.fr (Dieter Devlaminck)
Date: Wed, 28 Mar 2012 13:07:34 +0200 (CEST)
Subject: [FieldTrip] warning: the trial definition in the configuration
 is inconsistent with the actual data
In-Reply-To: <CABPNLUozQGCeGXm3DkH5eVrG5155RsBncFpjCfTwfTbPnSSmOg@mail.gmail.com>
Message-ID: <1504836263.656522.1332932854634.JavaMail.root@zmbs2.inria.fr>

Dear Eelke,

Thank you for answering so quickly.

> Do keep in mind, though (also for other people on the list, who might
> find this post in the future), that you cannot interpret the
> reconstructed sampleinfo in terms of the original recording anymore.
> This is not an issue with the plotting functions (since you do not
> directly use the manipulated data anyway), but might become relevant
> when you e.g. use ft_databrowser or ft_artifact_zvalue, which can
> return segments of interest in your data, specified in begin and end
> samples.

Indeed, this is the main reason why I asked this question, as it might have repercussions when calling other methods.

Is there a reason why the sampleinfo field disappears when calling the ft_timelockanalysis method? The field is still present in my data after calling the ft_redefinetrial method. I assume the normal operation is that the sampleinfo field is still present as it is normally used by subsequent methods?

A second thing I noticed is that now that I read my file with ft_preprocessing as one continuous trial and then partition my data into trials with ft_definetrials and ft_redefinetrials that the trialinfo (where I set some custom labels with my own trialfun) field has disappeared. If I first call ft_definetrials and the ft_preprocessing the trialinfo field is still there.

Best regards,
Dieter Devlaminck

----- Oorspronkelijk bericht -----
> Van: "Eelke Spaak" <eelke.spaak at donders.ru.nl>
> Aan: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
> Verzonden: Woensdag 28 maart 2012 11:39:05
> Onderwerp: Re: [FieldTrip] warning: the trial definition in the configuration is inconsistent with the actual data
> Dear Dieter,
> 
> You have correctly tracked down the cause of the warning: the actual
> data is inconsistent with a trl-matrix found somewhere in your
> data.cfg (.previous) tree.
> 
> The reason you are getting these warnings is that certain FieldTrip
> functions (apparently including ft_topoplotER and/or some of its
> dependencies) require a data.sampleinfo field in your data structure
> that is consistent with the actual data. In general, data.sampleinfo
> is an Nx2 matrix containing, for each trial in the data, the indices
> of the begin and end sample of that trial, with respect to the
> original data set (on disk). If such a consistent data.sampleinfo does
> not exist, as is the case with your data, fieldtrip will simply
> reconstruct this sampleinfo by using 1 as the begin sample of trial 1,
> and k as its end sample, where k is the number of samples in trial 1.
> Trial 2 will be numbered from k+1 to k+n, where n is trial 2's length,
> etc. This allows all FT functions depending on sampleinfo to function
> adequately. Thus, given that you understand where the warning comes
> from (as is the case), you should not worry about it and can safely
> ignore it.
> 
> Do keep in mind, though (also for other people on the list, who might
> find this post in the future), that you cannot interpret the
> reconstructed sampleinfo in terms of the original recording anymore.
> This is not an issue with the plotting functions (since you do not
> directly use the manipulated data anyway), but might become relevant
> when you e.g. use ft_databrowser or ft_artifact_zvalue, which can
> return segments of interest in your data, specified in begin and end
> samples.
> 
> Best,
> Eelke
> 
> On 28 March 2012 11:26, Dieter Devlaminck <dieter.devlaminck at inria.fr>
> wrote:
> > Dear All,
> >
> > When I try to invoke the 'ft_topoplotER(cfg,GA_FC)' command, I get
> > the
> > following warning
> >
> > Warning: the trial definition in the configuration is inconsistent
> > with the
> > actual data
> >
> > This happens both with the tutorial data as with my own data and is
> > apparently caused by the fact that in the data structure there is a
> > field
> > 'previous' which in turn contains a field 'trl' which contains
> > information
> > on all triggers found in my original data. As I only take the
> > average of the
> > trials corresponding to certain target stimuli with
> > ft_timelockanalysis
> > (using 'cfg.trials = find(data.cfg.trl(:,end));') and then try to
> > make a
> > plot of that, fieldtrip finds an inconsistency in the dimensions and
> > then
> > does some kind of reconstruction, stating the following
> >
> > Warning: reconstructing sampleinfo by assuming that the trials are
> > consecutive segments of a continuous recording
> >
> > This worries me a bit as I do not know exactly what it is doing
> > although the
> > tutorial plot seemed to be the same as the one on the website. What
> > can I do
> > to avoid this warning?
> >
> > I use fieldtrip version 20120308 and matlab R2010b on fedora 14.
> >
> > Thanks in advance,
> > Best regards,
> > Dieter Devlaminck
> >
> > _______________________________________________
> > 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 akiko.ikkai at gmail.com  Thu Mar 29 00:22:46 2012
From: akiko.ikkai at gmail.com (Akiko Ikkai)
Date: Wed, 28 Mar 2012 18:22:46 -0400
Subject: [FieldTrip] beamformer results smaller than brain
Message-ID: <CAKwx6Qc-TBiKARXJmJewk2Ob-CMZpTyXijCJ71iuOYGkH0ZbQA@mail.gmail.com>

Hi Fieldtrip users,

I'm hoping that someone could give me advice on segmentation and beamformer
on EEG data. I have EEG data set based on 128 channel cap. Thanks to the
help I got in mid-Feb, I'm now able to create a decent
segmentation (seg_results image attached) and volume conduction model.
However, when I run beamformer based on these models, resulting beamforming
image is often smaller than the brain (beamformer_result attached).
Particularly posterior parietal and occipital map is NaN.

I have tried going back to segmentation and expanded brain by
using imdilate after ft_volumesegment such as:

newbrain = imdilate(seg2.brain,strel_bol(1)); % seg2.brain is original
brain tissue from segmentation

seg2.brain = newbrain;
seg2.seg = seg2.scalp + seg2.skull*3 + seg2.brain*6;

and run ft_prepare_mesh_new on seg2. Of course, I have to make sure there
is no intersect between different tissue types, so using imdilate has
limitation.

Could someone explain why this shrinkage might be happening, and how I
could fix it?

Thanks in advance! Akiko

-- 
Akiko Ikkai, Ph.D.
Postdoctoral Fellow
Department of Psychological and Brain Sciences
Johns Hopkins University
Ames Hall, 3400 N. Charles St.
Baltimore, MD 21218
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From a.stolk at fcdonders.ru.nl  Thu Mar 29 10:19:47 2012
From: a.stolk at fcdonders.ru.nl (Stolk, A.)
Date: Thu, 29 Mar 2012 10:19:47 +0200 (CEST)
Subject: [FieldTrip] beamformer results smaller than brain
In-Reply-To: <CAKwx6Qc-TBiKARXJmJewk2Ob-CMZpTyXijCJ71iuOYGkH0ZbQA@mail.gmail.com>
Message-ID: <1939595059.215032.1333009187080.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Akiko, I'm not sure whether this is causing it, but w hat size inwardshift did you use when preparing your sourcemodel? Also check this page on our wiki: http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space Best, Arjen ----- Oorspronkelijk bericht -----
> Van: "Akiko Ikkai" <akiko.ikkai at gmail.com>
> Aan: fieldtrip at donders.ru.nl
> Verzonden: Donderdag 29 maart 2012 00:22:46
> Onderwerp: [FieldTrip] beamformer results smaller than brain
> Hi Fieldtrip users,
> I'm hoping that someone could give me advice on segmentation and
> beamformer on EEG data. I have EEG data set based on 128 channel cap.
> Thanks to the help I got in mid-Feb, I'm now able to create a decent
> segmentation (seg_results image attached) and volume conduction model.
> However, when I run beamformer based on these models, resulting
> beamforming image is often smaller than the brain (beamformer_result
> attached). Particularly posterior parietal and occipital map is NaN. 
> I have tried going back to segmentation and expanded brain by
> using imdilate after ft_volumesegment such as:
> newbrain = imdilate(seg2.brain,strel_bol(1)); % seg2.brain is original
> brain tissue from segmentation
> seg2.brain = newbrain;
> seg2.seg = seg2.scalp + seg2.skull*3 + seg2.brain*6;
> and run ft_prepare_mesh_new on seg2. Of course, I have to make sure
> there is no intersect between different tissue types, so using
> imdilate has limitation. 
> Could someone explain why this shrinkage might be happening, and how I
> could fix it? 
> Thanks in advance! Akiko
> --
> Akiko Ikkai, Ph.D.
> Postdoctoral Fellow
> Department of Psychological and Brain Sciences
> Johns Hopkins University
> Ames Hall, 3400 N. Charles St.
> Baltimore, MD 21218
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From g.piantoni at nin.knaw.nl  Thu Mar 29 11:13:19 2012
From: g.piantoni at nin.knaw.nl (Gio Piantoni)
Date: Thu, 29 Mar 2012 11:13:19 +0200
Subject: [FieldTrip] beamformer results smaller than brain
In-Reply-To: <CAKwx6Qc-TBiKARXJmJewk2Ob-CMZpTyXijCJ71iuOYGkH0ZbQA@mail.gmail.com>
References: <CAKwx6Qc-TBiKARXJmJewk2Ob-CMZpTyXijCJ71iuOYGkH0ZbQA@mail.gmail.com>
Message-ID: <CAHeOcruuVvKPDwhwXfozS8s6VciGf8T_stFcjYLMjOEvVOJiMg@mail.gmail.com>

Hi Akiko,

Your headmodel looks pretty good and your beamformer plot seems to
cover most of the gray matter.

However, it's good to check the location of your dipoles in respect to
your headmodel. For example, you can plot the .pos field of your
leadfield. Something like:

ft_plot_mesh(bnd(3), 'facealpha', .5)
hold on
plot3(lead.pos(:,1), lead.pos(:,2), lead.pos(:,3), '.')

It might well be that your grid is too coarse and some dipoles just
happen to be over the edge of the brain. Remember that your
"beamformer_result.png" is just an interpolation of the values of this
dipole grid.

You can either try to make your grid more refined (but remember that
your computation time will significantly increase). Or you can
manipulate the way dipoles are considered inside or outside the brain
with "inwardshift" for ft_prepare_leadfield (although I'd advise
against using a negative value as some dipoles might really end up
outside of your brain mesh, with some numerical instabilities).
Another option (the easiest) is to nudge your grid by, say, a few
millimeters, so that the parietal dipoles will be just inside the
brain mesh.

HTH,

Gio

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

+31 20 5665492
gio at gpiantoni.com
www.gpiantoni.com

On Thu, Mar 29, 2012 at 00:22, Akiko Ikkai <akiko.ikkai at gmail.com> wrote:
> Hi Fieldtrip users,
>
> I'm hoping that someone could give me advice on segmentation and beamformer
> on EEG data. I have EEG data set based on 128 channel cap. Thanks to the
> help I got in mid-Feb, I'm now able to create a decent
> segmentation (seg_results image attached) and volume conduction model.
> However, when I run beamformer based on these models, resulting beamforming
> image is often smaller than the brain (beamformer_result attached).
> Particularly posterior parietal and occipital map is NaN.
>
> I have tried going back to segmentation and expanded brain by using imdilate
> after ft_volumesegment such as:
>
> newbrain = imdilate(seg2.brain,strel_bol(1)); % seg2.brain is original brain
> tissue from segmentation
>
> seg2.brain = newbrain;
>
> seg2.seg = seg2.scalp + seg2.skull*3 + seg2.brain*6;
>
> and run ft_prepare_mesh_new on seg2. Of course, I have to make sure there is
> no intersect between different tissue types, so using imdilate has
> limitation.
>
> Could someone explain why this shrinkage might be happening, and how I could
> fix it?
>
> Thanks in advance! Akiko
>
> --
> Akiko Ikkai, Ph.D.
> Postdoctoral Fellow
> Department of Psychological and Brain Sciences
> Johns Hopkins University
> Ames Hall, 3400 N. Charles St.
> Baltimore, MD 21218
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From fredericroux at hotmail.de  Thu Mar 29 12:37:59 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 12:37:59 +0200
Subject: [FieldTrip] segmented volume not aligned with individual mri
Message-ID: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>


Dear all,

I am trying to create mni-aligned grids in individual head-space
and have followed the code provided in the corresponding example-script 
on the fieldtrip site to the line.

However when I plot the segmented volume it looks as if something
is going wrong. I am attaching the plots of the gray and white matter,
as well as of the csf.

I tried flipping the dimensions as suggested in the example script, however
this had zero effect.

My code looks like this.

addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
ft_defaults;

mri = ft_read_mri([path2files,'ID_V2.mri']);

cfg = [];
cfg.coordsys = 'ctf';
cfg.downsample = 2;
seg = ft_volumesegment(cfg,mri);

seg.transform = mri.transform;
seg.anatomy = mri.anatomy;

figure;
cfg = [];
ft_sourceplot(cfg,seg);
figure;
cfg = [];
cfg.funparameter = 'gray';

ft_sourceplot(cfg,seg);

figure;

cfg = [];

cfg.funparameter = 'white';


ft_sourceplot(cfg,seg);


figure;

cfg = [];

cfg.funparameter = 'csf';


ft_sourceplot(cfg,seg);



Anybody an idea why this is happening?
Any help would be highly appreciated.

Fred
-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From ali at cs.ru.nl  Thu Mar 29 12:46:54 2012
From: ali at cs.ru.nl (Ali Bahramisharif)
Date: Thu, 29 Mar 2012 12:46:54 +0200
Subject: [FieldTrip] segmented volume not aligned with individual mri
In-Reply-To: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>
References: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>
Message-ID: <165141044b7f16d8ba3fa0bc824d2c59.squirrel@squirrel.science.ru.nl>

Dear Fred,

Why do you enforce:

seg.transform = mri.transform;

after segmentation? I do not do it, and it looks fine!

Cheers,
Ali

>
> Dear all,
>
> I am trying to create mni-aligned grids in individual head-space
> and have followed the code provided in the corresponding example-script
> on the fieldtrip site to the line.
>
> However when I plot the segmented volume it looks as if something
> is going wrong. I am attaching the plots of the gray and white matter,
> as well as of the csf.
>
> I tried flipping the dimensions as suggested in the example script,
> however
> this had zero effect.
>
> My code looks like this.
>
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
> ft_defaults;
>
> mri = ft_read_mri([path2files,'ID_V2.mri']);
>
> cfg = [];
> cfg.coordsys = 'ctf';
> cfg.downsample = 2;
> seg = ft_volumesegment(cfg,mri);
>
> seg.transform = mri.transform;
> seg.anatomy = mri.anatomy;
>
> figure;
> cfg = [];
> ft_sourceplot(cfg,seg);
> figure;
> cfg = [];
> cfg.funparameter = 'gray';
>
> ft_sourceplot(cfg,seg);
>
> figure;
>
> cfg = [];
>
> cfg.funparameter = 'white';
>
>
> ft_sourceplot(cfg,seg);
>
>
> figure;
>
> cfg = [];
>
> cfg.funparameter = 'csf';
>
>
> ft_sourceplot(cfg,seg);
>
>
>
> Anybody an idea why this is happening?
> Any help would be highly appreciated.
>
> Fred
> --
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
>
>
>  		 	   		  _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Address:
        HG02.517
        Intelligent Systems
        Radboud University Nijmegen
        Heyendaalseweg 135
        6525 AJ Nijmegen
        The Netherlands

http://www.cs.ru.nl/~ali
Tel.:   +31 (0)24 36 52634



From jan.schoffelen at donders.ru.nl  Thu Mar 29 13:22:40 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 29 Mar 2012 13:22:40 +0200
Subject: [FieldTrip] segmented volume not aligned with individual mri
In-Reply-To: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>
References: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>
Message-ID: <9CDB7D6C-A8FC-4000-A234-3CD5913EBD12@donders.ru.nl>

Hi Fred,

You specify the seg to be downsampled. Therefore, I guess that the seg.dim and the mri.dim don't match anymore. Nor will the dimensions of the mri.anatomy match those of the seg.gray/white/csf. Also, as Ali suggests, the transformation matrices cannot be exchanged anymore.
I suspect that if you do: cfg = []; cfg.downsample = 2; mri2=ft_volumedownsample(cfg, mri); seg.anatomy = mri2.anatomy (and leave out seg.transform = mri.transform) that things will look a bit better.

JM

On Mar 29, 2012, at 12:37 PM, Frederic Roux wrote:

> Dear all,
> 
> I am trying to create mni-aligned grids in individual head-space
> and have followed the code provided in the corresponding example-script 
> on the fieldtrip site to the line.
> 
> However when I plot the segmented volume it looks as if something
> is going wrong. I am attaching the plots of the gray and white matter,
> as well as of the csf.
> 
> I tried flipping the dimensions as suggested in the example script, however
> this had zero effect.
> 
> My code looks like this.
> 
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
> ft_defaults;
> 
> mri = ft_read_mri([path2files,'ID_V2.mri']);
> 
> cfg = [];
> cfg.coordsys = 'ctf';
> cfg.downsample = 2;
> seg = ft_volumesegment(cfg,mri);
> 
> seg.transform = mri.transform;
> seg.anatomy = mri.anatomy;
> 
> figure;
> cfg = [];
> ft_sourceplot(cfg,seg);
> figure;
> cfg = [];
> cfg.funparameter = 'gray';
> ft_sourceplot(cfg,seg);
> figure;
> cfg = [];
> cfg.funparameter = 'white';
> ft_sourceplot(cfg,seg);
> figure;
> cfg = [];
> cfg.funparameter = 'csf';
> ft_sourceplot(cfg,seg);
> 
> Anybody an idea why this is happening?
> Any help would be highly appreciated.
> 
> Fred
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 
> <segmented_1.jpg>_______________________________________________
> 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

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From fredericroux at hotmail.de  Thu Mar 29 16:05:18 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 16:05:18 +0200
Subject: [FieldTrip] segmentation and individual grids
Message-ID: <DUB113-W1130856191D4A2E13FDACDCB7480@phx.gbl>


Dear Ali, Dear JM,

thanks a lot for your help.

According to your suggestions I have modified
my code as following:

mri = ft_read_mir('MRI_FILE_V2.mri');

cfg = [];
cfg.downsample = 2;
cfg.coordsys = 'ctf';

mri = ft_volume_downsample(cfg,mri);

cfg = [];
cfg.coordsys = 'ctf';
seg = ft_volumesegment(cfg,mri);
seg.anatomy = mri.anatomy;

Now the comparison of the segmented volumes and the MRI look fine,
but it seems that there is still a problem when I compute the individual grids (see attached figure).

I am also attaching the code I am using.

Would be great if you could help me to get this working.

Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From jan.schoffelen at donders.ru.nl  Thu Mar 29 16:17:00 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 29 Mar 2012 16:17:00 +0200
Subject: [FieldTrip] Fwd: segmentation and individual grids
References: <DUB113-W1130856191D4A2E13FDACDCB7480@phx.gbl>
Message-ID: <E9FA494C-82EA-4CCE-8951-1B020914FB2B@donders.ru.nl>

Hi Fred,

I forwarded your question to the list, so that other people get the opportunity to answer, and/or benefit from the answer ;-).

JM


Begin forwarded message:

> From: Frederic Roux <fredericroux at hotmail.de>
> Date: March 29, 2012 4:05:18 PM GMT+02:00
> To: <fieldtrip at donders.ru.nl>, <jan.schoffelen at donders.ru.nl>, <ali at cs.ru.nl>
> Subject: segmentation and individual grids
> Reply-To: <fredericrouxw at gmail.com>
> 
> Dear Ali, Dear JM,
> 
> thanks a lot for your help.
> 
> According to your suggestions I have modified
> my code as following:
> 
> mri = ft_read_mir('MRI_FILE_V2.mri');
> 
> cfg = [];
> cfg.downsample = 2;
> cfg.coordsys = 'ctf';
> 
> mri = ft_volume_downsample(cfg,mri);
> 
> cfg = [];
> cfg.coordsys = 'ctf';
> seg = ft_volumesegment(cfg,mri);
> seg.anatomy = mri.anatomy;
> 
> Now the comparison of the segmented volumes and the MRI look fine,
> but it seems that there is still a problem when I compute the individual grids (see attached figure).
> 
> I am also attaching the code I am using.
> 
> Would be great if you could help me to get this working.
> 
> Fred
> 
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 

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

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From fredericroux at hotmail.de  Thu Mar 29 17:45:52 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 17:45:52 +0200
Subject: [FieldTrip] alignment channel array, head model & individual grid
Message-ID: <DUB113-W104C6E0B399243CBB06024BB7480@phx.gbl>


Dear all,

I have trouble finding the right alignment for my head models and individual grids
with the MEG channel array.

The code I use is the following:

addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/fieltdrip_private/');
ft_defaults;

spm2path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm2/';
spm8path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm8/';

rmpath(spm2path,spm8path);


mri = ft_read_mri('ID_V2.mri');

cfg = [];
cfg.coordsys = 'ctf';
seg = ft_volumesegment(cfg,mri);

cfg = [];
hdm = ft_prepare_singleshell(cfg,seg);

cfg = [];
cfg.template = '/data/common/SPM8current/spm8/canonical/single_subj_T1.nii';
cfg.coordsys = 'ctf';
cfg.nonlinear = 'no';

norm = ft_volumenormalise(cfg,mri);

load template_grid.mat % template created from the SPM8 single_subj_T1.nii template located in the canonical folder of SPM8

grid = [];
grid.pos = warp_apply(inv(norm.cfg.final), template_grid.pos, 'homogenous')/10;
grid.inside = template_gird.inside;
grid.outside = template_grid.outside;

transfrom_ctf2spm = norm.cfg.final;

figure;
hold on;
ft_plot_sens(ft_read_sens('ID.ds'));
ft_plot_vol(hdm);
ft_plot_mesh(grid.pos(grid.inside,:));


Would be great if you could help me to figure out what is going wrong here.

Best,
Fred


-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From fredericroux at hotmail.de  Thu Mar 29 18:39:01 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 18:39:01 +0200
Subject: [FieldTrip] alignment channel array, head model & individual grid
Message-ID: <DUB113-W824234F69AD703490B557DB7480@phx.gbl>


I forgot to the mention that the left plot shows the headmodel and the channel array
whereas the rigth plot shows the grid and the channel array.

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From fredericroux at hotmail.de  Thu Mar 29 19:03:02 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 19:03:02 +0200
Subject: [FieldTrip] fieldtrip Digest, Vol 16, Issue 51
In-Reply-To: <mailman.715.1333035969.902.fieldtrip@donders.ru.nl>
References: <mailman.715.1333035969.902.fieldtrip@donders.ru.nl>
Message-ID: <DUB113-W63BCB0620F89F65ED05E6DB7480@phx.gbl>


Hi Julian,

thank you for response. That did indeed solve the problem.
I had commented out the section where everything is converted
from mm to cm.

Now the grid is at least on the same scale as the head model.
However, when I compare the template grid (Figure1) with
the individual grid (Figure6) it seems as if there is still a difference.

Is this normal and a consequence of the warping or should the
plot look different?

Best, Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225




> From: fieldtrip-request at donders.ru.nl
> Subject: fieldtrip Digest, Vol 16, Issue 51
> To: fieldtrip at donders.ru.nl
> Date: Thu, 29 Mar 2012 17:46:09 +0200
> 
> Send fieldtrip mailing list submissions to
> 	fieldtrip at donders.ru.nl
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> 	fieldtrip-request at donders.ru.nl
> 
> You can reach the person managing the list at
> 	fieldtrip-owner at donders.ru.nl
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
> 
> 
> Today's Topics:
> 
>    1. alignment channel array, head model & individual grid
>       (Frederic Roux)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 29 Mar 2012 17:45:52 +0200
> From: Frederic Roux <fredericroux at hotmail.de>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] alignment channel array, head model & individual
> 	grid
> Message-ID: <DUB113-W104C6E0B399243CBB06024BB7480 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 
> Dear all,
> 
> I have trouble finding the right alignment for my head models and individual grids
> with the MEG channel array.
> 
> The code I use is the following:
> 
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/fieltdrip_private/');
> ft_defaults;
> 
> spm2path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm2/';
> spm8path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm8/';
> 
> rmpath(spm2path,spm8path);
> 
> 
> mri = ft_read_mri('ID_V2.mri');
> 
> cfg = [];
> cfg.coordsys = 'ctf';
> seg = ft_volumesegment(cfg,mri);
> 
> cfg = [];
> hdm = ft_prepare_singleshell(cfg,seg);
> 
> cfg = [];
> cfg.template = '/data/common/SPM8current/spm8/canonical/single_subj_T1.nii';
> cfg.coordsys = 'ctf';
> cfg.nonlinear = 'no';
> 
> norm = ft_volumenormalise(cfg,mri);
> 
> load template_grid.mat % template created from the SPM8 single_subj_T1.nii template located in the canonical folder of SPM8
> 
> grid = [];
> grid.pos = warp_apply(inv(norm.cfg.final), template_grid.pos, 'homogenous')/10;
> grid.inside = template_gird.inside;
> grid.outside = template_grid.outside;
> 
> transfrom_ctf2spm = norm.cfg.final;
> 
> figure;
> hold on;
> ft_plot_sens(ft_read_sens('ID.ds'));
> ft_plot_vol(hdm);
> ft_plot_mesh(grid.pos(grid.inside,:));
> 
> 
> Would be great if you could help me to figure out what is going wrong here.
> 
> Best,
> Fred
> 
> 
> -- 
> Fr?d?ric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 
>  		 	   		  
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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 16, Issue 51
> *****************************************
 		 	   		  
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From Ulrich.Pomper at charite.de  Fri Mar 30 10:37:06 2012
From: Ulrich.Pomper at charite.de (Pomper, Ulrich)
Date: Fri, 30 Mar 2012 10:37:06 +0200
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <203022dc538e40168d5b72ded3195dcc@EXCCAHT-1.mail.uke.ads>
References: <4F71B9F0.8080106@charite.de>
	<203022dc538e40168d5b72ded3195dcc@EXCCAHT-1.mail.uke.ads>
Message-ID: <4F7570B2.5040707@charite.de>

Thanks Mark + Jörn for the replies!
I'll have a look at the NAI.

On 27.03.2012 15:48, "Jörn M. Horschig" wrote:

Dear Ulrich,


First of all, you might want to use the Neural Activity Index (NAI), as
also described in the tutorial:
http://fieldtrip.fcdonders.nl/tutorial/beamformer#source_analysiswithout_contrasting_condition

Then, to answer your question, I am tempted to say that this would be an
invalid approach when dealing with power, so in frequency-space. Power
obviously has a lower bound, so that the average of any random
collection of power values will never be 0.

That sounds plausible for raw power data, but actually, I want to compare whether my power change to baseline activity is different from zero (maybe that wasn't evident in my first post). I think that's a correct approach.




Though, what you are
suggesting is the same as a regular t-test, isn't it?
In case you are dealing e.g. with am LCMV beamformer, I am not quite
sure, but the null-hypothesis you suggested (amplitude==0)  sounds fair.

In any case, building a surrogate distribution same mean and variance
than your data might be a better way to deal with your problem. That
should be easily doable in Matlab without any need to implement this in
FieldTrip. And note that the MC problem is always present, but a
cluster-based correction (similar to Bonferroni, but correcting by the
number of voxels in the cluster not by the number of all voxels) sounds
legitimate to me. Afair, that's how it's done in FT.

Are you sure? I am not aware of any correction to the alpha level that is done by the cluster-based correction in FT. Afaik all it does is look for a certain number of significant voxels that are close in time, freq and space.
Best, Ulrich

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From yoni.levy at inserm.fr  Fri Mar 30 10:40:25 2012
From: yoni.levy at inserm.fr (yoni.levy at inserm.fr)
Date: Fri, 30 Mar 2012 10:40:25 +0200
Subject: [FieldTrip] actvsblT test statistic when running ft_freqstatistic
Message-ID: <20120330104025.kbc1vye188wwcoc8@imp.inserm.fr>

Dear All,

Would anyone know how to run ft_freqstatistics using the actvsblT?

I intend to statistically test activation period with baseline  
activity. For this, I followed the "Within trial experiments" tutorial  
in fieldtrip
(http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq#within_trial_experiments).
The tutorial emphasizes that one should select equal length time
windows. However, the number of trials in both conditions (activation
and baseline) remains unequal. Therefore, when I run ft_freqstatistics
with the design mentioned in the tutorial (inserting only the number
of trials of the activation condition), I receive the following error
message:
"the number of observations in the design does not match the number of
observations in the data"

Is there an error in the turorial, or is the script intended to create
two frequency output-files, with different total number of trials.

Any advice would be appreciated,

Thanks,

Yoni

----
Yoni Levy, Ph.D.,
INSERM U825,
Address: Pavillon BAUDOT / CHU Purpan,
Place du Docteur Joseph Baylac,
31024 TOULOUSE cédex 3, FRANCE.
E-Mail : yoni.levy at inserm.fr

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





From Ulrich.Pomper at charite.de  Fri Mar 30 10:56:52 2012
From: Ulrich.Pomper at charite.de (Pomper, Ulrich)
Date: Fri, 30 Mar 2012 10:56:52 +0200
Subject: [FieldTrip] =?utf-8?q?Postdoctoral_Position_-_Charit=C3=A9_Berlin?=
In-Reply-To: <8B8CE00B-155C-41D9-9F50-16EA83EB9314@charite.de>
References: <8B8CE00B-155C-41D9-9F50-16EA83EB9314@charite.de>
Message-ID: <4F757554.10703@charite.de>

The Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin invites applications for a Post-doctoral position.

A Starting Grant of the European Research Council (ERC) will fund the position. The main objective of this ERC research program is to examine neural and neurochemical markers of multisensory integration and to test a new hypothesis that considers dynamic interplay of synchronized neural populations as a key to multisensory processes. The studies within this program include healthy subjects and patients with schizophrenia, as an example of a mental disorder with deficits in multisensory integration. Multisensory processes will be examined in a series of experiments requiring both bottom-up and top-down processing.

Applicants should have a background in psychology, medicine, biology, physics, engineering, or neuroscience. Experience in human EEG/MEG studies, Matlab programming skills, as well as German language skills for interacting with patients are prerequisites for the position. An interest in neurophysiological studies including clinical populations is expected.

Applicants are asked to submit their CV, a motivation letter, 2 names of referees, and documentation of relevant qualifications (e.g., copies of diplomas and/or transcripts of grades) until April 15, 2012, electronically to:

Daniel Senkowski, Department of Psychiatry and Psychotherapy, Charité, University Medicine Berlin, 10115 Berlin, Germany, Phone: +49-30-2311-2738, Fax: +49-30-2311-2209, www.danielsenkowski.com<http://www.danielsenkowski.com/>, daniel.senkowski at charite.de<mailto:daniel.senkowski at charite.de>






---------------------------------------------------------------
Daniel Senkowski, Ph.D

Head of the Multisensory Integration research group
Department of Psychiatry and Psychotherapy
Charité, University Medicine Berlin
St. Hedwig Hospital, Große Hamburger Str. 5-11
10115 Berlin, Germany
Phone: +49-30-2311-2738
Fax:      +49-30-2311-2209
http://psy-ccm.charite.de/en/research/neuroimaging/multisensory_integration

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From jm.horschig at donders.ru.nl  Fri Mar 30 15:38:43 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Fri, 30 Mar 2012 15:38:43 +0200
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <4F7570B2.5040707@charite.de>
References: <4F71B9F0.8080106@charite.de>
	<203022dc538e40168d5b72ded3195dcc@EXCCAHT-1.mail.uke.ads>
	<4F7570B2.5040707@charite.de>
Message-ID: <4F75B763.9010906@donders.ru.nl>

Hi Ulrich,

>
> Are you sure? I am not aware of any correction to the alpha level that 
> is done by the cluster-based correction in FT. Afaik all it does is 
> look for a certain number of significant voxels that are close in 
> time, freq and space.

Oh indeed, I was mixing things up there. I couldn't find anything 
mentioned like this neither in the code nor in the Maris&Oostenveld 
paper. Then it was probably something I remembered from another 
test/tool, or I was mixing thoughts of mine with a simplistic 
explanation of random field theory. In any way, my apologies for the 
confusion.

Best,
Jörn


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

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 samarakm at mail.uc.edu  Fri Mar 30 21:04:42 2012
From: samarakm at mail.uc.edu (Samarasinghe, Kasun (samarakm))
Date: Fri, 30 Mar 2012 19:04:42 +0000
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <4F71B9F0.8080106@charite.de>
References: <4F71B9F0.8080106@charite.de>
Message-ID: <158540F0F1AD27479479077742EA83C515EA8C66@CH1PRD0102MB148.prod.exchangelabs.com>

Dear Fieldtrip members,

I am trying to construct a generic head model by following the tutorial "Build a geometrical description of the volume conduction model of the head". For some reason, I cannot download the zipped MRI file in the location : '"ftp://ftp.fcdonders.nl/pub/fieldtrip/". Any help regarding the correct location of this file would be appreciated.

Thank you,
Kasun

--------------------------------------------
Kasun M Samarasinghe
Doctoral Student
Electrical Engineering - Systems Track
University of Cincinnati








From samarakm at mail.uc.edu  Fri Mar 30 21:09:50 2012
From: samarakm at mail.uc.edu (Samarasinghe, Kasun (samarakm))
Date: Fri, 30 Mar 2012 19:09:50 +0000
Subject: [FieldTrip] Failure to access the MRI file in the Tutorial section
Message-ID: <158540F0F1AD27479479077742EA83C515EA8C74@CH1PRD0102MB148.prod.exchangelabs.com>

Dear Fieldtrip members,

I am trying to construct a generic head model by following the tutorial "Build a geometrical description of the volume conduction model of the head". For some reason, I cannot download the zipped MRI file in the location : '"ftp://ftp.fcdonders.nl/pub/fieldtrip/". Any help regarding the correct location of this file would be appreciated.

Please disregard my previous email since it had the wrong title.

Thank you,
Kasun

--------------------------------------------
Kasun M Samarasinghe
Doctoral Student
Electrical Engineering - Systems Track
University of Cincinnati



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From batrod at gmail.com  Fri Mar 30 21:24:56 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Fri, 30 Mar 2012 14:24:56 -0500
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <158540F0F1AD27479479077742EA83C515EA8C66@CH1PRD0102MB148.prod.exchangelabs.com>
References: <4F71B9F0.8080106@charite.de>
	<158540F0F1AD27479479077742EA83C515EA8C66@CH1PRD0102MB148.prod.exchangelabs.com>
Message-ID: <CAPy7a9CfQRDROZ6U_ksCddV8pMVyGdB--Uxhr1y3k6Lz3kKsoQ@mail.gmail.com>

Hi Kasun,

what software do you use to access this adress?
I know Chrome has issue with ftp, but Firefox handle that well. (I just
remade a test).

Rodolphe

On Fri, Mar 30, 2012 at 2:04 PM, Samarasinghe, Kasun (samarakm) <
samarakm at mail.uc.edu> wrote:

> Dear Fieldtrip members,
>
> I am trying to construct a generic head model by following the tutorial
> "Build a geometrical description of the volume conduction model of the
> head". For some reason, I cannot download the zipped MRI file in the
> location : '"ftp://ftp.fcdonders.nl/pub/fieldtrip/". Any help regarding
> the correct location of this file would be appreciated.
>
> Thank you,
> Kasun
>
> --------------------------------------------
> Kasun M Samarasinghe
> Doctoral Student
> Electrical Engineering - Systems Track
> University of Cincinnati
>
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From samarakm at mail.uc.edu  Fri Mar 30 21:42:27 2012
From: samarakm at mail.uc.edu (Samarasinghe, Kasun (samarakm))
Date: Fri, 30 Mar 2012 19:42:27 +0000
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <CAPy7a9CfQRDROZ6U_ksCddV8pMVyGdB--Uxhr1y3k6Lz3kKsoQ@mail.gmail.com>
References: <4F71B9F0.8080106@charite.de>
	<158540F0F1AD27479479077742EA83C515EA8C66@CH1PRD0102MB148.prod.exchangelabs.com>,
	<CAPy7a9CfQRDROZ6U_ksCddV8pMVyGdB--Uxhr1y3k6Lz3kKsoQ@mail.gmail.com>
Message-ID: <158540F0F1AD27479479077742EA83C515EA8C98@CH1PRD0102MB148.prod.exchangelabs.com>



Hi Rodolphe,



Yes, I can access using Firefox now, and thank you for your prompt response. I was using Chrome earlier, and yes it seems to have issues with the server.



Thank you again,

Kasun

--------------------------------------------
Kasun M Samarasinghe
Doctoral Student
Electrical Engineering - Systems Track
University of Cincinnati

________________________________
From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Rodolphe Nenert [batrod at gmail.com]
Sent: Friday, March 30, 2012 3:24 PM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] one-sample cluster test

Hi Kasun,

what software do you use to access this adress?
I know Chrome has issue with ftp, but Firefox handle that well. (I just remade a test).

Rodolphe

On Fri, Mar 30, 2012 at 2:04 PM, Samarasinghe, Kasun (samarakm) <samarakm at mail.uc.edu<mailto:samarakm at mail.uc.edu>> wrote:
Dear Fieldtrip members,

I am trying to construct a generic head model by following the tutorial "Build a geometrical description of the volume conduction model of the head". For some reason, I cannot download the zipped MRI file in the location : '"ftp://ftp.fcdonders.nl/pub/fieldtrip/". Any help regarding the correct location of this file would be appreciated.

Thank you,
Kasun

--------------------------------------------
Kasun M Samarasinghe
Doctoral Student
Electrical Engineering - Systems Track
University of Cincinnati






_______________________________________________
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 fredericroux at hotmail.de  Sat Mar 31 13:10:31 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Sat, 31 Mar 2012 13:10:31 +0200
Subject: [FieldTrip] restrict source reconstruction to gray matter
Message-ID: <DUB113-W1405024A1BD2BE5FF28CE14B74E0@phx.gbl>



Dear all,

I read that it is possible to restrict source reconstruction to gray matter.
Can anyone give me a hint on where can I find example code on how to do it?

I was searching for it on the fieldtrip-webstite but couldn't find anything.

Any help would as always be highly appreciated.

Fred



-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From jan.schoffelen at donders.ru.nl  Sat Mar 31 13:30:02 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Sat, 31 Mar 2012 13:30:02 +0200
Subject: [FieldTrip] restrict source reconstruction to gray matter
In-Reply-To: <DUB113-W1405024A1BD2BE5FF28CE14B74E0@phx.gbl>
References: <DUB113-W1405024A1BD2BE5FF28CE14B74E0@phx.gbl>
Message-ID: <A6ECCF8A-A40D-40CA-B560-578267AEABFC@donders.ru.nl>

Hi Fred,

I am not aware of any example code on the FT-website, but I would do something like this:

mri = ft_read_mri('...');
seg = ft_volumesegment([],mri);

cfg = [];
cfg.parameter = 'gray';
cfg.smooth = 10; % or some other value
cfg.downsample = 5; % downsample with a factor of 5
seg = ft_volumedownsample(cfg, seg);

% create a dipole grid
[X,Y,Z] = ndgrid(1:seg.dim(1), 1:seg.dim(2), 1:seg.dim(3));

grid = [];
grid.pos = warp_apply(seg.transform, [X(:) Y(:) Z(:)]); clear X Y Z
grid.dim = seg.dim;
grid.inside = find(seg.gray>0.5); % the threshold value needs to be verified, you can play with the value
grid.outside = find(seg.gray<=0.5);

grid = ft_convert_units(grid, 'cm'); % I assume that the sensors are defined in cm.

Just give it a shot. I would appreciate it very much if you could try this code and maybe optimize it. When you have done that, we could make a piece of documentation on the FT-website, i.e. I will create a page (because I don't think you could do that), and you'll write the documentation ;-). Sounds like a win-win situation to me. How does it sound to you?

Best wishes,

Jan-Mathijs


On Mar 31, 2012, at 1:10 PM, Frederic Roux wrote:

> 
> Dear all,
> 
> I read that it is possible to restrict source reconstruction to gray matter.
> Can anyone give me a hint on where can I find example code on how to do it?
> 
> I was searching for it on the fieldtrip-webstite but couldn't find anything.
> 
> Any help would as always be highly appreciated.
> 
> Fred
> 
> 
> 
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 
> _______________________________________________
> 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

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From litvak.vladimir at gmail.com  Thu Mar  1 16:02:28 2012
From: litvak.vladimir at gmail.com (Vladimir Litvak)
Date: Thu, 1 Mar 2012 15:02:28 +0000
Subject: [FieldTrip] Missing triggers with Biosemi EEG data
In-Reply-To: <f0f5f26cc301f41af598ca01ebe2a853.squirrel@www.drcmr.dk>
References: <f0f5f26cc301f41af598ca01ebe2a853.squirrel@www.drcmr.dk>
Message-ID: <CACq1BhKUJwiXMGEWM-OeD2tzbKOaQo=iR15VJ6qFr4HOMMcJ_A@mail.gmail.com>

Dear Mark,

I'm not sure what the reason is for not supporting downgoing triggers
in Biosemi, but there probably is one. I'm CCing your message to
Fieldtrip mailing list where it might be better answered. Are you sure
that the missing triggers are recorded correctly? Can you see them
with any other software you have? Sometimes there is a problem with
connectors which leads to incorrect assignments of trigger codes.

Vladimir

On Thu, Mar 1, 2012 at 2:54 PM, Mark Schram Christensen <markc at drcmr.dk> wrote:
> Dear Vladimir Litvak
> I am currently analysing some EEG data with SPM8 obtained with the biosemi
> system, and I am missing quite a lot of my triggers. I get the warning
> that only upcoing flanks are supported for biosemi, and I suspect that
> that is the reason. I can see that the status channel changes when ever I
> should have had the trigger.
> I guess it is related to the field trip file ft_read_event.m, which seems
> to have this biosemi exception, that even though it should look for both
> up and down flanks it only finds up with biosemi.
> Do you know if there is a possibility of also getting downflank triggers?
> Looking forward to hear from you.
> Best wishes
> Mark Schram Christensen
>
>
> _______________________________________________
> Mark Schram Christensen, MSc, PhD
> Copenhagen Neural Control of Movement &
> Danish Research Centre for Magnetic Resonance
> Department of Exercise and Sport Sciences
> Copenhagen University Hospital Hvidovre
> Kettegård Allé 30
> DK-2650 Hvidovre
> Phone: +45 3862 3407
> E-mail: markc at drcmr.dk
> http://www.ifi.ku.dk/
> http://www.cph-ncm.ku.dk/
> http://www.drcmr.dk/markc
>
>
>
>



From ghahremani.aida at gmail.com  Fri Mar  2 00:56:57 2012
From: ghahremani.aida at gmail.com (aida ghahremani)
Date: Thu, 1 Mar 2012 18:56:57 -0500
Subject: [FieldTrip] fieldtrip Digest, Vol 16, Issue 1
In-Reply-To: <mailman.1.1330599616.2810.fieldtrip@donders.ru.nl>
References: <mailman.1.1330599616.2810.fieldtrip@donders.ru.nl>
Message-ID: <CAM50FKDcYrPq2oSYnLkFHFNrX5ALT9Q2jVc9vU9PMxUc0tEYTQ@mail.gmail.com>

Dear Fieldtrip group

I have got a problem with a very simple program to solve a forward problem.
I used the below program to compute leadfield from a source in the origin
for two electrodes in different locations. I noticed that when I change the
position of one of the electrodes, it affects on the leadfield of the
other. I know it should not be like that, since electrodes do not affect
each other. Would you please help me?


elec.pnt=[4.6*cos(pi/3) 4.6*sin(pi/3) 7.96;4.6*cos(pi/6) 4.6*sin(pi/6)
7.96];
for i=1:2
   elec.label{i} = sprintf('%03d', i);
end

% create a concentric 3-sphere volume conductor, the radius is the same as
for the electrodes
vol = [];
vol.r = [8 8.1 8.6 9.2]; % radii of spheres
vol.c = [1 1 1/80 1];       % conductivity
vol.o = [0 0 0];          % center of sphere

% compute the leadfield for a dipole at position [0 0 0]
pos = [0 0 0];
lf = ft_compute_leadfield(pos, elec, vol);

% compute the potential distribution for a dipole with z-orientation
mom = [0 0 1]';
pot = lf * mom;
end

Best
Ayda

On Thu, Mar 1, 2012 at 6:00 AM, <fieldtrip-request at donders.ru.nl> wrote:

> Send fieldtrip mailing list submissions to
>        fieldtrip at donders.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>        fieldtrip-request at donders.ru.nl
>
> You can reach the person managing the list at
>        fieldtrip-owner at donders.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>   1. question about MNI alignment (Ali Bahramisharif)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 29 Feb 2012 21:10:54 +0100
> From: "Ali Bahramisharif" <ali at cs.ru.nl>
> To: fieldtrip at donders.ru.nl
> Subject: [FieldTrip] question about MNI alignment
> Message-ID:
>        <fac73988589583150fc4a6a7a958a215.squirrel at squirrel.science.ru.nl>
> Content-Type: text/plain;charset=iso-8859-1
>
> Dear Fieldtrip users,
>
> I want to create MNI-aligned grids in individual head-space, and I follow
> the guidelines in :
>
>
> http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space?s[]=template&s[]=grid
>
>
> I do not know how old this page is, but I noticed that for example in the
> current version "cfg.coordinates" should be "cfg.coordsys". I have the
> following problems:
>
> 1- When I run "ft_plot_mesh(template_grid);", I get a cubic grid which is
> apparently different from the one shown in the page.
>
> 2- When I run, ft_plot_vol(hdm), it does not seem to be aligned to
> "ft_plot_sens(ft_read_sens(dataset{i}));"
>
> I checked my segmented volumes, and they seem to be fine, and I did not
> need to run flipdim. I am wondering whether my segmented data is correct
> or it should be flipped somewhere. Please let me know if anybody knows how
> to resolve this problem.
>
> Cheers,
> Ali
>
>
>
>
> ------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> End of fieldtrip Digest, Vol 16, Issue 1
> ****************************************
>
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From r.oostenveld at donders.ru.nl  Mon Mar  5 12:27:53 2012
From: r.oostenveld at donders.ru.nl (Robert Oostenveld)
Date: Mon, 5 Mar 2012 12:27:53 +0100
Subject: [FieldTrip] FieldTrip course at the Donders in Nijmegen: 7-10 May
Message-ID: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>

Dear FieldTrip users,

The registration for our yearly toolkit course on "MEG and EEG data analysis" at the Donders Institute has opened. This year's MEG/EEG toolkit will take place from 7-10 May 2012. 

This 4-day toolkit course will teach you advanced MEG and EEG data analysis skills. Preprocessing, frequency analysis, source reconstruction and various statistical methods will be covered. The toolkit will consist of a number of lectures, followed by hands-on sessions in which you will be tutored through the complete analysis of a MEG data set using the FieldTrip toolbox. The fee for senior participants is € 400. The (PhD) student fee is € 200. Registration fee includes coffee/tea, Dutch sandwich lunches and one dinner.

Have a look at http://www.ru.nl/donders/agenda-news/courses/toolkits-2012/ for the preliminary programme and to register. Please do note that the number of seats is limited and that in the previous years the course was oversubscribed. We therefore expect to have to select participants; this is done on the basis of the information that you provide on your background, skills and research interest. Note that the registration closes 31 March. You will be informed about whether you can participate before mid-April.

Best wishes,

Robert Oostenveld & Jan-Mathijs Schoffelen

-----------------------------------------------------------
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
tel.: +31 (0)24 3619695
e-mail: r.oostenveld at donders.ru.nl
web: http://www.ru.nl/neuroimaging
skype: r.oostenveld
-----------------------------------------------------------



From ugabrewer at gmail.com  Mon Mar  5 18:58:33 2012
From: ugabrewer at gmail.com (Gene Brewer)
Date: Mon, 5 Mar 2012 10:58:33 -0700
Subject: [FieldTrip] Postdoctoral Fellowship at Arizona State University
In-Reply-To: <CADo-6W+m9eKFykATMtJhHEgEvZuA5xY09y3Y1s-bNwZgf573=Q@mail.gmail.com>
References: <CADo-6W+m9eKFykATMtJhHEgEvZuA5xY09y3Y1s-bNwZgf573=Q@mail.gmail.com>
Message-ID: <CADo-6WJRiPNv+KyL9cSAnbHonaGWX5=tV=KDMOcNmsz_njzmXg@mail.gmail.com>

List Members,

*Arizona State University Postdoctoral Fellowship in Neuropsychology of
Strategic Communication*

The Center for Strategic Communication (CSC) and the Department of
Psychology at Arizona State University are pleased to announce a new
Postdoctoral Fellowship program beginning May 2012.

*Postdoctoral Fellowship*

A postdoctoral fellowship will be awarded beginning in the May/June 2012
time frame. The appointment is for full time employment (40 hours per week)
for 18 months.  Renewal for up to two additional 18 month periods is
possible, contingent on additional funding by the sponsor and satisfactory
job performance. Salary is $60,000 and the University offers subsidized
health insurance. Support for travel to conferences will be available.
Fellows are responsible for relocation and housing expenses.  Fellows will
support a research project sponsored by the Defense Advanced Research
Projects Agency (DARPA) involving multi-modal neuroimaging (fMRI + EEG) of
narrative comprehension and persuasion.

For additional information regarding postdoctoral fellowships at ASU,
please see: http://provost.asu.edu/postdoc.

*Eligibility*

Applicants must have an earned or pending doctoral degree in Neuroscience,
Statistics, Social Psychology, Cognitive Psychology, or a related
field/discipline. The degree must have been earned no earlier than 2010.
Candidates with pending degrees who will have successfully defended their
dissertations by May 1, 2012 will also be considered. Applicants must have
no more than two years of formal postdoctoral experience.

*Required Expertise*

Applicants must have relevant expertise in fMRI data acquisition and
analysis and/or EEG data acquisition and analysis, as applied to the study
of cognitive or social psychological processes.

*Desired Expertise*

Relevant expertise or experience in multi-modal mapping (fMRI + EEG) of
cognitive and social psychological processes and/or neuropsychology of
narrative or persuasion is desirable.

*Responsibilities*

Postdoctoral scholars are expected to carry out the research plan and
fulfill the goals established with the supervising faculty members, Drs.
Gene Brewer and Leslie Baxter; to assist the supervising faculty members
and other Principal Investigators in fulfilling the requirements of the
grant in a timely manner; to communicate regularly with the supervising
faculty member and other members of the research team; and to notify the
faculty member of any change in research plans.

Beyond grant-related activities, our facilities will help create valuable
opportunities for the postdoctoral scholar to continue their fMRI and EEG
research agenda, develop new multi-modal techniques, teach, and get
training experience.

For further information about the position contact Prof. Gene Brewer,
gene.brewer at asu.edu

*Application*

Submit application materials electronically with all documents included in
a single PDF file, to include the following:

1. A cover letter stating your interest in the Postdoctoral Fellowship.
Provide details on

a. how your research and expertise relates to neuroimaging, especially with
regard to combining data from fMRI and EEG.

b. how your research and expertise relates to the project described above,
and

c. your long-term professional goals.

2. An up to date curriculum vitae.

3. Names and contact information for two references who agree to be
contacted.

4. Copies of up to three published papers/scholarly work.

5. Scanned copies of current academic transcript from all degree awarding
institutions. Official transcripts will be requested from those who
received formal offers.

The search will initially close with applications received by* April 15,
2012*.  If the position is not filled, then applications will be accepted
every subsequent Friday until search is closed.

Send materials to:

Josephine Wong, Program Manager

Center for Strategic Communication

jody at asu.edu

ASU is an equal opportunity/affirmative action employer committed to
excellence through diversity.  Women and minorities are encouraged to apply.
ASU’s complete non-discrimination statement can be found at:
http://www.asu.edu/titleIX/

-- 
Gene A. Brewer Jr.
Arizona State University
Department of Psychology
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From alotof_xd at yahoo.com  Tue Mar  6 21:52:37 2012
From: alotof_xd at yahoo.com (alotof eve)
Date: Tue, 6 Mar 2012 12:52:37 -0800 (PST)
Subject: [FieldTrip] error message in databrowser
In-Reply-To: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
References: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
Message-ID: <1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>

Hello, experts,

I am using ICA following the tutirial steps. 
I got IC dataset "comp" with the command: comp = ft_componentanalysis (cfg, data);
and ft_topoplotIC(cfg, comp) works.

However, then I used ft_databrowser(cfg, comp), I got an error message:
Operands to the || and && operators must be
convertible to logical scalar values.

Error in ft_databrowser (line 135)
if hasdata && isfield(data, 'topo') &&
strmatch (cfg.viewmode, 'component')

Can anyone know the way to settle this? 
Thanks in advance.

Eve
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From alotof_xd at yahoo.com  Wed Mar  7 09:01:59 2012
From: alotof_xd at yahoo.com (alotof eve)
Date: Wed, 7 Mar 2012 00:01:59 -0800 (PST)
Subject: [FieldTrip] error message in databrowser
In-Reply-To: <1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>
References: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
	<1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>
Message-ID: <1331107319.55433.YahooMailNeo@web125502.mail.ne1.yahoo.com>

Updated: I changed "&&" to "&", it worked but later a new error happened:

Reference to non-existent field 'hlim'.

Error in ft_databrowser>redraw_cb (line 1015)
             eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - opt.hlim(1)); 

 
Error in ft_databrowser (line 434)
redraw_cb(h);
_____
Thanks,
Eve



________________________________
 From: alotof eve <alotof_xd at yahoo.com>
To: Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
Sent: Tuesday, March 6, 2012 12:52 PM
Subject: [FieldTrip] error message in databrowser
 

Hello, experts,

I am using ICA following the tutirial steps. 
I got IC dataset "comp" with the command: comp = ft_componentanalysis (cfg, data);
and ft_topoplotIC(cfg, comp) works.

However, then I used ft_databrowser(cfg, comp), I got an error message:
Operands to the || and && operators must be
convertible to logical scalar values.

Error in ft_databrowser (line 135)
if hasdata && isfield(data, 'topo') &&
strmatch (cfg.viewmode, 'component')

Can anyone know the way to settle this? 
Thanks in advance.

Eve


_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From mcoskun at mail.uh.edu  Wed Mar  7 14:26:04 2012
From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun)
Date: Wed, 07 Mar 2012 07:26:04 -0600
Subject: [FieldTrip] error message in databrowser
In-Reply-To: <1331107319.55433.YahooMailNeo@web125502.mail.ne1.yahoo.com>
References: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
	<1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>
	<1331107319.55433.YahooMailNeo@web125502.mail.ne1.yahoo.com>
Message-ID: <7050dbcfcd6be.4f570d8c@mail.uh.edu>

Hi Eve,


I have posted same error earlier but got no suggestions. In my case, the error started popping up after i tried using parallel processing, but i don't know if this has anything to do with the error. I tried many things but no result.


finally, i simply uninstalled and re-installed matlab and everything worked perfectly there after. You may want to try this as a final option if you don't hear any other solution.


Mehmet

----- Original Message -----
From: alotof eve <alotof_xd at yahoo.com>
Date: Wednesday, March 7, 2012 2:03 am
Subject: Re: [FieldTrip] error message in databrowser
To: alotof eve <alotof_xd at yahoo.com>, Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl>



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



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



> Updated: I changed "&&" to "&", it worked but later a new error happened:

> 

> Reference to non-existent field 'hlim'.
> 

> Error in ft_databrowser>redraw_cb (line 1015)
>              eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - opt.hlim(1)); 

>  
> Error in ft_databrowser (line 434)
> redraw_cb(h);
> _____
> Thanks,
> Eve

> 
>
-----------------------------------------------------------
From: alotof eve <alotof_xd at yahoo.com>
> To: Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
> Sent: Tuesday, March 6, 2012 12:52 PM
> Subject: [FieldTrip] error message in databrowser
>
> 

> Hello, experts,
> 
> I am using ICA following the tutirial steps. 
> I got IC dataset "comp" with the command: comp = ft_componentanalysis (cfg, data);
> and ft_topoplotIC(cfg, comp) works.
> 
> However, then I used ft_databrowser(cfg, comp), I got an error message:
> Operands to the || and && operators must be
> convertible to logical scalar values.
> 
> Error in ft_databrowser (line 135)
> if hasdata && isfield(data, 'topo') &&
> strmatch (cfg.viewmode, 'component')
> 
> Can anyone know the way to settle this? 
> Thanks in advance.
> 
> Eve
>

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



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From MEpstein at NKI.RFMH.ORG  Wed Mar  7 18:28:48 2012
From: MEpstein at NKI.RFMH.ORG (Epstein, Michael)
Date: Wed, 7 Mar 2012 12:28:48 -0500
Subject: [FieldTrip] Error -> ft_databrowser
Message-ID: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>

Hi - I am actually encountering the same error with databrowser, and was
wondering if you ever came up with a solution to this problem - or if
anyone else has a solution - I didn't find a response on the mailing
list.

 

-Michael

 

 

 

________________________________

Dear Fieldtrippers,

 

 

I am encountering a strange error while i try to use ft_databrowser. The
error code is as below. I have never seen this error earlier. I used
ft_databrowser many times and its only last 2 days that i am getting the
error. I downloaded a newer version of fieldtrip (fieldtrip-20120130)
and used the newer version but still the same error. Strangely, i dont
get this error when i tried with other computers (same matlab version
(R2010a), same operating system (windows 7) on both computers. Has
anyone got this error before? what may cause this error?

 

 

fieldtrip version 20120130, matlab version R2010a, operating system
windows 7.

 

 

Thanks in advance for any suggestions.

 

 

 

??? Error using ==> ft_fetch_data at 57

data does not contain a consistent trial definition, fetching data is
not

possible

 

 

Error in ==> ft_databrowser>redraw_cb at 1159

art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample',
endsample);

 

 

Error in ==> ft_databrowser at 535

redraw_cb(h);

 



Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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From max-philipp.stenner at med.ovgu.de  Wed Mar  7 18:46:06 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Wed, 07 Mar 2012 17:46:06 +0000
Subject: [FieldTrip] ft_sourcestatistics
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830C999B@ESEN4.imed.uni-magdeburg.de>

Dear fieldtrip users,



I am encountering a problem with ft_sourcestatistics when using output from ft_sourcegrandaverage. My parameter of interest is a logratio: log(mean(moments(time of interest))/mean(moments(baseline))) which I simply named 'pow' to be compatible with ft functions. Apart from this, nothing else deviates from how fieldtrip handles the data/nothing else was changed 'manually'.



The problem arises from the fact that the existence of 10 different subjects in the grandaverage (in the usual 1x10 struct field 'trial') isn't represented in the 'powdimord' field of the data after ft_checkdata(varargin{i}, 'datatype', {'source', 'volume'}, 'feedback', 'no', 'inside', 'index', 'sourcerepresentation', 'new'); in the new implementation of ft_sourcestatistics:



varargin{1}

ans =



(before ft_checkdata:)



        pos: [8196x3 double]
        var: [1x1 struct]
     dimord: 'voxel'
      trial: [1x10 struct]
     inside: [8196x1 double]
    outside: [0x1 double]
         df: [8196x1 double]
        cfg: [1x1 struct]



(after ft_checkdata:)



          pos: [8196x3 double]
          var: [1x1 struct]
       dimord: 'pos'
       inside: [8196x1 double]
      outside: [0x1 double]
           df: [8196x1 double]
          cfg: [1x1 struct]
          pow: [8196x10 double]
    powdimord: 'pos'



This leads to a (wrong) transpose of the design (originally row1 = uvar, row2 = ivar [with two conditions for a depsamples T test]) and ultimately to the message

'The data must contain at least two units (usually subjects).'



Any help would be much appreciated, thanks very much!

Max

(fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)


From mcoskun at mail.uh.edu  Wed Mar  7 18:55:38 2012
From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun)
Date: Wed, 07 Mar 2012 11:55:38 -0600
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
Message-ID: <7270aa3bcbfd9.4f574cba@mail.uh.edu>

Hi Michael,


I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. 


just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution.


But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution.


Mehmet





----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
Date: Wednesday, March 7, 2012 11:29 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: fieldtrip at donders.ru.nl



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



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


> Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list.
>  
> -Michael
>  
>  
>  
-----------------------------------------------------------
> Dear Fieldtrippers,
>  
>  
> I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error?
>  
>  
> fieldtrip version 20120130, matlab version R2010a, operating system windows 7.
>  
>  
> Thanks in advance for any suggestions.
>  
>  
>  
> ??? Error using ==> ft_fetch_data at 57
> data does not contain a consistent trial definition, fetching data is not
> possible
>  
>  
> Error in ==> ft_databrowser>redraw_cb at 1159
> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample);
>  
>  
> Error in ==> ft_databrowser at 535
> redraw_cb(h);
>  



-----------------------------------------------------------
> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. 

|-----------------------------------------------------------



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From MEpstein at NKI.RFMH.ORG  Wed Mar  7 18:57:25 2012
From: MEpstein at NKI.RFMH.ORG (Epstein, Michael)
Date: Wed, 7 Mar 2012 12:57:25 -0500
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <7270aa3bcbfd9.4f574cba@mail.uh.edu>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
	<7270aa3bcbfd9.4f574cba@mail.uh.edu>
Message-ID: <2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>

Interesting... can I ask what version of matlab you were running? and
was it 64 bit?

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Mehmet-Akif Coskun
Sent: Wednesday, March 07, 2012 12:56 PM
To: Email discussion list for the FieldTrip project
Cc: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Michael,


I have posted the question actually but I didn't hear any suggestions
about it. The same error was posted yesterday by someone else. 


just to repeat what i have replied in the other post, i tried many
things to solve it (changed the code, run the databrowser code line by
line, updated fieldtrip version at etc.), but none of them solved the
problem. I started getting the error after I tried using parallel
processing scripts in matlab. But as i said, i have no basis to say that
this caused the problem. So basically, i do not know any scientific
solution.


But an old school method solved the problem in my case. Simply i
uninstalled and re-installed matlab. Never got the error again. You may
want to try this. I have no other solution.


Mehmet





----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
Date: Wednesday, March 7, 2012 11:29 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: fieldtrip at donders.ru.nl

> Hi - I am actually encountering the same error with databrowser, and
was wondering if you ever came up with a solution to this problem - or
if anyone else has a solution - I didn't find a response on the mailing
list.

>  

> -Michael

>  

>  

>  

________________________________

> Dear Fieldtrippers,

>  

>  

> I am encountering a strange error while i try to use ft_databrowser.
The error code is as below. I have never seen this error earlier. I used
ft_databrowser many times and its only last 2 days that i am getting the
error. I downloaded a newer version of fieldtrip (fieldtrip-20120130)
and used the newer version but still the same error. Strangely, i dont
get this error when i tried with other computers (same matlab version
(R2010a), same operating system (windows 7) on both computers. Has
anyone got this error before? what may cause this error?

>  

>  

> fieldtrip version 20120130, matlab version R2010a, operating system
windows 7.

>  

>  

> Thanks in advance for any suggestions.

>  

>  

>  

> ??? Error using ==> ft_fetch_data at 57

> data does not contain a consistent trial definition, fetching data is
not

> possible

>  

>  

> Error in ==> ft_databrowser>redraw_cb at 1159

> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample',
endsample);

>  

>  

> Error in ==> ft_databrowser at 535

> redraw_cb(h);

>  

 

________________________________

> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the
intended recipient. It may contain confidential information which is
legally privilegedor otherwise protected by law. If you received this
e-mail in error or from someone who is not authorized to send it to you,
you are strictly prohibited from reviewing, using, disseminating,
distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE
ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank
you for your cooperation. 

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



Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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From jnortonf at uci.edu  Wed Mar  7 19:05:43 2012
From: jnortonf at uci.edu (Jessamy Norton-Ford)
Date: Wed, 7 Mar 2012 10:05:43 -0800
Subject: [FieldTrip] EEG layout help
Message-ID: <CACvc6xQXFTQ+wnLafdrx7nFnjwZNF6GMOPMYOh2BvjasELDdpw@mail.gmail.com>

Hello,

I am trying to use the plotting functions with my 34-channel data (32
standard EEG channels + VEOG and HEOG).  In EEGLAB, I use the
'standard-10-5-cap385.elp' file for the locations, however I get the
following error in Fieldtrip (v. 20120220).

cfg = [];
cfg.baseline         = [-0.5 -0.1];
cfg.baselinetype     = 'absolute';
cfg.zlim             = [-3e-25 3e-25];
cfg.showlabels       = 'yes';
cfg.layout           = 'standard-10-5-cap385.elp';
figure
ft_multiplotTFR(cfg, TFRwave)
creating layout from electrode file standard-10-5-cap385.elp
??? Error using ==> ft_read_sens at 84
unknown fileformat for electrodes or gradiometers

Error in ==> ft_prepare_layout at 253
  lay = sens2lay(ft_read_sens(cfg.layout), cfg.rotate, cfg.projection,
  cfg.style);

Error in ==> ft_multiplotTFR at 241
lay = ft_prepare_layout(cfg, data);

In ft_read_sens, it appears as though fieldtrip cannot yet deal with such
.elp files?  I wonder if (1) I am making an easy mistake as I am still new
to Fieldtrip, or (2) if there is perhaps an easy workaround for this .elp
incompatibility?

In case it is useful, here are the channels that I am using:

1 Fp1  2 Fpz  3 Fp2  4 F7  5 F3  6 Fz  7 F4  8 F8  9 FC5  10 FC1  11 FC2  12
FC6  13 M1  14 T7  15 C3  16 Cz  17 C4  18 T8  19 M2  20 CP5  21 CP1
22 CP2  23
CP6  24 P7  25 P3  26 Pz  27 P4  28 P8  29 POz  30 O1  31 Oz  32 O2
33 VEOG  34
HEOG

Thanks very much,

Jessamy Norton-Ford








-- 
Jessamy Norton-Ford
Doctoral Student, Department of Cognitive Sciences
University of California, Irvine
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From mcoskun at mail.uh.edu  Wed Mar  7 19:17:33 2012
From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun)
Date: Wed, 07 Mar 2012 12:17:33 -0600
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
	<7270aa3bcbfd9.4f574cba@mail.uh.edu>
	<2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
Message-ID: <72b0dfc7cc8ec.4f5751dd@mail.uh.edu>

Matlab R2010a 64-bit under windows 7. I did not update matlab version. just uninstalled and re-installed the same version. 


Mehmet

----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
Date: Wednesday, March 7, 2012 11:58 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl>



| 


> Interesting... can I ask what version of matlab you were running? and was it 64 bit?
>  
> -Michael
>  
> From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Mehmet-Akif Coskun
> Sent: Wednesday, March 07, 2012 12:56 PM
> To: Email discussion list for the FieldTrip project
> Cc: fieldtrip at donders.ru.nl
> Subject: Re: [FieldTrip] Error -> ft_databrowser
>  
> Hi Michael,
> 
> 
> I have posted the question actually but I didn't hear any suggestions about it. The same error was posted yesterday by someone else. 
> 
> 
> just to repeat what i have replied in the other post, i tried many things to solve it (changed the code, run the databrowser code line by line, updated fieldtrip version at etc.), but none of them solved the problem. I started getting the error after I tried using parallel processing scripts in matlab. But as i said, i have no basis to say that this caused the problem. So basically, i do not know any scientific solution.
> 
> 
> But an old school method solved the problem in my case. Simply i uninstalled and re-installed matlab. Never got the error again. You may want to try this. I have no other solution.
> 
> 
> Mehmet
> 
> 
> 
> 
> 
> ----- Original Message -----
> From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
> Date: Wednesday, March 7, 2012 11:29 am
> Subject: Re: [FieldTrip] Error -> ft_databrowser
> To: fieldtrip at donders.ru.nl

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

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



-----------------------------------------------------------
> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. 

|-----------------------------------------------------------


> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
-----------------------------------------------------------
|
> > Hi - I am actually encountering the same error with databrowser, and was wondering if you ever came up with a solution to this problem - or if anyone else has a solution - I didn't find a response on the mailing list.
>  
> -Michael
>  
>  
>  
-----------------------------------------------------------
> > Dear Fieldtrippers,
> >  
> >  
> > I am encountering a strange error while i try to use ft_databrowser. The error code is as below. I have never seen this error earlier. I used ft_databrowser many times and its only last 2 days that i am getting the error. I downloaded a newer version of fieldtrip (fieldtrip-20120130) and used the newer version but still the same error. Strangely, i dont get this error when i tried with other computers (same matlab version (R2010a), same operating system (windows 7) on both computers. Has anyone got this error before? what may cause this error?
> >  
> >  
> > fieldtrip version 20120130, matlab version R2010a, operating system windows 7.
> >  
> >  
> > Thanks in advance for any suggestions.
> >  
> >  
> >  
> > ??? Error using ==> ft_fetch_data at 57
> > data does not contain a consistent trial definition, fetching data is not
> > possible
> >  
> >  
> > Error in ==> ft_databrowser>redraw_cb at 1159
> > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', endsample);
> >  
> >  
> > Error in ==> ft_databrowser at 535
> > redraw_cb(h);
> >  
>  
-----------------------------------------------------------
> > Conserve Resources. Print only when necessary.
> > 
> > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. 
| -----------------------------------------------------------



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From alotof_xd at yahoo.com  Thu Mar  8 08:04:14 2012
From: alotof_xd at yahoo.com (alotof eve)
Date: Wed, 7 Mar 2012 23:04:14 -0800 (PST)
Subject: [FieldTrip] error message in databrowser
In-Reply-To: <7050dbcfcd6be.4f570d8c@mail.uh.edu>
References: <D0BF906E-A026-4685-B100-ACA077034DB3@donders.ru.nl>
	<1331067157.67890.YahooMailNeo@web125504.mail.ne1.yahoo.com>
	<1331107319.55433.YahooMailNeo@web125502.mail.ne1.yahoo.com>
	<7050dbcfcd6be.4f570d8c@mail.uh.edu>
Message-ID: <1331190254.90650.YahooMailNeo@web125502.mail.ne1.yahoo.com>

Hi, Mehmet,

Thank you so much for the suggestion. I will try this and will report the result.

Thanks,
Eve



________________________________
 From: Mehmet-Akif Coskun <mcoskun at mail.uh.edu>
To: alotof eve <alotof_xd at yahoo.com>; Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
Cc: alotof eve <alotof_xd at yahoo.com>; Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
Sent: Wednesday, March 7, 2012 5:26 AM
Subject: Re: [FieldTrip] error message in databrowser
 

Hi Eve,


I have posted same error earlier but got no suggestions. In my case, the error started popping up after i tried using parallel processing, but i don't know if this has anything to do with the error. I tried many things but no result.


finally, i simply uninstalled and re-installed matlab and everything worked perfectly there after. You may want to try this as a final option if you don't hear any other solution.


Mehmet

----- Original Message -----
From: alotof eve <alotof_xd at yahoo.com>
Date: Wednesday, March 7, 2012 2:03 am
Subject: Re: [FieldTrip] error message in databrowser
To: alotof eve <alotof_xd at yahoo.com>, Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl>


> Updated: I changed "&&" to "&", it worked but later a new error happened:
> 

> Reference to non-existent field 'hlim'.
> 

> Error in ft_databrowser>redraw_cb (line 1015)
>              eventtim = (eventtim - opt.hlim(1)) / (opt.hlim(2) - opt.hlim(1)); 

>  
> Error in ft_databrowser (line 434)
> redraw_cb(h);
> _____
> Thanks,
> Eve

> 
>  

________________________________
 From: alotof eve <alotof_xd at yahoo.com>
>  To: Email discussion list for the FieldTrip project <fieldtrip at donders.ru.nl> 
>  Sent: Tuesday, March 6, 2012 12:52 PM
>  Subject: [FieldTrip] error message in databrowser
>   >  



> Hello, experts,
> 
> I am using ICA following the tutirial steps. 
> I got IC dataset "comp" with the command: comp = ft_componentanalysis (cfg, data);
> and ft_topoplotIC(cfg, comp) works.
> 
> However, then I used ft_databrowser(cfg, comp), I got an error message:
> Operands to the || and && operators must be
> convertible to logical scalar values.
> 
> Error in ft_databrowser (line 135)
> if hasdata && isfield(data, 'topo') &&
> strmatch (cfg.viewmode, 'component')
> 
> Can anyone know the way to settle this? 
> Thanks in advance.
> 
> Eve
>  

>  >  > 
> _______________________________________________
> 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 h.morgan at bangor.ac.uk  Thu Mar  8 10:49:59 2012
From: h.morgan at bangor.ac.uk (Helen Morgan)
Date: Thu, 08 Mar 2012 09:49:59 +0000
Subject: [FieldTrip] Call for abstracts - HIVE workshop - Berlin,
	April 27-28th, 2012
Message-ID: <4F5880C7.7020608@bangor.ac.uk>

Call for abstracts

HIVE WORKSHOP - Berlin, April 27-28th, 2012.

Could computers someday interact directly with the human brain? The 
vision of HIVE is that in the next 50 years we will witness the coming 
of age of technologies for fluent brain-computer and computer-mediated 
brain-to-brain interaction. While recent research has delivered 
important breakthroughs in brain-to-computer transmission, little has 
been achieved in the other direction––computer-controlled brain 
stimulation. The goal of the workshop is to present research toward 
developing a new generation of powerful and controllable non-invasive 
brain stimulation technologies.

State-of-the-art presentations on current distribution models and 
multi-scale neuron current interaction modeling will be presented. 
Results from stimulation experiments using tDCS, TMS, EEG and fMRI in 
different scenarios are given in overview and original presentations. 
Discussions during the workshop will lead to the design of multisite 
transcranial current stimulation technologies using real time EEG 
monitoring and feedback.

Keynote speakers:

Dr. Michael Nitsche
Dr. Klaus-Robert Müller
Dr. Lisa Marshall
Dr. Fabio Babiloni

The HIVE project has opened this workshop to all researchers from in 
this new multi-disciplinary field, based on acceptance of an abstract. 
You can find the Call for Abstracts here.

http://hive-eu.org/hive2012/call_for_papers

Best abstracts and presentations will be selected for publication in a 
Special Issue of the journal "Physiological Measurement".

Download the flyer here 
http://hive-eu.org/sites/hive-eu.org/files/Hive%20workshop%202012_final.pdf

-- 
Dr. Helen M. Morgan
Research Officer
Wolfson Centre for Clinical and Cognitive Neuroscience
School of Psychology
Bangor University
tel: 01248 388172
email: h.morgan at bangor.ac.uk

-- 
Rhif Elusen Gofrestredig / Registered Charity No. 1141565

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From max-philipp.stenner at med.ovgu.de  Thu Mar  8 13:26:13 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Thu, 08 Mar 2012 12:26:13 +0000
Subject: [FieldTrip] monte-carlo on LCMV moments
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830C9AB1@ESEN4.imed.uni-magdeburg.de>

Dear fieldtrip users, 

in addition to the question on the new implementation of ft_sourcestatistics for sourcegrandaveraged data which I sent yesterday, I have a second question regarding sourcestatistics on grandaveraged data obtained from LCMV beamforming of ERF. 

I would like to perfrom cluster corrected monte-carlo statistics on subj_voxel_time dipole moments, comparable (in its dimensions) to the sensor-level ERF cluster permutation test on subj_channel_time data that is described in the respective tutorial and that worked well. 

However, ft_sourcegrandaverage doesn't seem to permit "averaging" (with keepindividual = yes) of parameters that have more than one value per gridpoint (i.e. other than pow, nai etc.). 

In addition, the get_source_lcmv_mom subfunction in statistics_wrapper requires 4 rather than 3 dimensions. 

Is there any way that subj_voxel_time dipole moment data can be used for monte-carlo statistics comparable to the respective sensor-level ERF test?

Thanks very much, 

best wishes
Max
(fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)






________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]&quot; im Auftrag von &quot;Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de]
Gesendet: Mittwoch, 7. März 2012 18:46
Bis: Email discussion list for the FieldTrip project
Betreff: [FieldTrip] ft_sourcestatistics

Dear fieldtrip users,



I am encountering a problem with ft_sourcestatistics when using output from ft_sourcegrandaverage. My parameter of interest is a logratio: log(mean(moments(time of interest))/mean(moments(baseline))) which I simply named 'pow' to be compatible with ft functions. Apart from this, nothing else deviates from how fieldtrip handles the data/nothing else was changed 'manually'.



The problem arises from the fact that the existence of 10 different subjects in the grandaverage (in the usual 1x10 struct field 'trial') isn't represented in the 'powdimord' field of the data after ft_checkdata(varargin{i}, 'datatype', {'source', 'volume'}, 'feedback', 'no', 'inside', 'index', 'sourcerepresentation', 'new'); in the new implementation of ft_sourcestatistics:



varargin{1}

ans =



(before ft_checkdata:)



        pos: [8196x3 double]
        var: [1x1 struct]
     dimord: 'voxel'
      trial: [1x10 struct]
     inside: [8196x1 double]
    outside: [0x1 double]
         df: [8196x1 double]
        cfg: [1x1 struct]



(after ft_checkdata:)



          pos: [8196x3 double]
          var: [1x1 struct]
       dimord: 'pos'
       inside: [8196x1 double]
      outside: [0x1 double]
           df: [8196x1 double]
          cfg: [1x1 struct]
          pow: [8196x10 double]
    powdimord: 'pos'



This leads to a (wrong) transpose of the design (originally row1 = uvar, row2 = ivar [with two conditions for a depsamples T test]) and ultimately to the message

'The data must contain at least two units (usually subjects).'



Any help would be much appreciated, thanks very much!

Max

(fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From jan.schoffelen at donders.ru.nl  Thu Mar  8 13:38:46 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 8 Mar 2012 13:38:46 +0100
Subject: [FieldTrip] ft_sourcestatistics
In-Reply-To: <FBEFFA1F493D8944969D2F5AE78E58830C999B@ESEN4.imed.uni-magdeburg.de>
References: <FBEFFA1F493D8944969D2F5AE78E58830C999B@ESEN4.imed.uni-magdeburg.de>
Message-ID: <23891D6F-057F-4DBE-8C52-C43DAB74608E@donders.ru.nl>

Hi Max,

At the moment we are designing some major code changes to deal with source level data, and we need to ask you for some patience in this regard.
For now, you could try to move the call to ft_checkdata to outside ft_sourcestatistics, and change the powdimord into 'pos_rpt'; 
Does it work if you subsequently call ft_sourcestatistics (with cfg.implementation = 'new')? This new implementation has never fully matured and may be instable. It has been found to work in certain situations, but it has never been fully tested on all possible processing histories that users may throw at it. Hence the urgent need to clean up the code. 

Best,

Jan-Mathijs



On Mar 7, 2012, at 6:46 PM, Stenner, Max-Philipp wrote:

> Dear fieldtrip users,
> 
> 
> 
> I am encountering a problem with ft_sourcestatistics when using output from ft_sourcegrandaverage. My parameter of interest is a logratio: log(mean(moments(time of interest))/mean(moments(baseline))) which I simply named 'pow' to be compatible with ft functions. Apart from this, nothing else deviates from how fieldtrip handles the data/nothing else was changed 'manually'.
> 
> 
> 
> The problem arises from the fact that the existence of 10 different subjects in the grandaverage (in the usual 1x10 struct field 'trial') isn't represented in the 'powdimord' field of the data after ft_checkdata(varargin{i}, 'datatype', {'source', 'volume'}, 'feedback', 'no', 'inside', 'index', 'sourcerepresentation', 'new'); in the new implementation of ft_sourcestatistics:
> 
> 
> 
> varargin{1}
> 
> ans =
> 
> 
> 
> (before ft_checkdata:)
> 
> 
> 
>        pos: [8196x3 double]
>        var: [1x1 struct]
>     dimord: 'voxel'
>      trial: [1x10 struct]
>     inside: [8196x1 double]
>    outside: [0x1 double]
>         df: [8196x1 double]
>        cfg: [1x1 struct]
> 
> 
> 
> (after ft_checkdata:)
> 
> 
> 
>          pos: [8196x3 double]
>          var: [1x1 struct]
>       dimord: 'pos'
>       inside: [8196x1 double]
>      outside: [0x1 double]
>           df: [8196x1 double]
>          cfg: [1x1 struct]
>          pow: [8196x10 double]
>    powdimord: 'pos'
> 
> 
> 
> This leads to a (wrong) transpose of the design (originally row1 = uvar, row2 = ivar [with two conditions for a depsamples T test]) and ultimately to the message
> 
> 'The data must contain at least two units (usually subjects).'
> 
> 
> 
> Any help would be much appreciated, thanks very much!
> 
> Max
> 
> (fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)
> _______________________________________________
> 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

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From r.vandermeij at donders.ru.nl  Thu Mar  8 13:59:07 2012
From: r.vandermeij at donders.ru.nl (Roemer van der Meij)
Date: Thu, 08 Mar 2012 13:59:07 +0100
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org>
	<7270aa3bcbfd9.4f574cba@mail.uh.edu>
	<2586A1048152BE4D861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
Message-ID: <4F58AD1B.906@donders.ru.nl>

Hi Eve, Hi Michael,

I cannot find the specific line of code in the latest version, so I 
assume you are using an old version? If you update to the latest 
version, the problem should be solved.

Just for your curiosity, the bug was most likely caused by using the 
ancient strmatch (deprecated in later version of matlab). Changing it 
strcmp would have most likely fixed the problem.

Cheers,
Roemer




On 07-03-12 18:57, Epstein, Michael wrote:
>
> Interesting... can I ask what version of matlab you were running? and 
> was it 64 bit?
>
> -Michael
>
> *From:*fieldtrip-bounces at donders.ru.nl 
> [mailto:fieldtrip-bounces at donders.ru.nl] *On Behalf Of *Mehmet-Akif Coskun
> *Sent:* Wednesday, March 07, 2012 12:56 PM
> *To:* Email discussion list for the FieldTrip project
> *Cc:* fieldtrip at donders.ru.nl
> *Subject:* Re: [FieldTrip] Error -> ft_databrowser
>
> Hi Michael,
>
>
> I have posted the question actually but I didn't hear any suggestions 
> about it. The same error was posted yesterday by someone else.
>
>
> just to repeat what i have replied in the other post, i tried many 
> things to solve it (changed the code, run the databrowser code line by 
> line, updated fieldtrip version at etc.), but none of them solved the 
> problem. I started getting the error after I tried using parallel 
> processing scripts in matlab. But as i said, i have no basis to say 
> that this caused the problem. So basically, i do not know any 
> scientific solution.
>
>
> But an old school method solved the problem in my case. Simply i 
> uninstalled and re-installed matlab. Never got the error again. You 
> may want to try this. I have no other solution.
>
>
> Mehmet
>
>
>
>
>
> ----- Original Message -----
> From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
> Date: Wednesday, March 7, 2012 11:29 am
> Subject: Re: [FieldTrip] Error -> ft_databrowser
> To: fieldtrip at donders.ru.nl
>
> > Hi - I am actually encountering the same error with databrowser, and 
> was wondering if you ever came up with a solution to this problem - or 
> if anyone else has a solution - I didn't find a response on the 
> mailing list.
>
> >
>
> > -Michael
>
> >
>
> >
>
> >
>
> ------------------------------------------------------------------------
>
> > Dear Fieldtrippers,
>
> >
>
> >
>
> > I am encountering a strange error while i try to use ft_databrowser. 
> The error code is as below. I have never seen this error earlier. I 
> used ft_databrowser many times and its only last 2 days that i am 
> getting the error. I downloaded a newer version of fieldtrip 
> (fieldtrip-20120130) and used the newer version but still the same 
> error. Strangely, i dont get this error when i tried with other 
> computers (same matlab version (R2010a), same operating system 
> (windows 7) on both computers. Has anyone got this error before? what 
> may cause this error?
>
> >
>
> >
>
> > fieldtrip version 20120130, matlab version R2010a, operating system 
> windows 7.
>
> >
>
> >
>
> > Thanks in advance for any suggestions.
>
> >
>
> >
>
> >
>
> > ??? Error using ==> ft_fetch_data at 57
>
> > data does not contain a consistent trial definition, fetching data is not
>
> > possible
>
> >
>
> >
>
> > Error in ==> ft_databrowser>redraw_cb at 1159
>
> > art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample', 
> endsample);
>
> >
>
> >
>
> > Error in ==> ft_databrowser at 535
>
> > redraw_cb(h);
>
> >
>
> ------------------------------------------------------------------------
>
> > Conserve Resources. Print only when necessary.
> >
> > IMPORTANT NOTICE: This e-mail is meant only for the use of the 
> intended recipient. It may contain confidential information which is 
> legally privilegedor otherwise protected by law. If you received this 
> e-mail in error or from someone who is not authorized to send it to 
> you, you are strictly prohibited from reviewing, using, disseminating, 
> distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF 
> THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. 
> Thank you for your cooperation.
>
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> ------------------------------------------------------------------------
> Conserve Resources. Print only when necessary.
>
> IMPORTANT NOTICE: This e-mail is meant only for the use of the 
> intended recipient. It may contain confidential information which is 
> legally privilegedor otherwise protected by law. If you received this 
> e-mail in error or from someone who is not authorized to send it to 
> you, you are strictly prohibited from reviewing, using, disseminating, 
> distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF 
> THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. 
> Thank you for your cooperation.
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

-- 
Roemer van der Meij M.Sc.
PhD student
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 max-philipp.stenner at med.ovgu.de  Thu Mar  8 14:36:16 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Thu, 08 Mar 2012 13:36:16 +0000
Subject: [FieldTrip] ft_sourcestatistics
In-Reply-To: <23891D6F-057F-4DBE-8C52-C43DAB74608E@donders.ru.nl>
References: <FBEFFA1F493D8944969D2F5AE78E58830C999B@ESEN4.imed.uni-magdeburg.de>
	<23891D6F-057F-4DBE-8C52-C43DAB74608E@donders.ru.nl>
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830C9AD3@ESEN4.imed.uni-magdeburg.de>

Hi Jan-Mathijs,



thank you for your response, since it worked for cfg.implementation = 'old' I haven't tried your suggestion of calling ft_checkdata outside of ft_sourcestatistics so far but will later during the day,



thanks again,

best

Max



________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]" im Auftrag von "jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl]
Gesendet: Donnerstag, 8. März 2012 13:38
Bis: Email discussion list for the FieldTrip project
Betreff: Re: [FieldTrip] ft_sourcestatistics

Hi Max,

At the moment we are designing some major code changes to deal with source level data, and we need to ask you for some patience in this regard.
For now, you could try to move the call to ft_checkdata to outside ft_sourcestatistics, and change the powdimord into 'pos_rpt';
Does it work if you subsequently call ft_sourcestatistics (with cfg.implementation = 'new')? This new implementation has never fully matured and may be instable. It has been found to work in certain situations, but it has never been fully tested on all possible processing histories that users may throw at it. Hence the urgent need to clean up the code.

Best,

Jan-Mathijs



On Mar 7, 2012, at 6:46 PM, Stenner, Max-Philipp wrote:

Dear fieldtrip users,



I am encountering a problem with ft_sourcestatistics when using output from ft_sourcegrandaverage. My parameter of interest is a logratio: log(mean(moments(time of interest))/mean(moments(baseline))) which I simply named 'pow' to be compatible with ft functions. Apart from this, nothing else deviates from how fieldtrip handles the data/nothing else was changed 'manually'.



The problem arises from the fact that the existence of 10 different subjects in the grandaverage (in the usual 1x10 struct field 'trial') isn't represented in the 'powdimord' field of the data after ft_checkdata(varargin{i}, 'datatype', {'source', 'volume'}, 'feedback', 'no', 'inside', 'index', 'sourcerepresentation', 'new'); in the new implementation of ft_sourcestatistics:



varargin{1}

ans =



(before ft_checkdata:)



       pos: [8196x3 double]
       var: [1x1 struct]
    dimord: 'voxel'
     trial: [1x10 struct]
    inside: [8196x1 double]
   outside: [0x1 double]
        df: [8196x1 double]
       cfg: [1x1 struct]



(after ft_checkdata:)



         pos: [8196x3 double]
         var: [1x1 struct]
      dimord: 'pos'
      inside: [8196x1 double]
     outside: [0x1 double]
          df: [8196x1 double]
         cfg: [1x1 struct]
         pow: [8196x10 double]
   powdimord: 'pos'



This leads to a (wrong) transpose of the design (originally row1 = uvar, row2 = ivar [with two conditions for a depsamples T test]) and ultimately to the message

'The data must contain at least two units (usually subjects).'



Any help would be much appreciated, thanks very much!

Max

(fieldtrip version: fieldtrip-lite-20111130 on a Windows7 PC)
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl<mailto: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<mailto:J.Schoffelen at donders.ru.nl>
Telephone: +31-24-3614793




From MEpstein at NKI.RFMH.ORG  Thu Mar  8 16:17:56 2012
From: MEpstein at NKI.RFMH.ORG (Epstein, Michael)
Date: Thu, 8 Mar 2012 10:17:56 -0500
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <4F58AD1B.906@donders.ru.nl>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org><7270aa3bcbfd9.4f574cba@mail.uh.edu><2586A1048152BE4D
	861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org>
	<4F58AD1B.906@donders.ru.nl>
Message-ID: <2586A1048152BE4D861E64A98700AD420A999DCD@nki-mail.NKI.rfmh.org>

Interesting... I'll look into that if I ever have the issue again.
However following Mehmet's advice and simply reinstalling the same
version of MATLAB seems to have fixed the problem anyway - not exactly
sure how that happened, but at least it worked. 

 

Thanks for the advice anyway though,

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Roemer van der
Meij
Sent: Thursday, March 08, 2012 7:59 AM
To: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Eve, Hi Michael,

I cannot find the specific line of code in the latest version, so I
assume you are using an old version? If you update to the latest
version, the problem should be solved.

Just for your curiosity, the bug was most likely caused by using the
ancient strmatch (deprecated in later version of matlab). Changing it
strcmp would have most likely fixed the problem.

Cheers,
Roemer




On 07-03-12 18:57, Epstein, Michael wrote: 

Interesting... can I ask what version of matlab you were running? and
was it 64 bit?

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Mehmet-Akif Coskun
Sent: Wednesday, March 07, 2012 12:56 PM
To: Email discussion list for the FieldTrip project
Cc: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Michael,


I have posted the question actually but I didn't hear any suggestions
about it. The same error was posted yesterday by someone else. 


just to repeat what i have replied in the other post, i tried many
things to solve it (changed the code, run the databrowser code line by
line, updated fieldtrip version at etc.), but none of them solved the
problem. I started getting the error after I tried using parallel
processing scripts in matlab. But as i said, i have no basis to say that
this caused the problem. So basically, i do not know any scientific
solution.


But an old school method solved the problem in my case. Simply i
uninstalled and re-installed matlab. Never got the error again. You may
want to try this. I have no other solution.


Mehmet





----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
<mailto:MEpstein at NKI.RFMH.ORG> 
Date: Wednesday, March 7, 2012 11:29 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: fieldtrip at donders.ru.nl

> Hi - I am actually encountering the same error with databrowser, and
was wondering if you ever came up with a solution to this problem - or
if anyone else has a solution - I didn't find a response on the mailing
list.

>  

> -Michael

>  

>  

>  

________________________________

> Dear Fieldtrippers,

>  

>  

> I am encountering a strange error while i try to use ft_databrowser.
The error code is as below. I have never seen this error earlier. I used
ft_databrowser many times and its only last 2 days that i am getting the
error. I downloaded a newer version of fieldtrip (fieldtrip-20120130)
and used the newer version but still the same error. Strangely, i dont
get this error when i tried with other computers (same matlab version
(R2010a), same operating system (windows 7) on both computers. Has
anyone got this error before? what may cause this error?

>  

>  

> fieldtrip version 20120130, matlab version R2010a, operating system
windows 7.

>  

>  

> Thanks in advance for any suggestions.

>  

>  

>  

> ??? Error using ==> ft_fetch_data at 57

> data does not contain a consistent trial definition, fetching data is
not

> possible

>  

>  

> Error in ==> ft_databrowser>redraw_cb at 1159

> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample',
endsample);

>  

>  

> Error in ==> ft_databrowser at 535

> redraw_cb(h);

>  

 

________________________________

> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the
intended recipient. It may contain confidential information which is
legally privilegedor otherwise protected by law. If you received this
e-mail in error or from someone who is not authorized to send it to you,
you are strictly prohibited from reviewing, using, disseminating,
distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE
ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank
you for your cooperation. 

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

________________________________

Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally
privilegedor otherwise protected by law. If you received this e-mail in
error or from someone who is not authorized to send it to you, you are
strictly prohibited from reviewing, using, disseminating, distributing
or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY
RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for
your cooperation. 






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

 

-- 
Roemer van der Meij M.Sc.
PhD student
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



Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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From MEpstein at NKI.RFMH.ORG  Thu Mar  8 16:27:03 2012
From: MEpstein at NKI.RFMH.ORG (Epstein, Michael)
Date: Thu, 8 Mar 2012 10:27:03 -0500
Subject: [FieldTrip] Error -> ft_databrowser
In-Reply-To: <2586A1048152BE4D861E64A98700AD420A999DCD@nki-mail.NKI.rfmh.org>
References: <2586A1048152BE4D861E64A98700AD420A999C0B@nki-mail.NKI.rfmh.org><7270aa3bcbfd9.4f574cba@mail.uh.edu><2586A1048152BE4D
	861E64A98700AD420A999C27@nki-mail.NKI.rfmh.org><4F58AD1B.906@donders.ru.nl>
	<2586A1048152BE4D861E64A98700AD420A999DCD@nki-mail.NKI.rfmh.org>
Message-ID: <2586A1048152BE4D861E64A98700AD420A999DE5@nki-mail.NKI.rfmh.org>

Stephan said David is a 'guru' so that sounds good. He actually said
that he uses EEGLAB for ICA too, so I guess that really is the way to
go.

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Epstein, Michael
Sent: Thursday, March 08, 2012 10:18 AM
To: r.vandermeij at donders.ru.nl; Email discussion list for the FieldTrip
project
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Interesting... I'll look into that if I ever have the issue again.
However following Mehmet's advice and simply reinstalling the same
version of MATLAB seems to have fixed the problem anyway - not exactly
sure how that happened, but at least it worked. 

 

Thanks for the advice anyway though,

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Roemer van der
Meij
Sent: Thursday, March 08, 2012 7:59 AM
To: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Eve, Hi Michael,

I cannot find the specific line of code in the latest version, so I
assume you are using an old version? If you update to the latest
version, the problem should be solved.

Just for your curiosity, the bug was most likely caused by using the
ancient strmatch (deprecated in later version of matlab). Changing it
strcmp would have most likely fixed the problem.

Cheers,
Roemer




On 07-03-12 18:57, Epstein, Michael wrote: 

Interesting... can I ask what version of matlab you were running? and
was it 64 bit?

 

-Michael

 

From: fieldtrip-bounces at donders.ru.nl
[mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Mehmet-Akif Coskun
Sent: Wednesday, March 07, 2012 12:56 PM
To: Email discussion list for the FieldTrip project
Cc: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Error -> ft_databrowser

 

Hi Michael,


I have posted the question actually but I didn't hear any suggestions
about it. The same error was posted yesterday by someone else. 


just to repeat what i have replied in the other post, i tried many
things to solve it (changed the code, run the databrowser code line by
line, updated fieldtrip version at etc.), but none of them solved the
problem. I started getting the error after I tried using parallel
processing scripts in matlab. But as i said, i have no basis to say that
this caused the problem. So basically, i do not know any scientific
solution.


But an old school method solved the problem in my case. Simply i
uninstalled and re-installed matlab. Never got the error again. You may
want to try this. I have no other solution.


Mehmet





----- Original Message -----
From: "Epstein, Michael" <MEpstein at NKI.RFMH.ORG>
<mailto:MEpstein at NKI.RFMH.ORG> 
Date: Wednesday, March 7, 2012 11:29 am
Subject: Re: [FieldTrip] Error -> ft_databrowser
To: fieldtrip at donders.ru.nl

> Hi - I am actually encountering the same error with databrowser, and
was wondering if you ever came up with a solution to this problem - or
if anyone else has a solution - I didn't find a response on the mailing
list.

>  

> -Michael

>  

>  

>  

________________________________

> Dear Fieldtrippers,

>  

>  

> I am encountering a strange error while i try to use ft_databrowser.
The error code is as below. I have never seen this error earlier. I used
ft_databrowser many times and its only last 2 days that i am getting the
error. I downloaded a newer version of fieldtrip (fieldtrip-20120130)
and used the newer version but still the same error. Strangely, i dont
get this error when i tried with other computers (same matlab version
(R2010a), same operating system (windows 7) on both computers. Has
anyone got this error before? what may cause this error?

>  

>  

> fieldtrip version 20120130, matlab version R2010a, operating system
windows 7.

>  

>  

> Thanks in advance for any suggestions.

>  

>  

>  

> ??? Error using ==> ft_fetch_data at 57

> data does not contain a consistent trial definition, fetching data is
not

> possible

>  

>  

> Error in ==> ft_databrowser>redraw_cb at 1159

> art = ft_fetch_data(opt.artdata, 'begsample', begsample, 'endsample',
endsample);

>  

>  

> Error in ==> ft_databrowser at 535

> redraw_cb(h);

>  

 

________________________________

> Conserve Resources. Print only when necessary.
> 
> IMPORTANT NOTICE: This e-mail is meant only for the use of the
intended recipient. It may contain confidential information which is
legally privilegedor otherwise protected by law. If you received this
e-mail in error or from someone who is not authorized to send it to you,
you are strictly prohibited from reviewing, using, disseminating,
distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE
ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank
you for your cooperation. 

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

________________________________

Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally
privilegedor otherwise protected by law. If you received this e-mail in
error or from someone who is not authorized to send it to you, you are
strictly prohibited from reviewing, using, disseminating, distributing
or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY
RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for
your cooperation. 





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

 

-- 
Roemer van der Meij M.Sc.
PhD student
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

________________________________

Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended
recipient. It may contain confidential information which is legally
privilegedor otherwise protected by law. If you received this e-mail in
error or from someone who is not authorized to send it to you, you are
strictly prohibited from reviewing, using, disseminating, distributing
or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY
RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for
your cooperation. 



Conserve Resources. Print only when necessary.

IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
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From frerap at gist.ac.kr  Fri Mar  9 12:56:13 2012
From: frerap at gist.ac.kr (MinKyu Ahn)
Date: Fri, 9 Mar 2012 20:56:13 +0900 (KST)
Subject: [FieldTrip] question for ft_freqanalysis()
Message-ID: <1182294678.1331294173648.JavaMail.root@eunhasu>

I am new fieldtrip and wavelet analysis.



Fortunately, fieldtrip webpage has some examples for that.



While I follow it, I found that the scale between the resuts of fixed hann method and wavelet method in http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis.



When it plots results, the zlimt is used  as cfg.zlim         = [-3e-27 3e-27] while  it is used as [-3e-25 3e-25]    for wavelet.



The scale difference is about 10^2, why this happen?





Please let me know about it.







Thank you.






============================================================ MinKyu Ahn, Ph.D. Student, Member of BioComputing Lab. School of Information and Communications Gwangju Institute of Science and Technology (GIST)  261 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, Korea  Tel : +82-62-715-3126/2266  Cell : +82-10-7360-8232  E-mail : frerap at gist.ac.kr  URL : http://biocomput.gist.ac.kr ============================================================

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From matt.mollison at gmail.com  Fri Mar  9 20:16:42 2012
From: matt.mollison at gmail.com (Matt Mollison)
Date: Fri, 9 Mar 2012 12:16:42 -0700
Subject: [FieldTrip] Oscillatory power normalization
Message-ID: <CAJB8axm9J3=ktKM16bVhjFiToBOcD1RrVbn+1xxD4HiiqP1_WA@mail.gmail.com>

My questions essentially boil down to: what do people do for power
normalization when assessing statistical differences?

It gets more detailed below regarding examining event-related power changes
relative to a baseline (within-subjects, comparing two conditions, stimulus
onset = 0 ms). I didn't find much discussion of this on the list or the
wiki. Any references for these issues would also be appreciated.

(1) Does power data need to be baseline normalized for statistical tests
comparing conditions? Normalization would put power on equal footing across
all subjects, conditions, sensors, times, frequencies, etc., but it will
surely affect power during the stimulus period in a particular way. If so,
do the two (or more) conditions need to use the same baseline condition, or
can each trial be normalized to its own pre-stim baseline period (a la
ft_freqbaseline)? For either, it seems like you'd always need
keeptrials='yes' in ft_freqanalysis. However, it does not seem to get
normalized in the cluster_permutation_freq tutorial (within-subjects)---am
I missing something?

If we should normalize:
(2) I've read a number of papers that Z-transform stimulus period power
relative to pre-stim activity (subtract mean, divide by std) before doing
statistics. I've also read a lot that don't mention baselines, or e.g. do a
decibel [dB] transform. ft_freqbaseline does not have a Z-transform option.
There is ft_preproc_standardize, but this seems to operate at a lower level
than is usually recommended. Z-transforming seems like a good option, but
how can I use it in the FT pipeline for within-subjects analyses
(especially with keeptrials='no')? Alternatively, when should one use
'absolute', 'relative', or 'relchange'?

Regarding choosing the baseline period:
(3) It seems that the baseline period needs to precede stimulus onset by a
sufficient amount of time so that the stimulus period doesn't bleed into
the baseline; this time would be specific to both the frequency and either
wavelet width or taper window length. For example, at 4 Hz with wavelet
width=6 or a taper with 6 cycles per time window (t_ftimwin) the
wavelet/window would be 1500 ms long, and the end of the baseline must
precede stimulus onset by at least half this to keep them separate. At
lower frequencies this could get quite unruly (e.g., 1 Hz would require
ending 3000 ms before stimulus). Is this correct? Maybe that's why it's
better to have a single separate baseline condition. Anyway, the
timefrequencyanalysis tutorial seems to disregard this separation of
baseline and stimulus activity (as have many papers I've read), so maybe
I'm wrong about this being necessary.

Thanks for your time,
Matt Mollison

--
Univ. of Colorado at Boulder
Dept. of Psychology and Neuroscience
matthew.mollison at colorado.edu
http://psych.colorado.edu/~mollison/
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From cas243 at georgetown.edu  Sun Mar 11 22:52:15 2012
From: cas243 at georgetown.edu (Clara A. Scholl)
Date: Sun, 11 Mar 2012 17:52:15 -0400
Subject: [FieldTrip] clustering, spatial neighbors and minnbchan
In-Reply-To: <CAAHOyr7pc8qkmeJ4X9NOsGQAmEUsg3viPPYo5v+4d5rE3bQ-Mw@mail.gmail.com>
References: <CAAHOyr7pc8qkmeJ4X9NOsGQAmEUsg3viPPYo5v+4d5rE3bQ-Mw@mail.gmail.com>
Message-ID: <CAAHOyr6APDwrRwfONA0xuYXNJbhYKtNrpd0QuVxcKcAXTUL5Yg@mail.gmail.com>

Hi,

I have a question about how to identify appropriate parameters for
neighbor distance in ft_neighbourselection and how to set minnbchan
for space-time cluster analysis.

I identified a neighbor distance based on our sensor layout, so that
spatially adjacent channels were defined as neighbors, and spatially
non-adjacent channels were not defined as neighbors.  I then ran
space-time cluster analysis and identified a cluster with a large
spatial and temporal extent which appears to be the continuation of
several effects lumped together.  I subsequently increased minnbchan,
so that this cluster gets separated into separate clusters following
the logic in this discussion thread:
http://mailman.science.ru.nl/pipermail/fieldtrip/2011-February/003501.html

However now a new problem appears: it seems that channels near the
periphery of the sensor layout, which have few adjacent spatial
neighbors, are not included in the clusters when minnbchan has a value
greater than the number of neighbors the channels have according to
the neighbor distance used in ft_neighbourselection.  Is this correct?
 Put differently, increasing minnbchan appears to bias clusters toward
including only channels at the center of the sensor layout, with many
adjacent other channels (and channels at the periphery of the layout,
which have fewer spatial neighbors, are excluded from the identified
clusters).

Obviously I want a principled, data-independent selection of cluster
identification parameters so I want to ask what the "correct" way to
identify these parameters (neighbor distance, and minnbchan) is.
Should minnbchan be used differently for channel-time cluster analysis
(what I'm doing) compared to channel-time-frequency cluster analysis?

Thanks,
Clara



From jm.horschig at donders.ru.nl  Mon Mar 12 09:48:53 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 12 Mar 2012 09:48:53 +0100
Subject: [FieldTrip] clustering, spatial neighbors and minnbchan
In-Reply-To: <CAAHOyr6APDwrRwfONA0xuYXNJbhYKtNrpd0QuVxcKcAXTUL5Yg@mail.gmail.com>
References: <CAAHOyr7pc8qkmeJ4X9NOsGQAmEUsg3viPPYo5v+4d5rE3bQ-Mw@mail.gmail.com>
	<CAAHOyr6APDwrRwfONA0xuYXNJbhYKtNrpd0QuVxcKcAXTUL5Yg@mail.gmail.com>
Message-ID: <4F5DB875.9080501@donders.ru.nl>

Dear Clara,

First of all, defining neighbours based on a sensor layout may not be 
the best approach. If you have 3D positions of your sensors available, I 
would suggest that you use these for neighbour selection (note that for 
EEG sensors, this is much less an issue than for MEG sensors, but you 
didn't mention what system you are using)

Second, for minnbchan, I think you are right. Of course sensors at the 
outer rim have, by definition, less neighbouring sensors than other 
sensors. As far as I know, minnbchan is defined as the number of 
neighbouring significant sensors. So, if you specify it to be e.g. 10, 
than of course all sensors with less than 10 neighbours can never be 
part of a cluster. Those with more than 10 need to have also at least 10 
neighbouring sensors that are significant as well. Of course, sensors in 
the center have more neighbouring sensors, thus higher minnbchan will 
have a less tremendous effect there. So as far as I can see, there are 
four ways out for you:

1) If you didn't do so already, you can choose a finer time-scale, 
hoping that this will separate the different neural effects (if they are 
different)

2) Do the same on source level - maybe this will reduce spatial leakage.

3) Define a wider range of neighbours for sensors at the outer rim, 
thereby forcing a minimum number of neighbouring sensors. Instead (or 
additionally), you could try to use cfg.method = 'triangulation' or 
'template' for neighbour selection. For more information, see here: 
http://fieldtrip.fcdonders.nl/faq/how_does_ft_prepare_neighbours_work
I would suggest that you use cfg.feedback = 'yes' and choose the 
method/parameters that seem most optimal to you (there is not *the* best 
way, unfortunately)

4) Live with it, as there are technical limitations with our recording 
equipment, and of course physiological limitations. As Eric pointed out 
in the old mails you referred to:
"

In fact, it is looking for isolated blobs that one would like to interpret as separate physiological entities.
This contrast with the nature of the EEG/MEG data, which has poor spatial resolution (due to volume conduction and common pick-up),
often poor spectral resolution (due to the short time windows of our time-resolved spectral analysis), and often poor time resolution
(due to latency jitter over trials).
"



Hope this helps.
Best,
Jörn



On 3/11/2012 10:52 PM, Clara A. Scholl wrote:
> Hi,
>
> I have a question about how to identify appropriate parameters for
> neighbor distance in ft_neighbourselection and how to set minnbchan
> for space-time cluster analysis.
>
> I identified a neighbor distance based on our sensor layout, so that
> spatially adjacent channels were defined as neighbors, and spatially
> non-adjacent channels were not defined as neighbors.  I then ran
> space-time cluster analysis and identified a cluster with a large
> spatial and temporal extent which appears to be the continuation of
> several effects lumped together.  I subsequently increased minnbchan,
> so that this cluster gets separated into separate clusters following
> the logic in this discussion thread:
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-February/003501.html
>
> However now a new problem appears: it seems that channels near the
> periphery of the sensor layout, which have few adjacent spatial
> neighbors, are not included in the clusters when minnbchan has a value
> greater than the number of neighbors the channels have according to
> the neighbor distance used in ft_neighbourselection.  Is this correct?
>   Put differently, increasing minnbchan appears to bias clusters toward
> including only channels at the center of the sensor layout, with many
> adjacent other channels (and channels at the periphery of the layout,
> which have fewer spatial neighbors, are excluded from the identified
> clusters).
>
> Obviously I want a principled, data-independent selection of cluster
> identification parameters so I want to ask what the "correct" way to
> identify these parameters (neighbor distance, and minnbchan) is.
> Should minnbchan be used differently for channel-time cluster analysis
> (what I'm doing) compared to channel-time-frequency cluster analysis?
>
> Thanks,
> Clara
>
> _______________________________________________
> 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

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 vitoria.piai at gmail.com  Mon Mar 12 11:06:19 2012
From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=)
Date: Mon, 12 Mar 2012 11:06:19 +0100
Subject: [FieldTrip] bug in new ft_checkdata?
Message-ID: <4F5DCA9B.5030208@gmail.com>

Hi everyone,

I've just got an error when running ft_megplanar and ft_multiplotER that 
I had never had before when running the exact same scripts on exact same 
data:

"Undefined function or method 'fixname' for input arguments of type 'char'.
The chain of errors makes reference to warning_once at 66, fixsampleinfo 
at 66/68, and ft_checkdata at 604.

I'm using the most up-to-date fieldtrip version since I'm working within 
the Donders.
Is this a bug or should I re-structure my data?

Thanks a lot, Vitória

-- 
** Please consider the environment - do you really need to print? **	



From ali at cs.ru.nl  Mon Mar 12 11:32:53 2012
From: ali at cs.ru.nl (Ali Bahramisharif)
Date: Mon, 12 Mar 2012 11:32:53 +0100
Subject: [FieldTrip] bug in new ft_checkdata?
In-Reply-To: <4F5DCA9B.5030208@gmail.com>
References: <4F5DCA9B.5030208@gmail.com>
Message-ID: <8590fee73375ab9349c94481d6a98ebf.squirrel@squirrel.science.ru.nl>

Hi Vitória,

Just be sure that you have removed SPM from your path. SPM has an old
version of fieldtrip and if you have it in your path, it causes a lot of
troubles.

Cheers,
Ali

> Hi everyone,
>
> I've just got an error when running ft_megplanar and ft_multiplotER that
> I had never had before when running the exact same scripts on exact same
> data:
>
> "Undefined function or method 'fixname' for input arguments of type
> 'char'.
> The chain of errors makes reference to warning_once at 66, fixsampleinfo
> at 66/68, and ft_checkdata at 604.
>
> I'm using the most up-to-date fieldtrip version since I'm working within
> the Donders.
> Is this a bug or should I re-structure my data?
>
> Thanks a lot, Vitória
>
> --
> ** Please consider the environment - do you really need to print? **
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>


-- 
Address:
        HG02.517
        Intelligent Systems
        Radboud University Nijmegen
        Heyendaalseweg 135
        6525 AJ Nijmegen
        The Netherlands

http://www.cs.ru.nl/~ali
Tel.:   +31 (0)24 36 52634



From bibi.raquel at gmail.com  Mon Mar 12 13:03:33 2012
From: bibi.raquel at gmail.com (Raquel Bibi)
Date: Mon, 12 Mar 2012 08:03:33 -0400
Subject: [FieldTrip] bug in new ft_checkdata?
In-Reply-To: <4F5DCA9B.5030208@gmail.com>
References: <4F5DCA9B.5030208@gmail.com>
Message-ID: <D550BDC5-8AED-45A9-A8F9-DBEDB52BDB82@gmail.com>

I had the had same error running ft_redefinetrial. As a quick fix I put fixname.m (in private folder) into fieldtrip folder. 

Best,

Raquel

Sent from my iPhone

On Mar 12, 2012, at 6:06 AM, Vitória Magalhães Piai <vitoria.piai at gmail.com> wrote:

> Hi everyone,
> 
> I've just got an error when running ft_megplanar and ft_multiplotER that I had never had before when running the exact same scripts on exact same data:
> 
> "Undefined function or method 'fixname' for input arguments of type 'char'.
> The chain of errors makes reference to warning_once at 66, fixsampleinfo at 66/68, and ft_checkdata at 604.
> 
> I'm using the most up-to-date fieldtrip version since I'm working within the Donders.
> Is this a bug or should I re-structure my data?
> 
> Thanks a lot, Vitória
> 
> -- 
> ** Please consider the environment - do you really need to print? **    
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From g.piantoni at nin.knaw.nl  Mon Mar 12 14:22:39 2012
From: g.piantoni at nin.knaw.nl (Gio Piantoni)
Date: Mon, 12 Mar 2012 14:22:39 +0100
Subject: [FieldTrip] bug in new ft_checkdata?
In-Reply-To: <D550BDC5-8AED-45A9-A8F9-DBEDB52BDB82@gmail.com>
References: <4F5DCA9B.5030208@gmail.com>
	<D550BDC5-8AED-45A9-A8F9-DBEDB52BDB82@gmail.com>
Message-ID: <CAHeOcrtUjpEaVA_bnkWFCHUe3H5P1a6oDJ-fB9HwdRk2VuU2ag@mail.gmail.com>

Hi all,

Raquel is correct. fixname.m was missing from utilities/private

I added it to the dev version, should be fixed now and available on FTP tonight.

Gio

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

+31 20 5665492
gio at gpiantoni.com
www.gpiantoni.com

On Mon, Mar 12, 2012 at 13:03, Raquel Bibi <bibi.raquel at gmail.com> wrote:
> I had the had same error running ft_redefinetrial. As a quick fix I put fixname.m (in private folder) into fieldtrip folder.
>
> Best,
>
> Raquel
>
> Sent from my iPhone
>
> On Mar 12, 2012, at 6:06 AM, Vitória Magalhães Piai <vitoria.piai at gmail.com> wrote:
>
>> Hi everyone,
>>
>> I've just got an error when running ft_megplanar and ft_multiplotER that I had never had before when running the exact same scripts on exact same data:
>>
>> "Undefined function or method 'fixname' for input arguments of type 'char'.
>> The chain of errors makes reference to warning_once at 66, fixsampleinfo at 66/68, and ft_checkdata at 604.
>>
>> I'm using the most up-to-date fieldtrip version since I'm working within the Donders.
>> Is this a bug or should I re-structure my data?
>>
>> Thanks a lot, Vitória
>>
>> --
>> ** Please consider the environment - do you really need to print? **
>>
>> _______________________________________________
>> 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 fredericroux at hotmail.de  Mon Mar 12 15:11:07 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Mon, 12 Mar 2012 15:11:07 +0100
Subject: [FieldTrip] read_fcdc_mri error
Message-ID: <DUB113-W99483229B6AF1ABB816C85B75B0@phx.gbl>


Dear all,

I am getting an error when trying to read CTF-V2 formatted
MRI data using the read_fcdc_mri function.

??? Error using ==> reshape
To RESHAPE the number of elements must not change.

Error in ==> fieldtrip-20081208/private/read_ctf_mri at 113
mri = reshape(mri, [256 256 256]);

Error in ==> read_fcdc_mri at 95
 [img,hdr] = read_ctf_mri(filename);

Error in ==> warpMRI_DEV at 18
 mri = read_fcdc_mri([path2files,mrifiles(sujIt).name]);

The error results because at line 105 of the read_fcfc_mri.m function

mri = unint16(fread(fid,256*256*256,'uint16'));

returns a vector of  length = 16777215 when in fact it should be of
lentgh = 16777216. This means that 1 single value is missing.

The ackward thing is that I can open the MR-file without problem
in the MRIViewer and that there it appears to have 256 values
in the x,y and z dimension. Also this error appears only in 
a subset of files. 

I suspect that there is an error somewhere maybe in the data
acquisition or conversion pipeline.
Any suggestions or help would be highly appreciated.

Have a nice day!

Fred


-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From fredericroux at hotmail.de  Mon Mar 12 17:15:58 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Mon, 12 Mar 2012 17:15:58 +0100
Subject: [FieldTrip] how to set lambda for resting state lcmv-beamformer
Message-ID: <DUB113-W27C7B2A586CF97AE4D0EC8B75B0@phx.gbl>


Dear fieldtrip users,

I am trying to compute a spatial filter
to localize alpha-band activity in an
eyes closed resting state meg recording
using the LCMV-method.

The condition of my covariance matrix is > 1*10e6
so I set lambda = 0.01. When I then plot the NAI
I find two clusters of activity: 
one in the center of the head,
one in the occipital cortex.

In Exercise 5 of the tutorial, it is 
mentioned to set lambda to 1e-29 in order 
to suppresses the center of head artifact.

I wanted to ask if anybody could tell me what the
rationale was to set lambda = 1e-29? 
Is there a standardized way to compute lambda?

Best regards,

Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225

 		 	   		  
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From ali at cs.ru.nl  Mon Mar 12 18:30:52 2012
From: ali at cs.ru.nl (Ali Bahramisharif)
Date: Mon, 12 Mar 2012 18:30:52 +0100
Subject: [FieldTrip] how to set lambda for resting state lcmv-beamformer
In-Reply-To: <DUB113-W27C7B2A586CF97AE4D0EC8B75B0@phx.gbl>
References: <DUB113-W27C7B2A586CF97AE4D0EC8B75B0@phx.gbl>
Message-ID: <b81684b6e207fbd7cbfccb066a4fa413.squirrel@squirrel.science.ru.nl>

Hi Fred,

As far as I remember, lambda is used to regularize the covariance matrix.
I mean: regularized_covariance= XX'+lambda*Identity. To set it properly,
you need to look at the eigen-values of XX'. Normally you want to get rid
of the small eigen values. One way is to choose lambda to be 1/1000 of the
largest eigen-value.

Hope this helps.
Ali

>
> Dear fieldtrip users,
>
> I am trying to compute a spatial filter
> to localize alpha-band activity in an
> eyes closed resting state meg recording
> using the LCMV-method.
>
> The condition of my covariance matrix is > 1*10e6
> so I set lambda = 0.01. When I then plot the NAI
> I find two clusters of activity:
> one in the center of the head,
> one in the occipital cortex.
>
> In Exercise 5 of the tutorial, it is
> mentioned to set lambda to 1e-29 in order
> to suppresses the center of head artifact.
>
> I wanted to ask if anybody could tell me what the
> rationale was to set lambda = 1e-29?
> Is there a standardized way to compute lambda?
>
> Best regards,
>
> Fred
>
> --
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
>
>  		 	   		  _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Address:
        HG02.517
        Intelligent Systems
        Radboud University Nijmegen
        Heyendaalseweg 135
        6525 AJ Nijmegen
        The Netherlands

http://www.cs.ru.nl/~ali
Tel.:   +31 (0)24 36 52634



From nathanweisz at mac.com  Mon Mar 12 20:59:42 2012
From: nathanweisz at mac.com (Nathan Weisz)
Date: Mon, 12 Mar 2012 20:59:42 +0100
Subject: [FieldTrip] Master Cognitive Science Trento
Message-ID: <5BE61BE0-E292-4EF6-B6DD-82814DD0F62A@mac.com>

Dear all,

sorry for (mis-)using this mailing list as advertisement platform. 
http://international.unitn.it/sites/international.unitn.it/files/439_11_MCS_Cop_web.pdf


best,
n

International Masters in Cognitive Science, University of Trento, Italy:

1. COGNITIVE NEUROSCIENCE - CSCNS
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The Master’s course in Cognitive Neuroscience at the University of Trento provides research-focused training with a diverse, international group of faculty and researchers. The two year program combines courses in neuroscience, cognition, statistics, advanced signal and data analysis with hands-on training in cutting-edge research techniques. These include functional magnetic resonance imaging (fMRI), transcranial magnetic stimulation (TMS), magnetic encephalography (MEG), computational modelling, comparative cognition (animal models), EEG, eye tracking, cinematic motion tracking and psychophysics.

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The two-year program combines a solid foundation in scientific and cognitive methods - modules in mathematics, language science, neuroscience, and psychology, including an introduction to advanced methods such as eye tracking, EEG, and fMRI – with an extensive training in computational methods for the statistical analysis of large amounts of language and perceptual data, and in interface design. Theoretical knowledge will be supplemented by the experience acquired in substantial practical projects carried out in research and industry labs.

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In order to be considered for admission, a Bachelor’s degree and a certified English knowledge (e.g. TOEFL, IELTS, CPE) is required.
In the absence of a document certifying the level of English language, the candidate is encouraged to submit alternative proof of English proficiency (i.e. an official letter from the University stating that the candidate completed university courses taught entirely in English). The evaluation of this alternative document will be entirely at discretion of the admission committee.

Selection criteria
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Language
All courses are taught in English. For students wishing to familiarize with the Italian culture, Italian language courses will be offered by the Faculty of Cognitive Science.

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The program is intended for a small number of top level students. In the academic year 2009-2010, the program will admit at most 40 students.

Final degree
After successful completion of the curriculum and fulfilment of the Master’s requirements, students will be awarded a Master of Science degree (laurea magistrale) in Cognitive Science.
Please note that, thanks to an agreement with the University of Osnabrück, students will be awarded a double Master’s degree (Italian and German), valid in both countries.

Deadline
The deadline to complete the on-line application is 31st July, 2009. Please note that this call is for EU citizens only, or non-EU applicants who already have a valid visa to study in the EU.
We regret to inform that at this time the deadline for applications from non-EU students has already passed.
For more details about the opening of the next call please visit the web sitewww.cogsci.unitn.it<http://www.cogsci.unitn.it/>

The University advantage
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The Faculty advantage
The Faculty of Cognitive Science is specialized in mind and brain studies, psychology and human-computer interaction, and offers a wide range of programs at Master and Doctorate level.

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Contacts
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From cas243 at georgetown.edu  Tue Mar 13 02:29:39 2012
From: cas243 at georgetown.edu (Clara A. Scholl)
Date: Mon, 12 Mar 2012 21:29:39 -0400
Subject: [FieldTrip] clustering, spatial neighbors and minnbchan
In-Reply-To: <4F5DB875.9080501@donders.ru.nl>
References: <CAAHOyr7pc8qkmeJ4X9NOsGQAmEUsg3viPPYo5v+4d5rE3bQ-Mw@mail.gmail.com>
	<CAAHOyr6APDwrRwfONA0xuYXNJbhYKtNrpd0QuVxcKcAXTUL5Yg@mail.gmail.com>
	<4F5DB875.9080501@donders.ru.nl>
Message-ID: <CAAHOyr5S+U6ZRtBZ77hjQx9EPe0qcq3O8tL++mAkNeZ5aj2HtQ@mail.gmail.com>

Dear Jörn,

Thank you for directing me to ft_prepare_neighbours instead of
ft_neighbourselection, the triangulation method is excellent and I'll
be sure to stick to the most recent version of fieldtrip from now on.

I really like the spirit of the minnbchan parameter for tightening
cluster extent, but as long as different channels have different
numbers of neighbors (which seems both inevitable and sensible), I
find it problematic that for example, for minnbchan=2, a channel with
5 neighbors will be rejected at a given timepoint if fewer than 40% of
its neighbors belong to a cluster, while a channel with 10 neighbors
will be rejected only when fewer than 20% of its neighbors belong to
the cluster (if I understand what's going on correctly -- and I use 5
and 10 as examples because this is the range of neighbors I get using
triangulation for an EGI 128 channel EEG sensor layout).  I have two
questions about a possible modification to this parameter that I've
implemented:

1) Instead of setting minnbchan to a fixed number of channels, would
it make sense to use a percentage of neighbors so that, for the
example above, instead of using minnbchan=2, use
minnbchan=0.4*numneighbours (at each channel), so that a channel with
5 neighbors would need 2 neighboring channels in the cluster to
remain, while a channel with 10 neighbors would need 4 neighboring
channels in the cluster to remain?  Would this introduce problems I'm
not considering?

2) I implemented it by modifying beginning at line 83 of
findcluster.m, so that instead of looking for
remove=(onoff.*nsigneighb)<minnbchan;

I'm now adding an additional line for the number of neighbors at each
channel (in addition to nsigneighb, the number of significant
neighbors), followed by remove:

nneighb=reshape(selectmat*reshape(single(ones(size(onoff))),[spatdimlength
(nfreq*ntime)]),[spatdimlength nfreq ntime]);
remove=(onoff.*nsigneighb)<(nneighb.*minnbchan);

Where now the minnbchan input must be between 0 and 1 so that the
channels removed at each timepoint are some fraction of each channels
number of neighbors.  It seems to work but I want to run it by users
who are more familiar with the parameters & code than I am, because
it's very possible that (1) the concept is esoteric and problematic
and (2) my implementation is faulty.

Thanks enormously for any & all feedback,
Clara


On Mon, Mar 12, 2012 at 4:48 AM, "Jörn M. Horschig"
<jm.horschig at donders.ru.nl> wrote:
> Dear Clara,
>
> First of all, defining neighbours based on a sensor layout may not be the
> best approach. If you have 3D positions of your sensors available, I would
> suggest that you use these for neighbour selection (note that for EEG
> sensors, this is much less an issue than for MEG sensors, but you didn't
> mention what system you are using)
>
> Second, for minnbchan, I think you are right. Of course sensors at the outer
> rim have, by definition, less neighbouring sensors than other sensors. As
> far as I know, minnbchan is defined as the number of neighbouring
> significant sensors. So, if you specify it to be e.g. 10, than of course all
> sensors with less than 10 neighbours can never be part of a cluster. Those
> with more than 10 need to have also at least 10 neighbouring sensors that
> are significant as well. Of course, sensors in the center have more
> neighbouring sensors, thus higher minnbchan will have a less tremendous
> effect there. So as far as I can see, there are four ways out for you:
>
> 1) If you didn't do so already, you can choose a finer time-scale, hoping
> that this will separate the different neural effects (if they are different)
>
> 2) Do the same on source level - maybe this will reduce spatial leakage.
>
> 3) Define a wider range of neighbours for sensors at the outer rim, thereby
> forcing a minimum number of neighbouring sensors. Instead (or additionally),
> you could try to use cfg.method = 'triangulation' or 'template' for
> neighbour selection. For more information, see here:
> http://fieldtrip.fcdonders.nl/faq/how_does_ft_prepare_neighbours_work
> I would suggest that you use cfg.feedback = 'yes' and choose the
> method/parameters that seem most optimal to you (there is not *the* best
> way, unfortunately)
>
> 4) Live with it, as there are technical limitations with our recording
> equipment, and of course physiological limitations. As Eric pointed out in
> the old mails you referred to:
> "
>
> In fact, it is looking for isolated blobs that one would like to interpret
> as separate physiological entities.
> This contrast with the nature of the EEG/MEG data, which has poor spatial
> resolution (due to volume conduction and common pick-up),
> often poor spectral resolution (due to the short time windows of our
> time-resolved spectral analysis), and often poor time resolution
> (due to latency jitter over trials).
> "
>
>
>
> Hope this helps.
> Best,
> Jörn
>
>
>
>
> On 3/11/2012 10:52 PM, Clara A. Scholl wrote:
>>
>> Hi,
>>
>> I have a question about how to identify appropriate parameters for
>> neighbor distance in ft_neighbourselection and how to set minnbchan
>> for space-time cluster analysis.
>>
>> I identified a neighbor distance based on our sensor layout, so that
>> spatially adjacent channels were defined as neighbors, and spatially
>> non-adjacent channels were not defined as neighbors.  I then ran
>> space-time cluster analysis and identified a cluster with a large
>> spatial and temporal extent which appears to be the continuation of
>> several effects lumped together.  I subsequently increased minnbchan,
>> so that this cluster gets separated into separate clusters following
>> the logic in this discussion thread:
>> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-February/003501.html
>>
>> However now a new problem appears: it seems that channels near the
>> periphery of the sensor layout, which have few adjacent spatial
>> neighbors, are not included in the clusters when minnbchan has a value
>> greater than the number of neighbors the channels have according to
>> the neighbor distance used in ft_neighbourselection.  Is this correct?
>>  Put differently, increasing minnbchan appears to bias clusters toward
>> including only channels at the center of the sensor layout, with many
>> adjacent other channels (and channels at the periphery of the layout,
>> which have fewer spatial neighbors, are excluded from the identified
>> clusters).
>>
>> Obviously I want a principled, data-independent selection of cluster
>> identification parameters so I want to ask what the "correct" way to
>> identify these parameters (neighbor distance, and minnbchan) is.
>> Should minnbchan be used differently for channel-time cluster analysis
>> (what I'm doing) compared to channel-time-frequency cluster analysis?
>>
>> Thanks,
>> Clara
>>
>> _______________________________________________
>> 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
>
> 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



From olivia.mariani at epfl.ch  Tue Mar 13 11:44:53 2012
From: olivia.mariani at epfl.ch (Mariani Olivia)
Date: Tue, 13 Mar 2012 10:44:53 +0000
Subject: [FieldTrip] Mesh intersecting BEM headmodel
Message-ID: <BD7CF73B66D0674980FC749AE22A9BFD2B83B0A0@rexma.intranet.epfl.ch>

Hello,

I am using the "create a BEM headmodel" script but I am getting spikes and unwanted holes in the brain compartment when using the triplot function and don't know how to get rid of it.

I get the following warnings on matlab (R2011a):

%%%%%%%%%%%%%%%%%%%%%
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!! WARNING !!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Mesh is self intersecting !
Mesh Info :
    # points : 1000
    # triangles : 1996
    Euler characteristic : 2
    Min Area : 14
    Max Area : 152.381
Self intersection for mesh number 2
%%%%%%%%%%%%%%%%%%%%%%

I get this self intersecting warning for my three meshes and additional warnings that two meshes are intersecting.
My problem may come from ill-defined boundaries. Would you know how to better define the boundaries between the meshes?

And then I get the following error:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
| ------ om_minverser
| ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin
| ./tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin
| -----------------------
Exception: Unable to open the file ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin for reading Doing my best....
Warning: an error ocurred while running OpenMEEG
> In openmeeg at 127
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Error using ==> fread
Invalid file identifier.  Use fopen to generate a valid file identifier.
Warning: File 'tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin' not found.
> In openmeeg>cleaner at 142
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Warning: File 'tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin' not found.
> In openmeeg>cleaner at 143
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The file om_minverser from openmeeg closes and the figures open.

Thank you,

Olivia


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From lihqih at gmail.com  Tue Mar 13 18:10:16 2012
From: lihqih at gmail.com (qi li)
Date: Tue, 13 Mar 2012 13:10:16 -0400
Subject: [FieldTrip] ICA problem
Message-ID: <CAMWMXsDEoFUpC5JhfLBZgcN7PDEJHtJvA3zgrmYH=a36uV3z=A@mail.gmail.com>

Hi there,

I am having trouble to prepare neighbors of the channels after I do
the ICA with the following commands,

cfg            = [];
cfg.method = 'runica';
cfg.runica.pca=64;
comp           = ft_componentanalysis(cfg, datas)

Then I remove the bad components by

cfg=[];
cfg.component=[2 5];
data_c=ft_rejectcomponent(cfg,comp_o);

now I want to prepare the neighbors
cfg=[];
cfg.neighbours = ft_prepare_neighbours(cfg, data_c);

I have the following error message,

'undoing the invcomp balancing
Index exceeds matrix dimensions.

Error in undobalancing (line 25)
      tra3(iy,iy) = (eye(numel(ix))+tmp(ix,ix))*tra1(iy,iy);

Error in channelposition (line 39)
sens = undobalancing(sens);

Error in ft_datatype_sens (line 95)
        [chanpos, chanori, chanlab] = channelposition(sens, 'channel', 'all');

Error in ft_datatype_raw (line 95)
      data.grad = ft_datatype_sens(data.grad);

Error in ft_checkdata (line 177)
  data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo);

Error in ft_prepare_neighbours (line 84)
if hasdata, data = ft_checkdata(data); end'.


From k.muesch at uke.uni-hamburg.de  Tue Mar 13 19:13:31 2012
From: k.muesch at uke.uni-hamburg.de (=?iso-8859-1?Q?Kathrin_M=FCsch?=)
Date: Tue, 13 Mar 2012 19:13:31 +0100
Subject: [FieldTrip] ICA problem
In-Reply-To: <CAMWMXsDEoFUpC5JhfLBZgcN7PDEJHtJvA3zgrmYH=a36uV3z=A@mail.gmail.com>
References: <CAMWMXsDEoFUpC5JhfLBZgcN7PDEJHtJvA3zgrmYH=a36uV3z=A@mail.gmail.com>
Message-ID: <A1BDA1C1-3106-44E3-A0EA-45D9A92B0524@uke.uni-hamburg.de>

Hi Qi,

This error message pops up recently with many ft_functions after ICA and is due to some updates. I don't know with which FieldTrip version it started. After ICA component rejection, the number of gradiometers seems to change and this error message pops up. As a workaround, you can either remove the grad field if you don't need it for your analysis at hand or you can load the grad structure from a processing step before the ICA.

Hope that helps,
Kathrin

Am 13.03.2012 um 18:10 schrieb qi li:

> Hi there,
> 
> I am having trouble to prepare neighbors of the channels after I do
> the ICA with the following commands,
> 
> cfg            = [];
> cfg.method = 'runica';
> cfg.runica.pca=64;
> comp           = ft_componentanalysis(cfg, datas)
> 
> Then I remove the bad components by
> 
> cfg=[];
> cfg.component=[2 5];
> data_c=ft_rejectcomponent(cfg,comp_o);
> 
> now I want to prepare the neighbors
> cfg=[];
> cfg.neighbours = ft_prepare_neighbours(cfg, data_c);
> 
> I have the following error message,
> 
> 'undoing the invcomp balancing
> Index exceeds matrix dimensions.
> 
> Error in undobalancing (line 25)
>      tra3(iy,iy) = (eye(numel(ix))+tmp(ix,ix))*tra1(iy,iy);
> 
> Error in channelposition (line 39)
> sens = undobalancing(sens);
> 
> Error in ft_datatype_sens (line 95)
>        [chanpos, chanori, chanlab] = channelposition(sens, 'channel', 'all');
> 
> Error in ft_datatype_raw (line 95)
>      data.grad = ft_datatype_sens(data.grad);
> 
> Error in ft_checkdata (line 177)
>  data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo);
> 
> Error in ft_prepare_neighbours (line 84)
> if hasdata, data = ft_checkdata(data); end'.
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg

Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus 

From chan at med.uni-frankfurt.de  Wed Mar 14 17:28:49 2012
From: chan at med.uni-frankfurt.de (Jason Chan)
Date: Wed, 14 Mar 2012 17:28:49 +0100
Subject: [FieldTrip] missing pos in beamforming
Message-ID: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>

Greetings,

I am adapting the beamformer tutorial to my data.  When I sourceinterpolate
the subtracted sourceA from sourceB data, the 'pos'  disappears.  This seems
to be important for the volume normalization and Grand Average.  I am
running Fieldtrip version: 20110917.  I have placed the code below.

 

Many thanks in advance.

Jason

 

 

Young_CombineFilter_sourceDiff_16_3={};

for i=1:length(Young_CombineFilter_beamform_16_3);

    cfg=[];

    Young_CombineFilter_sourceDiff_16_3{i}
=Young_CombineFilter_beamform_16_3{i}.sourceA;

    Young_CombineFilter_sourceDiff_16_3{i}.avg.pow
=(Young_CombineFilter_beamform_16_3{i}.sourceA.avg.pow -
Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow)./Young_CombineFilter_b
eamform_16_3{i}.sourceB.avg.pow;

    

    cfg            = [];

    cfg.downsample = 2;

    cfg.parameter  = 'avg.pow';

    cfg.anatomy    = mri{i};

    cfg.keepfilter='yes';

    cfg.interpmethod='linear';

 
Young_CombineFilter_sourceDiffInt_16_3{i}=ft_sourceinterpolate(cfg,Young_Com
bineFilter_sourceDiff_16_3{i}, mri_young{i});

end;

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From michael.wibral at web.de  Wed Mar 14 20:28:31 2012
From: michael.wibral at web.de (Michael Wibral)
Date: Wed, 14 Mar 2012 20:28:31 +0100 (CET)
Subject: [FieldTrip] missing pos in beamforming
In-Reply-To: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
References: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
Message-ID: <trinity-f95591b5-c49e-407e-9e7e-edbf090da54e-1331753310885@3capp-webde-bs48.dlan.cinetic.de>

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From nathanweisz at mac.com  Wed Mar 14 20:29:56 2012
From: nathanweisz at mac.com (Nathan Weisz)
Date: Wed, 14 Mar 2012 20:29:56 +0100
Subject: [FieldTrip] missing pos in beamforming
In-Reply-To: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
References: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
Message-ID: <5AC98AFE-D119-411D-81A9-FE44B021847D@mac.com>

Hi,

don't have any data at hand right now. but i can't recall that a pos-field should be there after ft_sourceinterpolate (you get your data in 3D corresponding to the dimensions of your MRI). did you actually try ft_volumenormalise? did you run into problems and if yes what does the error look like?

totally unrelated to your problem (if there is any problem), I do not think that cfg.keepfilter is a meaningful input to this function.

best,
n

On 14.03.2012, at 17:28, Jason Chan wrote:

> Greetings,
> I am adapting the beamformer tutorial to my data.  When I sourceinterpolate the subtracted sourceA from sourceB data, the ‘pos’  disappears.  This seems to be important for the volume normalization and Grand Average.  I am running Fieldtrip version: 20110917.  I have placed the code below.
>  
> Many thanks in advance.
> Jason
>  
>  
> Young_CombineFilter_sourceDiff_16_3={};
> for i=1:length(Young_CombineFilter_beamform_16_3);
>     cfg=[];
>     Young_CombineFilter_sourceDiff_16_3{i} =Young_CombineFilter_beamform_16_3{i}.sourceA;
>     Young_CombineFilter_sourceDiff_16_3{i}.avg.pow =(Young_CombineFilter_beamform_16_3{i}.sourceA.avg.pow - Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow)./Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow;
>    
>     cfg            = [];
>     cfg.downsample = 2;
>     cfg.parameter  = 'avg.pow';
>     cfg.anatomy    = mri{i};
>     cfg.keepfilter='yes';
>     cfg.interpmethod='linear';
>     Young_CombineFilter_sourceDiffInt_16_3{i}=ft_sourceinterpolate(cfg,Young_CombineFilter_sourceDiff_16_3{i}, mri_young{i});
> end;
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From jeremiemattout at yahoo.fr  Wed Mar 14 21:22:55 2012
From: jeremiemattout at yahoo.fr (Jeremie MATTOUT)
Date: Wed, 14 Mar 2012 20:22:55 +0000 (GMT)
Subject: [FieldTrip] Post-doctoral Position
Message-ID: <1331756575.90158.YahooMailNeo@web29504.mail.ird.yahoo.com>



Two years Post-doctoral position available
 
Lyon Neuroscience Research Center, Brain Dynamics and Cognition Team, Lyon,
France 
 
----------------------------------------------------------------------------------------------------------------------------------------

Applications are invited for a Post-doctoral position at the Brain Dynamics and
Cognition Team, in the Lyon Neuroscience Research Center, in France. The focus
of the position is on the investigation of the electrophysiological markers of attention,
vigilance and conscious perception, in healthy subjects and non-communicating
and non-responsive patients.
 
The post-doctoral fellow will be part of a three years multi-partner
project. Within the laboratory, she/he will be incorporated in a team of
researchers, engineers, post-doctoral and doctoral fellows who work on various research
and clinical applications of human electrophysiology. Techniques range from
EEG, MEG to SEEG (in collaboration with the Neurological Hospital on site).
In interaction with the team members, the post-doctoral fellow will be in
charge of designing and performing new experiments to test hypothesis about the
functional role of electrophysiological markers.
 
The candidates should have a PhD in Neuroimaging, Human electrophysiology,
Cognitive neuroscience, Biomedical Engineering or a related area. Experience
with high density EEG or MEG in humans is highly desirable (acquisition,
processing, statistics) as well as programming skills (Matlab).  Application from candidates with previous
experience or special interest in related fields such as research in attention,
coma or vegetative state patients, real-time electrophysiology and
brain-computer interfaces are welcome.
 
The Lyon Neuroscience Research Center integrates the multidisciplinary
expertise of 14 teams (about 350 researchers), including university-researchers,
clinician-researchers, technicians and engineers, doctoral and post-doctoral
fellows, making possible a synergistic approach on integrative and cognitive
neurophysiology and its related brain disorders. The neural and molecular
substrates of brain functions, from sensory and motor processes to cognition
and mind, are investigated along two entwined strategic directions: from gene
to behavior, and from bench to patient. Our aim is to bridge the gaps between
the different levels of investigation, and to reinforce a translational
research with reciprocal exchanges between basic conceptual advances and
clinical challenges. The Neuroimaging facilities include an EEG, MEG, TMS, MR and
PET scans as well as access to SEEG recordings in epileptic patients.

Please address questions or send CV, letter of application with research
interests, and two references to Jérémie Mattout (jeremie.mattout at inserm.fr). Applications will be considered until position is
filled. Starting date is negotiable.
 
Jérémie Mattout,
PhD   and   Dominique Morlet, PhD
Lyon Neuroscience
Research Center
Brain Dynamics and
Cognition Team
CHS
Le Vinatier
95
Boulevard Pinel
69500
Bron
France
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From c.micheli at fcdonders.ru.nl  Wed Mar 14 21:48:42 2012
From: c.micheli at fcdonders.ru.nl (Micheli, C.)
Date: Wed, 14 Mar 2012 21:48:42 +0100 (CET)
Subject: [FieldTrip] Mesh intersecting BEM headmodel
In-Reply-To: <BD7CF73B66D0674980FC749AE22A9BFD2B83B0A0@rexma.intranet.epfl.ch>
Message-ID: <767172752.17756.1331758122289.JavaMail.root@draco.zimbra.ru.nl>

Dear Olivia, The documentation you are referring to is not up-to-date and I would not recommend to rely on it. Notwithstanding the old documentation, the problem that you encounter is a known issue with the automatic generation of triangulated surfaces. In fact, the surfaces created from any volumetric data (anatomical MRI or segmentations) should be topologically correct for the BEM to work correctly and at the moment FieldTrip does not check for this (we are working currently on this topic). If you plan to use a head model with 3 compartments I would recommend to start with the function ft_prepare_headmodel, and work with concentric spheres.You can call it like this: cfg=[]; cfg.method = 'concentricspheres'; bnd = ft_prepare_headmodel(cfg,seg) The variable seg is the output of ft_volume_segment containing the skin, skull, brain compartments as and you can refer to the standard documentation for this function: http://fieldtrip.fcdonders.nl/tutorial/headmodel This should automatically solve in most of the cases the problem of intersecting or self-intersecting surfaces. If you want to use the openmeeg toolbox with realistic head models the analysis is complicated by the non-correctness of the surfaces topologies, due probably to the outcome of the segmentation and the successive triangulation step (which happens within the ft_prepare_bemmodel function, now obsolete). The generation of the meshes might work straight away also with the realistic segmented compartments, but it would be difficult to visually check for surface correctness (for example by using the ft_plot_mesh function). When you have the three surfaces you can eventually attach them to your next mail, so that I can verify things with the prototype surface management functions, that we are developing/integrating (see http://code.google.com/p/fieldtrip/source). Let me know if this helps Cristiano ----- Oorspronkelijk bericht -----
> Van: "Mariani Olivia" <olivia.mariani at epfl.ch>
> Aan: fieldtrip at donders.ru.nl
> Verzonden: Dinsdag 13 maart 2012 11:44:53
> Onderwerp: [FieldTrip] Mesh intersecting BEM headmodel
> Hello,
> I am using the "create a BEM headmodel" script but I am getting spikes
> and unwanted holes in the brain compartment when using the triplot
> function and don't know how to get rid of it.
> I get the following warnings on matlab (R2011a):
> %%%%%%%%%%%%%%%%%%%%%
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!! WARNING !!!!!!!!!!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> Mesh is self intersecting !
> Mesh Info :
> # points : 1000
> # triangles : 1996
> Euler characteristic : 2
> Min Area : 14
> Max Area : 152.381
> Self intersection for mesh number 2
> %%%%%%%%%%%%%%%%%%%%%%
> I get this self intersecting warning for my three meshes and
> additional warnings that two meshes are intersecting.
> My problem may come from ill-defined boundaries. Would you know how to
> better define the boundaries between the meshes?
> And then I get the following error:
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> | ------ om_minverser
> | ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin
> | ./tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin
> | -----------------------
> Exception: Unable to open the file
> ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin for reading Doing my
> best....
> Warning: an error ocurred while running OpenMEEG
> > In openmeeg at 127
> In ft_prepare_bemmodel at 232
> In projet_mineur at 106
> Error using ==> fread
> Invalid file identifier. Use fopen to generate a valid file
> identifier.
> Warning: File 'tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin' not found.
> > In openmeeg>cleaner at 142
> In openmeeg at 129
> In ft_prepare_bemmodel at 232
> In projet_mineur at 106
> Warning: File 'tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin' not found.
> > In openmeeg>cleaner at 143
> In openmeeg at 129
> In ft_prepare_bemmodel at 232
> In projet_mineur at 106
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> The file om_minverser from openmeeg closes and the figures open.
> Thank you,
> Olivia
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From olivia.mariani at epfl.ch  Fri Mar 16 09:13:29 2012
From: olivia.mariani at epfl.ch (Mariani Olivia)
Date: Fri, 16 Mar 2012 08:13:29 +0000
Subject: [FieldTrip] RE :  Mesh intersecting BEM headmodel
In-Reply-To: <767172752.17756.1331758122289.JavaMail.root@draco.zimbra.ru.nl>
References: <BD7CF73B66D0674980FC749AE22A9BFD2B83B0A0@rexma.intranet.epfl.ch>,
	<767172752.17756.1331758122289.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <BD7CF73B66D0674980FC749AE22A9BFD2B83B1C3@rexma.intranet.epfl.ch>

Hello Cristiano,

yes it was useful thank you very much, I will use for now the concentric sphere model and will try with the ft_plot_mesh.

I forgot to mention that I am actually using the avg152T1 head model. Does an other method exist to extract the skin from an average? I was thinking of defining the skin and skull as outer and inner skull. Do you think it might solve the triangulation problem?

Thank you very much,

Olivia
________________________________
De : fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] de la part de Micheli, C. [c.micheli at fcdonders.ru.nl]
Date d'envoi : mercredi 14 mars 2012 21:48
À : Email discussion list for the FieldTrip project
Objet : Re: [FieldTrip] Mesh intersecting BEM headmodel

Dear Olivia,
The documentation you are referring to is not up-to-date and I would not recommend to rely on it.
Notwithstanding the old documentation, the problem that you encounter is a known issue with the automatic generation of triangulated surfaces. In fact, the surfaces created from any volumetric data (anatomical MRI or segmentations) should be topologically correct for the BEM to work correctly and at the moment FieldTrip does not check for this (we are working currently on this topic).
If you plan to use a head model with 3 compartments I would recommend to start with the function ft_prepare_headmodel, and work with concentric spheres.You can call it like this:

cfg=[];
cfg.method = 'concentricspheres';
bnd = ft_prepare_headmodel(cfg,seg)

The variable seg is the output of ft_volume_segment containing the skin, skull, brain compartments as
and you can refer to the standard documentation for this function:

http://fieldtrip.fcdonders.nl/tutorial/headmodel

This should automatically solve in most of the cases the problem of intersecting or self-intersecting surfaces.
If you want to use the openmeeg toolbox with realistic head models the analysis is complicated by the non-correctness of the surfaces topologies, due probably to the outcome of the segmentation and the successive triangulation step (which happens within the ft_prepare_bemmodel function, now obsolete).
The generation of the meshes might work straight away also with the realistic segmented compartments, but it would be difficult to visually check for surface correctness (for example by using the ft_plot_mesh function).
When you have the three surfaces you can eventually attach them to your next mail, so that I can verify things with the prototype surface management functions, that we are developing/integrating (see http://code.google.com/p/fieldtrip/source).

Let me know if this helps
Cristiano


________________________________
Van: "Mariani Olivia" <olivia.mariani at epfl.ch>
Aan: fieldtrip at donders.ru.nl
Verzonden: Dinsdag 13 maart 2012 11:44:53
Onderwerp: [FieldTrip] Mesh intersecting BEM headmodel

Hello,

I am using the "create a BEM headmodel" script but I am getting spikes and unwanted holes in the brain compartment when using the triplot function and don't know how to get rid of it.

I get the following warnings on matlab (R2011a):

%%%%%%%%%%%%%%%%%%%%%
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!! WARNING !!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Mesh is self intersecting !
Mesh Info :
    # points : 1000
    # triangles : 1996
    Euler characteristic : 2
    Min Area : 14
    Max Area : 152.381
Self intersection for mesh number 2
%%%%%%%%%%%%%%%%%%%%%%

I get this self intersecting warning for my three meshes and additional warnings that two meshes are intersecting.
My problem may come from ill-defined boundaries. Would you know how to better define the boundaries between the meshes?

And then I get the following error:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
| ------ om_minverser
| ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin
| ./tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin
| -----------------------
Exception: Unable to open the file ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin for reading Doing my best....
Warning: an error ocurred while running OpenMEEG
> In openmeeg at 127
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Error using ==> fread
Invalid file identifier.  Use fopen to generate a valid file identifier.
Warning: File 'tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin' not found.
> In openmeeg>cleaner at 142
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Warning: File 'tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin' not found.
> In openmeeg>cleaner at 143
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The file om_minverser from openmeeg closes and the figures open.

Thank you,

Olivia



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

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From ivano_triggiani at yahoo.it  Fri Mar 16 09:42:10 2012
From: ivano_triggiani at yahoo.it (Ivano Triggiani)
Date: Fri, 16 Mar 2012 08:42:10 +0000 (GMT)
Subject: [FieldTrip] channel type (EEG, EMG,etc.) and when to filter data
Message-ID: <1331887330.12945.YahooMailNeo@web132104.mail.ird.yahoo.com>

Hi everybody,


I'm back to use fieldtrip after a long period, and now everything seems to work (I used .edf file and I had problem with trigger).

Now I have some questions, if someone would be so kind to help me:

1. I'd like to label my channel to select among EEG type, EMG type etc. because my acquire system labeled them all as EEG. When is it specified in cfg ? I can't find it! And if I can't, how can I exclude EMG,TRIGGER and EOG channels from ICA computation? 


2. I have a lot of channel, but ICA gave me back just 33 of them. How can I proceed to obtain a correct ICA from my 56 channels?

3. is it wrong if I filter my data before ICA?


4. If I use ICA probably I can't use other source separation method (like BSS) to analyze my data, am I wrong?


Sorry
 if I post so much questions, but I'm back with fieldtrip and I want to improve my techniques.

Ivano 
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From nathanweisz at mac.com  Fri Mar 16 09:53:20 2012
From: nathanweisz at mac.com (Nathan Weisz)
Date: Fri, 16 Mar 2012 09:53:20 +0100
Subject: [FieldTrip] channel type (EEG, EMG,
	etc.) and when to filter data
In-Reply-To: <1331887330.12945.YahooMailNeo@web132104.mail.ird.yahoo.com>
References: <1331887330.12945.YahooMailNeo@web132104.mail.ird.yahoo.com>
Message-ID: <83DC888D-74CA-467E-90BE-8615B181E8AB@mac.com>

hi,

> I'm back to use fieldtrip after a long period, and now everything seems to work (I used .edf file and I had problem with trigger).

congratulations.

> 1. I'd like to label my channel to select among EEG type, EMG type etc. because my acquire system labeled them all as EEG. When is it specified in cfg ? I can't find it! And if I can't, how can I exclude EMG,TRIGGER and EOG channels from ICA computation? 

you must have had a consitent way of plugging in the channels into your amplifier, haven't you? if yes, then you should find out which channel corresponds to which row in your EEG data and you can relabel them within Matlab.

Your EMG, TRIGGER and EOG channels should also be easy to detect when looking at your data. but you should get back to your recording configurations (also data acquisition software) if you are interested in the positions / labels of the other EEG electrodes. You may want to keep your EOG channels if they have a common reference like the EEG channels.

> 2. I have a lot of channel, but ICA gave me back just 33 of them. How can I proceed to obtain a correct ICA from my 56 channels?

you mean components? 

> 3. is it wrong if I filter my data before ICA?

no.

> 4. If I use ICA probably I can't use other source separation method (like BSS) to analyze my data, am I wrong?

dunno.

good luck,
n

> 
> Sorry if I post so much questions, but I'm back with fieldtrip and I want to improve my techniques.
> 
> Ivano 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From olivia.mariani at epfl.ch  Fri Mar 16 11:16:39 2012
From: olivia.mariani at epfl.ch (Mariani Olivia)
Date: Fri, 16 Mar 2012 10:16:39 +0000
Subject: [FieldTrip] Concentricspheres method
Message-ID: <BD7CF73B66D0674980FC749AE22A9BFD2B83B1EF@rexma.intranet.epfl.ch>

Hello Cristiano,

I am using the concentricsphere but get the following errors:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

??? Error using ==> ft_prepare_headmodel at 233
no input available

Error in ==> Olivia at 29
vol = ft_prepare_headmodel(cfg, seg);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

My code is as follows:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%adds the path toward fieldtrip
addpath_projet;

%récupère les données du fichier mri
mri = ft_read_mri('avg152T1.nii');

%segmentation du volume
cfg = [];
cfg.coordinates = 'spm';

seg = ft_volumesegment(cfg, mri);

seg.anatomy = mri.anatomy;

cfg                = [];
cfg.tissue         = [1 2 3]; % value of each tissue type in the segmentation
cfg.numvertices    = [1000 2000 3000];
cfg.conductivity   = [1 1/80 1];
cfg.isolatedsource = true;
cfg.method         = 'concentricspheres';
cfg.smooth = 'no';

cfg.sourceunits = 'mm';
cfg.mriunits = 'mm';

vol = ft_prepare_headmodel(cfg, seg);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

It seems that I never have the good conditions to put some values in "geometry" but I can't find what I am missing.

Thank you very much,

Olivia
________________________________
De : fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] de la part de Micheli, C. [c.micheli at fcdonders.ru.nl]
Date d'envoi : mercredi 14 mars 2012 21:48
À : Email discussion list for the FieldTrip project
Objet : Re: [FieldTrip] Mesh intersecting BEM headmodel

Dear Olivia,
The documentation you are referring to is not up-to-date and I would not recommend to rely on it.
Notwithstanding the old documentation, the problem that you encounter is a known issue with the automatic generation of triangulated surfaces. In fact, the surfaces created from any volumetric data (anatomical MRI or segmentations) should be topologically correct for the BEM to work correctly and at the moment FieldTrip does not check for this (we are working currently on this topic).
If you plan to use a head model with 3 compartments I would recommend to start with the function ft_prepare_headmodel, and work with concentric spheres.You can call it like this:

cfg=[];
cfg.method = 'concentricspheres';
bnd = ft_prepare_headmodel(cfg,seg)

The variable seg is the output of ft_volume_segment containing the skin, skull, brain compartments as
and you can refer to the standard documentation for this function:

http://fieldtrip.fcdonders.nl/tutorial/headmodel

This should automatically solve in most of the cases the problem of intersecting or self-intersecting surfaces.
If you want to use the openmeeg toolbox with realistic head models the analysis is complicated by the non-correctness of the surfaces topologies, due probably to the outcome of the segmentation and the successive triangulation step (which happens within the ft_prepare_bemmodel function, now obsolete).
The generation of the meshes might work straight away also with the realistic segmented compartments, but it would be difficult to visually check for surface correctness (for example by using the ft_plot_mesh function).
When you have the three surfaces you can eventually attach them to your next mail, so that I can verify things with the prototype surface management functions, that we are developing/integrating (see http://code.google.com/p/fieldtrip/source).

Let me know if this helps
Cristiano


________________________________
Van: "Mariani Olivia" <olivia.mariani at epfl.ch>
Aan: fieldtrip at donders.ru.nl
Verzonden: Dinsdag 13 maart 2012 11:44:53
Onderwerp: [FieldTrip] Mesh intersecting BEM headmodel

Hello,

I am using the "create a BEM headmodel" script but I am getting spikes and unwanted holes in the brain compartment when using the triplot function and don't know how to get rid of it.

I get the following warnings on matlab (R2011a):

%%%%%%%%%%%%%%%%%%%%%
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!! WARNING !!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Mesh is self intersecting !
Mesh Info :
    # points : 1000
    # triangles : 1996
    Euler characteristic : 2
    Min Area : 14
    Max Area : 152.381
Self intersection for mesh number 2
%%%%%%%%%%%%%%%%%%%%%%

I get this self intersecting warning for my three meshes and additional warnings that two meshes are intersecting.
My problem may come from ill-defined boundaries. Would you know how to better define the boundaries between the meshes?

And then I get the following error:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
| ------ om_minverser
| ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin
| ./tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin
| -----------------------
Exception: Unable to open the file ./tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin for reading Doing my best....
Warning: an error ocurred while running OpenMEEG
> In openmeeg at 127
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Error using ==> fread
Invalid file identifier.  Use fopen to generate a valid file identifier.
Warning: File 'tpa072e3c1_0eb4_4007_ba7c_1f49bd581138.bin' not found.
> In openmeeg>cleaner at 142
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
Warning: File 'tpaf0e1a3b_e107_4728_bbb8_1f5309bb3861.bin' not found.
> In openmeeg>cleaner at 143
  In openmeeg at 129
  In ft_prepare_bemmodel at 232
  In projet_mineur at 106
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The file om_minverser from openmeeg closes and the figures open.

Thank you,

Olivia



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

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From michael.wibral at web.de  Fri Mar 16 14:32:21 2012
From: michael.wibral at web.de (Michael Wibral)
Date: Fri, 16 Mar 2012 14:32:21 +0100 (CET)
Subject: [FieldTrip] Workshop on Non-linear and model-free Interdependence
 Measures in Neuroscience and TRENTOOL course
Message-ID: <trinity-c81db96e-2921-4177-8653-0919d68bd344-1331904741681@3capp-webde-bs47.dlan.cinetic.de>

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From chan at med.uni-frankfurt.de  Fri Mar 16 15:17:09 2012
From: chan at med.uni-frankfurt.de (Jason Chan)
Date: Fri, 16 Mar 2012 15:17:09 +0100
Subject: [FieldTrip] missing pos in beamforming
In-Reply-To: <trinity-f95591b5-c49e-407e-9e7e-edbf090da54e-1331753310885@3capp-webde-bs48.dlan.cinetic.de>
References: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
	<trinity-f95591b5-c49e-407e-9e7e-edbf090da54e-1331753310885@3capp-webde-bs48.dlan.cinetic.de>
Message-ID: <002601cd037f$793ca580$6bb5f080$@med.uni-frankfurt.de>

Hi Michael,

 

Many thanks for your informative reply.  I was able to use the reverse normalization technique and eliminated the ft_sourceinterpolate and ft_volumenormalise commands.

However, after I subtract ‘sourceA’ from ‘sourceB’ I now get the error “different grid locations in source reconstructions” when I try to do a ft_sourcegrandaverage.  Any suggestions would be very welcome.

 

Thanks in advance.

Jason

 

From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Michael Wibral
Sent: Mittwoch, 14. März 2012 20:29
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] missing pos in beamforming

 

Dear Jason,

the pos indicates where the original sources were (i.e. on a regular grid with a certain spacing or self-defined). After interpolation this information does not reflect the data anymore. I would suggest to use Ingrid nieuwenhuis famous reverse normalization technique to create individual subject grids taht all match in MNI space - the script is found on the ft website. Sourceinterpoltae should really only be used for plotting IMHO.

Michael

Gesendet: Mittwoch, 14. März 2012 um 17:28 Uhr
Von: "Jason Chan" <chan at med.uni-frankfurt.de>
An: fieldtrip at donders.ru.nl
Betreff: [FieldTrip] missing pos in beamforming 

Greetings,

I am adapting the beamformer tutorial to my data.  When I sourceinterpolate the subtracted sourceA from sourceB data, the ‘pos’  disappears.  This seems to be important for the volume normalization and Grand Average.  I am running Fieldtrip version: 20110917.  I have placed the code below.

 

Many thanks in advance.

Jason

 

 

Young_CombineFilter_sourceDiff_16_3={};

for i=1:length(Young_CombineFilter_beamform_16_3);

    cfg=[];

    Young_CombineFilter_sourceDiff_16_3{i} =Young_CombineFilter_beamform_16_3{i}.sourceA;

    Young_CombineFilter_sourceDiff_16_3{i}.avg.pow =(Young_CombineFilter_beamform_16_3{i}.sourceA.avg.pow - Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow)./Young_CombineFilter_beamform_16_3{i}.sourceB.avg.pow;

    

    cfg            = [];

    cfg.downsample = 2;

    cfg.parameter  = 'avg.pow';

    cfg.anatomy    = mri{i};

    cfg.keepfilter='yes';

    cfg.interpmethod='linear';

    Young_CombineFilter_sourceDiffInt_16_3{i}=ft_sourceinterpolate(cfg,Young_CombineFilter_sourceDiff_16_3{i}, mri_young{i});

end;

 

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From michael.wibral at web.de  Fri Mar 16 16:21:46 2012
From: michael.wibral at web.de (Michael Wibral)
Date: Fri, 16 Mar 2012 16:21:46 +0100 (CET)
Subject: [FieldTrip] missing pos in beamforming
In-Reply-To: <002601cd037f$793ca580$6bb5f080$@med.uni-frankfurt.de>
References: <001b01cd01ff$89b919b0$9d2b4d10$@med.uni-frankfurt.de>
	<trinity-f95591b5-c49e-407e-9e7e-edbf090da54e-1331753310885@3capp-webde-bs48.dlan.cinetic.de>,
	<002601cd037f$793ca580$6bb5f080$@med.uni-frankfurt.de>
Message-ID: <trinity-d7e7ebe6-1de2-434c-a5e2-1f12f9f5681b-1331911306816@3capp-webde-bs47.dlan.cinetic.de>

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From mark.noordenbos at gmail.com  Fri Mar 16 18:05:39 2012
From: mark.noordenbos at gmail.com (Mark Noordenbos)
Date: Fri, 16 Mar 2012 18:05:39 +0100
Subject: [FieldTrip] Combine Grand Average
Message-ID: <CAJSb8nPaJcyFsKU7+nMzPd9r9trs70t=iRWvCgGSxw-k_QFZ0Q@mail.gmail.com>

Hi,

I'm looking for a function that combines two timelocked Grand Averages
(keeping the 'subj_chan_time' dimord).
I have for several conditions seperate Grand Averages, but now I need to
combine some of them into a new Grand Average while keeping the individual
data.

Does Fieldtrip has a buit-in function to do this?

When just calculating the mean, one dimension ('subj' or 'chan' or 'time')
is always lost.

Thanks,
Mark


-- 
Mark Noordenbos, MSc

Radboud University Nijmegen
Behavioural Science Institute

P.O. Box 9104, Room A05.36
6500 HE Nijmegen
The Netherlands

Email: m.noordenbos at bsi.ru.nl
Telephone: +31 24 3612070
Fax:          +31 24 3616211

http://www.ru.nl
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From michael.wibral at web.de  Fri Mar 16 21:51:42 2012
From: michael.wibral at web.de (Michael Wibral)
Date: Fri, 16 Mar 2012 21:51:42 +0100 (CET)
Subject: [FieldTrip] Post-doctoral position available at the Group of
 Michael Wibral, Brain Imaging Center, Frankurt Germany
Message-ID: <trinity-d1f8194a-a8c2-4ba5-b861-c808251892a8-1331931102882@3capp-webde-bs47.dlan.cinetic.de>

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From batrod at gmail.com  Fri Mar 16 18:49:09 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Fri, 16 Mar 2012 12:49:09 -0500
Subject: [FieldTrip] channel type (EEG, EMG,
	etc.) and when to filter data
In-Reply-To: <83DC888D-74CA-467E-90BE-8615B181E8AB@mac.com>
References: <1331887330.12945.YahooMailNeo@web132104.mail.ird.yahoo.com>
	<83DC888D-74CA-467E-90BE-8615B181E8AB@mac.com>
Message-ID: <CAPy7a9B2nCTYXDvr4o86wtxN1na1yAUnystjaMDRTXeWYaxQhA@mail.gmail.com>

Let me add my 2 cents :

I'm back to use fieldtrip after a long period, and now everything seems to
> work (I used .edf file and I had problem with trigger).
>
>
> congratulations.
>

Rodolphe: Congratulations too

>
> 1. I'd like to label my channel to select among EEG type, EMG type etc.
> because my acquire system labeled them all as EEG. When is it specified in
> cfg ? I can't find it! And if I can't, how can I exclude EMG,TRIGGER and
> EOG channels from ICA computation?
>
>
> you must have had a consitent way of plugging in the channels into your
> amplifier, haven't you? if yes, then you should find out which channel
> corresponds to which row in your EEG data and you can relabel them within
> Matlab.
>
> Your EMG, TRIGGER and EOG channels should also be easy to detect when
> looking at your data. but you should get back to your recording
> configurations (also data acquisition software) if you are interested in
> the positions / labels of the other EEG electrodes. You may want to keep
> your EOG channels if they have a common reference like the EEG channels.
>

Rodolphe: Same answer

>
> 2. I have a lot of channel, but ICA gave me back just 33 of them. How can
> I proceed to obtain a correct ICA from my 56 channels?
>
>
> you mean components?
>

Rodolphe: Did you use a PCA to reduce your components first?

>
> 3. is it wrong if I filter my data before ICA?
>
>
> no.
>

Rodolphe: I would tend to say yes. ICA needs a maximum of information to
separate the components,
See for example Snyder and Foxe (2010) where they used ICA to get
components with a dominant of alpha oscillations. They argued that
filtering before is making ICA analysis worse

>
> 4. If I use ICA probably I can't use other source separation method (like
> BSS) to analyze my data, am I wrong?
>
>
> dunno.
>
Rodolphe : as ICA is a BSS, what other method did you have in mind?

>
> good luck,
> n
>
>
> Rodolphe Nenert, PhD.
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From fredericroux at hotmail.de  Sun Mar 18 15:51:21 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Sun, 18 Mar 2012 15:51:21 +0100
Subject: [FieldTrip] indepsamplesF with sourcestatistics
Message-ID: <DUB113-W53D91DAF011D28E811FBE7B75D0@phx.gbl>


Dear all,

I noticed that the result of sourcestatistics can be quite different when using cfg.statistic = 'indepsamplesF'
or also cfg.statistic ='indepsamplesregrT', depending on whether you specify a unit of observations (UO's)
variable in the design matrix or not.

For example when running the code without the UOs-variable as following

cfg.design(1,:) = [ones(1,length(indx1)) 2*ones(1,length(indx1)) 3*ones(1,length(indx1)) 4*ones(1,length(indx1))];
cfg.ivar = 1;

I get a different result than if I run:

cfg.design(1,:) = [ones(1,length(indx1)) 2*ones(1,length(indx2)) 3*ones(1,length(indx3)) 4*ones(1,length(indx4))];
cfg.design(2,:) = [indx1' indx2' indx3' indx4'];
cfg.ivar = 1;

cfg.uvar = 2;

Note that in the second case the indexes in the UOs variable are not sorted.

I guess that you are not supposed to run the code as in the second case,
but I would still like to know why I get different results. Shouldn't it be the same anyways?

It would be great to get an explanation for the discrepancy between both codes.

Best,
Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From eelke.spaak at donders.ru.nl  Mon Mar 19 11:37:47 2012
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Mon, 19 Mar 2012 11:37:47 +0100
Subject: [FieldTrip] Combine Grand Average
In-Reply-To: <CAJSb8nPaJcyFsKU7+nMzPd9r9trs70t=iRWvCgGSxw-k_QFZ0Q@mail.gmail.com>
References: <CAJSb8nPaJcyFsKU7+nMzPd9r9trs70t=iRWvCgGSxw-k_QFZ0Q@mail.gmail.com>
Message-ID: <CABPNLUoTApRzDeyZGvWFfwJjxQcE_QgTwf+pRJcy-jjh+_E7iA@mail.gmail.com>

Hi Mark,

I am not entirely sure, but I think ft_appendtimelock might be what
you are looking for. If not, you could probably also just append the
timelocked information 'by hand':

tl_combined = tl1;
tl_combined.individual = [tl1.individual; tl2.individual];

But be aware that this could get messy, and you then need to make sure
the .avg and other fields are still consistent. So, if at all
possible, stick to ft_appendtimelock :)

Best,
Eelke

On 16 March 2012 18:05, Mark Noordenbos <mark.noordenbos at gmail.com> wrote:
> Hi,
>
> I'm looking for a function that combines two timelocked Grand Averages
> (keeping the 'subj_chan_time' dimord).
> I have for several conditions seperate Grand Averages, but now I need to
> combine some of them into a new Grand Average while keeping the individual
> data.
>
> Does Fieldtrip has a buit-in function to do this?
>
> When just calculating the mean, one dimension ('subj' or 'chan' or 'time')
> is always lost.
>
> Thanks,
> Mark
>
>
> --
> Mark Noordenbos, MSc
>
> Radboud University Nijmegen
> Behavioural Science Institute
>
> P.O. Box 9104, Room A05.36
> 6500 HE Nijmegen
> The Netherlands
>
> Email: m.noordenbos at bsi.ru.nl
> Telephone: +31 24 3612070
> Fax:          +31 24 3616211
>
> http://www.ru.nl
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From politzerahless at gmail.com  Mon Mar 19 12:08:49 2012
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Mon, 19 Mar 2012 06:08:49 -0500
Subject: [FieldTrip] Combine Grand Average
Message-ID: <CAJT2k_80VhT3oBTNCLipJz5J9PDg2y-DjuRecYWdP9ZaP1ZThQ@mail.gmail.com>

Hi Mark,

Do you mean to combine multiple conditions into a single condition? For
that I'm not sure of a built-in function that can do this using grand
averages; you might need to re-do ft_timelockanalysis for the new condition
and then make new grand averages. Since it's possible that a given subject
has more trials contributing to her average for condition A than for
condition B, simply averaging the two condition averages together might not
be accurate.

Best,
Steve Politzer-Ahles

Message: 2
> Date: Mon, 19 Mar 2012 11:37:47 +0100
> From: Eelke Spaak <eelke.spaak at donders.ru.nl>
> To: Email discussion list for the FieldTrip project
>        <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] Combine Grand Average
> Message-ID:
>        <CABPNLUoTApRzDeyZGvWFfwJjxQcE_QgTwf+pRJcy-jjh+_E7iA at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Mark,
>
> I am not entirely sure, but I think ft_appendtimelock might be what
> you are looking for. If not, you could probably also just append the
> timelocked information 'by hand':
>
> tl_combined = tl1;
> tl_combined.individual = [tl1.individual; tl2.individual];
>
> But be aware that this could get messy, and you then need to make sure
> the .avg and other fields are still consistent. So, if at all
> possible, stick to ft_appendtimelock :)
>
> Best,
> Eelke
>
> On 16 March 2012 18:05, Mark Noordenbos <mark.noordenbos at gmail.com> wrote:
> > Hi,
> >
> > I'm looking for a function that combines two timelocked Grand Averages
> > (keeping the 'subj_chan_time' dimord).
> > I have for several conditions seperate Grand Averages, but now I need to
> > combine some of them into a new Grand Average while keeping the
> individual
> > data.
> >
> > Does Fieldtrip has a buit-in function to do this?
> >
> > When just calculating the mean, one dimension ('subj' or 'chan' or
> 'time')
> > is always lost.
> >
> > Thanks,
> > Mark
> >
> >
> > --
> > Mark Noordenbos, MSc
> >
> > Radboud University Nijmegen
> > Behavioural Science Institute
> >
> > P.O. Box 9104, Room A05.36
> > 6500 HE Nijmegen
> > The Netherlands
> >
> > Email: m.noordenbos at bsi.ru.nl
> > Telephone: +31 24 3612070
> > Fax:? ? ? ? ? +31 24 3616211
> >
> > http://www.ru.nl
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
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From jm.horschig at donders.ru.nl  Mon Mar 19 13:35:17 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Mon, 19 Mar 2012 13:35:17 +0100
Subject: [FieldTrip] Combine Grand Average
In-Reply-To: <CAJT2k_80VhT3oBTNCLipJz5J9PDg2y-DjuRecYWdP9ZaP1ZThQ@mail.gmail.com>
References: <CAJT2k_80VhT3oBTNCLipJz5J9PDg2y-DjuRecYWdP9ZaP1ZThQ@mail.gmail.com>
Message-ID: <4F672805.5060404@donders.ru.nl>

Hi Mark,

I agree with Steve. Though, in order to not re-compute the averages, you 
could create the weighted average yourself. Just make a weight vector 
like this:

/weights = no_trials_cond_A / (no_trials_cond_A+no_trials_cond_B);/

Where /no_trials_cond_A /and /*_b/ contai  the number of trials in 
condition A and B, respectively.
Then you can take the weighted sum of the two grand-averages you have, 
something like:

/    grandavg.individual = condA.individual * weights + condB.individual 
* (1-weights);/

This is mathematically equivalent to re-computing the average on all 
trials (note that I am not sure whether this holds for spectral denisity 
matrices and stuff like that, but for ERPs and plain powerspectra, does).

Best,
Jörn

On 3/19/2012 12:08 PM, Stephen Politzer-Ahles wrote:
> Hi Mark,
>
> Do you mean to combine multiple conditions into a single condition? 
> For that I'm not sure of a built-in function that can do this using 
> grand averages; you might need to re-do ft_timelockanalysis for the 
> new condition and then make new grand averages. Since it's possible 
> that a given subject has more trials contributing to her average for 
> condition A than for condition B, simply averaging the two condition 
> averages together might not be accurate.
>
> Best,
> Steve Politzer-Ahles
>
>     Message: 2
>     Date: Mon, 19 Mar 2012 11:37:47 +0100
>     From: Eelke Spaak <eelke.spaak at donders.ru.nl
>     <mailto:eelke.spaak at donders.ru.nl>>
>     To: Email discussion list for the FieldTrip project
>     <fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>>
>     Subject: Re: [FieldTrip] Combine Grand Average
>     Message-ID:
>     <CABPNLUoTApRzDeyZGvWFfwJjxQcE_QgTwf+pRJcy-jjh+_E7iA at mail.gmail.com <mailto:CABPNLUoTApRzDeyZGvWFfwJjxQcE_QgTwf%2BpRJcy-jjh%2B_E7iA at mail.gmail.com>>
>     Content-Type: text/plain; charset=ISO-8859-1
>
>     Hi Mark,
>
>     I am not entirely sure, but I think ft_appendtimelock might be what
>     you are looking for. If not, you could probably also just append the
>     timelocked information 'by hand':
>
>     tl_combined = tl1;
>     tl_combined.individual = [tl1.individual; tl2.individual];
>
>     But be aware that this could get messy, and you then need to make sure
>     the .avg and other fields are still consistent. So, if at all
>     possible, stick to ft_appendtimelock :)
>
>     Best,
>     Eelke
>
>     On 16 March 2012 18:05, Mark Noordenbos <mark.noordenbos at gmail.com
>     <mailto:mark.noordenbos at gmail.com>> wrote:
>     > Hi,
>     >
>     > I'm looking for a function that combines two timelocked Grand
>     Averages
>     > (keeping the 'subj_chan_time' dimord).
>     > I have for several conditions seperate Grand Averages, but now I
>     need to
>     > combine some of them into a new Grand Average while keeping the
>     individual
>     > data.
>     >
>     > Does Fieldtrip has a buit-in function to do this?
>     >
>     > When just calculating the mean, one dimension ('subj' or 'chan'
>     or 'time')
>     > is always lost.
>     >
>     > Thanks,
>     > Mark
>     >
>     >
>     > --
>     > Mark Noordenbos, MSc
>     >
>     > Radboud University Nijmegen
>     > Behavioural Science Institute
>     >
>     > P.O. Box 9104, Room A05.36
>     > 6500 HE Nijmegen
>     > The Netherlands
>     >
>     > Email: m.noordenbos at bsi.ru.nl <mailto:m.noordenbos at bsi.ru.nl>
>     > Telephone: +31 24 3612070 <tel:%2B31%2024%203612070>
>     > Fax:? ? ? ? ? +31 24 3616211 <tel:%2B31%2024%203616211>
>     >
>     > http://www.ru.nl
>     >
>     >
>     > _______________________________________________
>     > 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

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 giulia.rizza at tiscali.it  Mon Mar 19 16:25:20 2012
From: giulia.rizza at tiscali.it (Giulia Rizza)
Date: Mon, 19 Mar 2012 16:25:20 +0100 (GMT+01:00)
Subject: [FieldTrip] Neuroscan .cnt files
Message-ID: <7171049.98631332170720589.JavaMail.defaultUser@defaultHost>

Dear Fieldtrippers,
hi to everyone and thanks in advance for your time.
I'm not 
an expert and I'd like to share with you a problem I found in reading cnt files 
acquired with Neuroscan.

I read the data with ft_read_data function and I find 
the attached link Plot1, for instance the first channel. It seems that the 
signal is forced to pass per zero every two samples, so I tried to read them  
excluding the even samples and I find the result in Plot2, while excluding the 
odd values I find the result in Plot3.

http://dl.dropbox.com/u/28258961/Plot01.
rar

Unfortunately there are still some problems since the maximum value that 
can be represented (about 900) is smaller than some values in the data and the 
result is that I find a sharp change of sign. How can I fix it?

Thanks to 
anyone who can help me

Giulia


E' nata indoona: chiama, videochiama e messaggia Gratis. Scarica indoona per iPhone, Android e PC: http://www.indoona.com/ 


From yuvharpaz at gmail.com  Mon Mar 19 16:46:04 2012
From: yuvharpaz at gmail.com (Yuval Harpaz)
Date: Mon, 19 Mar 2012 17:46:04 +0200
Subject: [FieldTrip] rejectcomponent after ica for 20 comps only
Message-ID: <CAGQZS_kvLUWndQijop+pjEwj0r2=k=-Efp+WLRs1VzhuMVj2bQ@mail.gmail.com>

Dear ft_emaillist

I want to reject components obtained with with fastica.

if I only run ft_componentanalysis with cfg.numcomponent=20, creating only
20 components, can I still reject a specific component by
ft_rejectcomponent(cfg,comp,data) or will it only reconstruct the date
based on the 20 components I calculated?

thanks,Yuval

-- 

Y.Harpaz

a link to the BIU MEG lab:
http://faculty.biu.ac.il/~goldsa/index.html
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From enzo.brunetti at gmail.com  Mon Mar 19 18:32:34 2012
From: enzo.brunetti at gmail.com (Enzo Brunetti)
Date: Mon, 19 Mar 2012 13:32:34 -0400
Subject: [FieldTrip] Neuroscan .cnt files
In-Reply-To: <7171049.98631332170720589.JavaMail.defaultUser@defaultHost>
References: <7171049.98631332170720589.JavaMail.defaultUser@defaultHost>
Message-ID: <2CD6708A-A08A-4AF0-92BB-B78029DF2B76@gmail.com>

Dear Giulia,
I could not see your dropbox link showing the plot, but a known reported problem with importing .cnt neuroscan files is that the file header does not specify the actual precision of your data (typically 32 bits with new neuroscan systems, 16 bits previously). If you are importing 32 bits data without explicitly defining it previously, you can obtain the type of signals you are talking about (the default importing option is '16bits'). If this is the case, you must to specify this in the cfg input structure of the reader function, as:

cfg.headerformat         =  'ns_cnt32';
cfg.dataformat              =  'ns_cnt32';
cfg.eventformat            =  'ns_cnt32';

in addition to the other specific fields of the structure.

Also, you can visit this link: http://fieldtrip.fcdonders.nl/faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_this for more information.

I hope this could help you.
Best

Dr. Enzo Brunetti F.
---------------------------
Institute of Biomedical Sciences
Faculty of Medicine
University of Chile


On Mar 19, 2012, at 11:25 AM, Giulia Rizza wrote:

> Dear Fieldtrippers,
> hi to everyone and thanks in advance for your time.
> I'm not 
> an expert and I'd like to share with you a problem I found in reading cnt files 
> acquired with Neuroscan.
> 
> I read the data with ft_read_data function and I find 
> the attached link Plot1, for instance the first channel. It seems that the 
> signal is forced to pass per zero every two samples, so I tried to read them  
> excluding the even samples and I find the result in Plot2, while excluding the 
> odd values I find the result in Plot3.
> 
> http://dl.dropbox.com/u/28258961/Plot01.
> rar
> 
> Unfortunately there are still some problems since the maximum value that 
> can be represented (about 900) is smaller than some values in the data and the 
> result is that I find a sharp change of sign. How can I fix it?
> 
> Thanks to 
> anyone who can help me
> 
> Giulia
> 
> 
> E' nata indoona: chiama, videochiama e messaggia Gratis. Scarica indoona per iPhone, Android e PC: http://www.indoona.com/ 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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From g.piantoni at nin.knaw.nl  Mon Mar 19 17:59:50 2012
From: g.piantoni at nin.knaw.nl (Gio Piantoni)
Date: Mon, 19 Mar 2012 17:59:50 +0100
Subject: [FieldTrip] rejectcomponent after ica for 20 comps only
In-Reply-To: <CAGQZS_kvLUWndQijop+pjEwj0r2=k=-Efp+WLRs1VzhuMVj2bQ@mail.gmail.com>
References: <CAGQZS_kvLUWndQijop+pjEwj0r2=k=-Efp+WLRs1VzhuMVj2bQ@mail.gmail.com>
Message-ID: <CAHeOcrv=saYUviSjchVn-mdnv53Y4Ky37LsG-hit+E=2CLSy2g@mail.gmail.com>

Hi Yuval,

If you pass data as third argument, the function will substract the
weights of rejected component(s) from your data. So, your data will
have the initial rank minus the number of rejected component. No
reconstruction occurs.

See line 121 of ft_rejectcomponent or try the code below.

nelec = 50;
fs = 1000;
ntrl = 5;

data = [];
data.label = cellfun(@(x)['E' num2str(x)], num2cell(1:nelec), 'uni', 0);
data.fsample = fs;
for i =1:ntrl
  data.trial{i} = randn(nelec, fs);
  data.time{i} = 1/fs:1/fs:1;
end

cfg = [];
cfg.method = 'fastica';
cfg.numcomponent = 10;
comp = ft_componentanalysis(cfg, data);

cfg = [];
cfg.component = 2;
data2 = ft_rejectcomponent(cfg, comp, data); % subtract comp from data
data3 = ft_rejectcomponent(cfg, comp); % reconstruct from comp

rank(data.trial{1}) % full rank
rank(data2.trial{1}) % full rank - 1 rejected
rank(data3.trial{1})  % rank of 'comp' - 1 rejected

On Mon, Mar 19, 2012 at 16:46, Yuval Harpaz <yuvharpaz at gmail.com> wrote:
> Dear ft_emaillist
>
> I want to reject components obtained with with fastica.
>
> if I only run ft_componentanalysis with cfg.numcomponent=20, creating only
> 20 components, can I still reject a specific component by
> ft_rejectcomponent(cfg,comp,data) or will it only reconstruct the date based
> on the 20 components I calculated?
>
> thanks,Yuval
>
> --
>
> Y.Harpaz
>
> a link to the BIU MEG lab:
> http://faculty.biu.ac.il/~goldsa/index.html
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From politzerahless at gmail.com  Mon Mar 19 18:56:21 2012
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Mon, 19 Mar 2012 12:56:21 -0500
Subject: [FieldTrip] fieldtrip Digest, Vol 16, Issue 25
In-Reply-To: <mailman.142.1332174700.1184.fieldtrip@donders.ru.nl>
References: <mailman.142.1332174700.1184.fieldtrip@donders.ru.nl>
Message-ID: <CAJT2k__WBFwXyOujLbn-vm6OGLmrMEWOHqy4BpYE5xUEwp=+eg@mail.gmail.com>

Hi Giulia,

The data certainly do look a bit weird to me, and as Enzo suggests
specifying 32 or 16 bits may help. Also, have you tried reading the data
using ft_preprocessing()<http://fieldtrip.fcdonders.nl/reference/ft_preprocessing>rather
than ft_read_data()? In my experience the high-level function
(ft_preprocessing) is easier to work with and handles a lot of the
complicated stuff for you, so unless you have a special reason to need to
read your data with the low-level functions then you might have more luck
just using ft_preprocessing.

Best,
Steve Politzer-Ahles

Message: 5
> Date: Mon, 19 Mar 2012 13:32:34 -0400
> From: Enzo Brunetti <enzo.brunetti at gmail.com>
> To: Giulia Rizza <giulia.rizza at tiscali.it>,     Email discussion list for
>        the FieldTrip project <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] Neuroscan .cnt files
> Message-ID: <2CD6708A-A08A-4AF0-92BB-B78029DF2B76 at gmail.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Giulia,
> I could not see your dropbox link showing the plot, but a known reported
> problem with importing .cnt neuroscan files is that the file header does
> not specify the actual precision of your data (typically 32 bits with new
> neuroscan systems, 16 bits previously). If you are importing 32 bits data
> without explicitly defining it previously, you can obtain the type of
> signals you are talking about (the default importing option is '16bits').
> If this is the case, you must to specify this in the cfg input structure of
> the reader function, as:
>
> cfg.headerformat         =  'ns_cnt32';
> cfg.dataformat              =  'ns_cnt32';
> cfg.eventformat            =  'ns_cnt32';
>
> in addition to the other specific fields of the structure.
>
> Also, you can visit this link:
> http://fieldtrip.fcdonders.nl/faq/i_have_problems_reading_in_neuroscan_.cnt_files._how_can_i_fix_thisfor more information.
>
> I hope this could help you.
> Best
>
> Dr. Enzo Brunetti F.
> ---------------------------
> Institute of Biomedical Sciences
> Faculty of Medicine
> University of Chile
>
>
> On Mar 19, 2012, at 11:25 AM, Giulia Rizza wrote:
>
> > Dear Fieldtrippers,
> > hi to everyone and thanks in advance for your time.
> > I'm not
> > an expert and I'd like to share with you a problem I found in reading
> cnt files
> > acquired with Neuroscan.
> >
> > I read the data with ft_read_data function and I find
> > the attached link Plot1, for instance the first channel. It seems that
> the
> > signal is forced to pass per zero every two samples, so I tried to read
> them
> > excluding the even samples and I find the result in Plot2, while
> excluding the
> > odd values I find the result in Plot3.
> >
> > http://dl.dropbox.com/u/28258961/Plot01.
> > rar
> >
> > Unfortunately there are still some problems since the maximum value that
> > can be represented (about 900) is smaller than some values in the data
> and the
> > result is that I find a sharp change of sign. How can I fix it?
> >
> > Thanks to
> > anyone who can help me
> >
> > Giulia
> >
> >
> > E' nata indoona: chiama, videochiama e messaggia Gratis. Scarica indoona
> per iPhone, Android e PC: http://www.indoona.com/
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From yuvharpaz at gmail.com  Mon Mar 19 20:49:31 2012
From: yuvharpaz at gmail.com (Yuval Harpaz)
Date: Mon, 19 Mar 2012 21:49:31 +0200
Subject: [FieldTrip] rejectcomponent after ica for 20 comps only
In-Reply-To: <CAHeOcrv=saYUviSjchVn-mdnv53Y4Ky37LsG-hit+E=2CLSy2g@mail.gmail.com>
References: <CAGQZS_kvLUWndQijop+pjEwj0r2=k=-Efp+WLRs1VzhuMVj2bQ@mail.gmail.com>
	<CAHeOcrv=saYUviSjchVn-mdnv53Y4Ky37LsG-hit+E=2CLSy2g@mail.gmail.com>
Message-ID: <CAGQZS_=SbL+U2YumY0HyFc4OpJ2j81199Y_8ke8TddoFoC-29w@mail.gmail.com>

thanks a lot. it clears the matter
Yuval

On 19 March 2012 18:59, Gio Piantoni <g.piantoni at nin.knaw.nl> wrote:

> Hi Yuval,
>
> If you pass data as third argument, the function will substract the
> weights of rejected component(s) from your data. So, your data will
> have the initial rank minus the number of rejected component. No
> reconstruction occurs.
>
> See line 121 of ft_rejectcomponent or try the code below.
>
> nelec = 50;
> fs = 1000;
> ntrl = 5;
>
> data = [];
> data.label = cellfun(@(x)['E' num2str(x)], num2cell(1:nelec), 'uni', 0);
> data.fsample = fs;
> for i =1:ntrl
>  data.trial{i} = randn(nelec, fs);
>  data.time{i} = 1/fs:1/fs:1;
> end
>
> cfg = [];
> cfg.method = 'fastica';
> cfg.numcomponent = 10;
> comp = ft_componentanalysis(cfg, data);
>
> cfg = [];
> cfg.component = 2;
> data2 = ft_rejectcomponent(cfg, comp, data); % subtract comp from data
> data3 = ft_rejectcomponent(cfg, comp); % reconstruct from comp
>
> rank(data.trial{1}) % full rank
> rank(data2.trial{1}) % full rank - 1 rejected
> rank(data3.trial{1})  % rank of 'comp' - 1 rejected
>
> On Mon, Mar 19, 2012 at 16:46, Yuval Harpaz <yuvharpaz at gmail.com> wrote:
> > Dear ft_emaillist
> >
> > I want to reject components obtained with with fastica.
> >
> > if I only run ft_componentanalysis with cfg.numcomponent=20, creating
> only
> > 20 components, can I still reject a specific component by
> > ft_rejectcomponent(cfg,comp,data) or will it only reconstruct the date
> based
> > on the 20 components I calculated?
> >
> > thanks,Yuval
> >
> > --
> >
> > Y.Harpaz
> >
> > a link to the BIU MEG lab:
> > http://faculty.biu.ac.il/~goldsa/index.html
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>



-- 

Y.Harpaz

a link to the BIU MEG lab:
http://faculty.biu.ac.il/~goldsa/index.html
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From mark.noordenbos at gmail.com  Tue Mar 20 09:37:51 2012
From: mark.noordenbos at gmail.com (Mark Noordenbos)
Date: Tue, 20 Mar 2012 09:37:51 +0100
Subject: [FieldTrip] Combine Grand Average
Message-ID: <CAJSb8nPtg+d6dFPtWLgNXmasLFXHkOFeHEhrw7FNABMA1pE_fg@mail.gmail.com>

Hi Jörn, Steve and Eelke,

Thanks for the suggestions for combining grand averages.
Unfortunately, ft_appendtimelock did not work for the grand averages.

Probably, the only proper way to this is to make completely new grand
averages with all conditions included, instead of a grand average for each
condition and combine them later.

To quickly view the outcome of combining the grand averages of 2 conditions
a calculated the mean by hand:

datatot.individual = (data1.individual + data2.individual)/2;

Kind regards,
Mark


-- 
Mark Noordenbos, MSc

Radboud University Nijmegen
Behavioural Science Institute

P.O. Box 9104, Room A05.36
6500 HE Nijmegen
The Netherlands

Email: m.noordenbos at bsi.ru.nl
Telephone: +31 24 3612070
Fax:          +31 24 3616211

http://www.ru.nl
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From batrod at gmail.com  Tue Mar 20 18:53:03 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Tue, 20 Mar 2012 12:53:03 -0500
Subject: [FieldTrip] Clusterplot scale?
Message-ID: <CAPy7a9CGu275wjBvMJiUsnaHYSpTpWOwMbhrTovMdvGNXGb26A@mail.gmail.com>

dear Fieldtrippers,

Im using the Montecarlo randomization method with cluster correction to
compare 2 conditions with a t-test.
When i plot the significant cluster with the ft_clusterplot function, it
creates a topoplot with highlighted electrodes.
I was just wondering what values were represented in the topoplot, as it
seems to be the difference between my two conditions, but with a higher
scale.

Rodolphe.
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From jm.horschig at donders.ru.nl  Wed Mar 21 09:45:11 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 21 Mar 2012 09:45:11 +0100
Subject: [FieldTrip] Clusterplot scale?
In-Reply-To: <CAPy7a9CGu275wjBvMJiUsnaHYSpTpWOwMbhrTovMdvGNXGb26A@mail.gmail.com>
References: <CAPy7a9CGu275wjBvMJiUsnaHYSpTpWOwMbhrTovMdvGNXGb26A@mail.gmail.com>
Message-ID: <4F699517.6050407@donders.ru.nl>

Dear Rodolphe,

By default, the corresponding values do not reflect power differences 
directly, but the test-statistic, in your case t-values (that's the 
/stat.stat/ field)
You can see on what scale the plot is by typing /colorbar /in the 
command window or by pressing the colorbar button in the icon bar of the 
matlab figure.

Best,
Jörn


On 3/20/2012 6:53 PM, Rodolphe Nenert wrote:
> dear Fieldtrippers,
>
> Im using the Montecarlo randomization method with cluster correction 
> to compare 2 conditions with a t-test.
> When i plot the significant cluster with the ft_clusterplot function, 
> it creates a topoplot with highlighted electrodes.
> I was just wondering what values were represented in the topoplot, as 
> it seems to be the difference between my two conditions, but with a 
> higher scale.
>
> Rodolphe.
>
>
> _______________________________________________
> 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

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 m.leszczynski.m at googlemail.com  Wed Mar 21 10:51:14 2012
From: m.leszczynski.m at googlemail.com (Marcin)
Date: Wed, 21 Mar 2012 10:51:14 +0100
Subject: [FieldTrip] statfun_depsamplesregrT
Message-ID: <CAAVVtzDY5stRD-XE2Pa5TjrO1L8AJXXSZToy7XhA72hK22bu+w@mail.gmail.com>

Dear Fieldtripers,

Could anyone explain me what is being calculated with the
statfun_depsamplesregrT function, please.

David Groppe (thank you David) suggested in a previous thread on the list
that I might calculate permutation test based on rank correlation to
account for monotonic relationships within the permutation framework. I was
wondering if this is the kind of test that statfun_depsamplesregrT function
calculates.
http://mailman.science.ru.nl/pipermail/fieldtrip/2011-December/004578.html

Best,
Marcin
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From ole.jensen at donders.ru.nl  Wed Mar 21 15:28:58 2012
From: ole.jensen at donders.ru.nl (Ole Jensen)
Date: Wed, 21 Mar 2012 15:28:58 +0100
Subject: [FieldTrip] data analysis competition / Biomag2012
Message-ID: <4F69E5AA.5010507@donders.ru.nl>

Dear colleagues,

We would like to announce (2nd announcement) the data analysis 
competition at the Biomag2012 meeting (Paris, Aug 26-30). Please 
encourage students and postdocs to participate. There were some 
technical glitches in the data after the 1st announcement. They are now 
corrected.

With best wishes,

Ole Jensen and Ali Bahramisharif


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

*Biomag2012 analysis competition - distributed representations
*
http://www.biomag2012.org/content/data-analysis-competition

The decoding of mental states and neuronal representations from brain 
imaging data is a research field in rapid development (Spiers HJ, 
Maguire EA. Decoding human brain activity during real-world experiences. 
Trends Cogn Sci. 2007 ; Haynes JD, Rees G. Decoding mental states from 
brain activity in humans. Nat Rev Neurosci. 2006). These decoding 
approaches have a great potential in MEG research where data are 
recorded from hundreds of sensors with a millisecond time resolution. In 
particular cognitive neuroscience could benefit from further development 
of decoding approaches in order to identify representational specific 
brain activity.
The aim of the competition is to:

  * Promote the development and application of new multivariate analysis
    techniques for decoding of brain activity
  * Make the audience aware of novel approaches
  * Elucidate the pros and cons of the different techniques
      o Which assumptions are behind a given approach?
      o What are the limitations?
  * Attract signal-processing experts from outside the MEG field
  * Encourage a discussion on the cognitive insight the techniques can
    bring about

The deadline for submitting results is Aug 17, 2012.

-- 
Ole Jensen
http://www.neuosc.com

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From vitoria.piai at gmail.com  Wed Mar 21 16:17:24 2012
From: vitoria.piai at gmail.com (=?ISO-8859-1?Q?Vit=F3ria_Magalh=E3es_Piai?=)
Date: Wed, 21 Mar 2012 16:17:24 +0100
Subject: [FieldTrip] a function for averaging over freq x time x channel
Message-ID: <4F69F104.1000406@gmail.com>

Hi there,

Is there an easy way for averaging over frequency x time x channel if my 
data is the output of ft_freqanalysis with keeptrials = 'no' (so 
chan_freq_time)?

ft_redefinetrial requires rpt to be present, so that's not an option. 
ft_selectdata_old is also complaining about the wrong structure for the 
input data and ft_selectdata_new is outputting exactly the same 
chan_freq_time as the input (I'm using the most recent FT version at the 
DCCN).

I may be missing some really obvious function, but so far I've been 
doing it in the hard way by hand.

Any suggestions are very much appreciated.

Thanks, Vitoria


From jm.horschig at donders.ru.nl  Wed Mar 21 16:21:55 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 21 Mar 2012 16:21:55 +0100
Subject: [FieldTrip] a function for averaging over freq x time x channel
In-Reply-To: <4F69F104.1000406@gmail.com>
References: <4F69F104.1000406@gmail.com>
Message-ID: <4F69F213.5040609@donders.ru.nl>

Hi Vitoria,

try ft_freqdescriptives

Best,
Jörn

On 3/21/2012 4:17 PM, Vitória Magalhães Piai wrote:
> Hi there,
>
> Is there an easy way for averaging over frequency x time x channel if 
> my data is the output of ft_freqanalysis with keeptrials = 'no' (so 
> chan_freq_time)?
>
> ft_redefinetrial requires rpt to be present, so that's not an option. 
> ft_selectdata_old is also complaining about the wrong structure for 
> the input data and ft_selectdata_new is outputting exactly the same 
> chan_freq_time as the input (I'm using the most recent FT version at 
> the DCCN).
>
> I may be missing some really obvious function, but so far I've been 
> doing it in the hard way by hand.
>
> Any suggestions are very much appreciated.
>
> Thanks, Vitoria
> _______________________________________________
> 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

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 jm.horschig at donders.ru.nl  Wed Mar 21 16:32:42 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 21 Mar 2012 16:32:42 +0100
Subject: [FieldTrip] a function for averaging over freq x time x channel
In-Reply-To: <4F69F213.5040609@donders.ru.nl>
References: <4F69F104.1000406@gmail.com> <4F69F213.5040609@donders.ru.nl>
Message-ID: <4F69F49A.5080005@donders.ru.nl>

Hey again,

sorry, it doesn't work with ft_freqdescriptives, then you have to do it 
manually:
squeeze(nanmean(nanmean(nanmean(data.powspctrm, 1), 2), 3))

Best,
Jörn

On 3/21/2012 4:21 PM, "Jörn M. Horschig" wrote:
> Hi Vitoria,
>
> try ft_freqdescriptives
>
> Best,
> Jörn
>
> On 3/21/2012 4:17 PM, Vitória Magalhães Piai wrote:
>> Hi there,
>>
>> Is there an easy way for averaging over frequency x time x channel if 
>> my data is the output of ft_freqanalysis with keeptrials = 'no' (so 
>> chan_freq_time)?
>>
>> ft_redefinetrial requires rpt to be present, so that's not an option. 
>> ft_selectdata_old is also complaining about the wrong structure for 
>> the input data and ft_selectdata_new is outputting exactly the same 
>> chan_freq_time as the input (I'm using the most recent FT version at 
>> the DCCN).
>>
>> I may be missing some really obvious function, but so far I've been 
>> doing it in the hard way by hand.
>>
>> Any suggestions are very much appreciated.
>>
>> Thanks, Vitoria
>> _______________________________________________
>> 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

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 Jan.Hirschmann at med.uni-duesseldorf.de  Wed Mar 21 16:36:39 2012
From: Jan.Hirschmann at med.uni-duesseldorf.de (Jan.Hirschmann at med.uni-duesseldorf.de)
Date: Wed, 21 Mar 2012 16:36:39 +0100
Subject: [FieldTrip] error ft_read_mri
Message-ID: <72E993C35FB11743B79FF9286E5B6D8B03ADFF9E@Mail2-UKD.VMED.UKD>

Dear fieldtrip programmers,

 

with the latest version of fieldtrip I am experiencing problems reading
MRs:

 

a=ft_read_mri('/data/apps/spm/spm8/canonical/avg152T1.nii')

Undefined function or variable "out".

 

Error in fixname (line 55)

while(out(1) == '_'),   out = out(2:end); end;   % remove all underscore
at the begin of the

string

 

Error in ft_hastoolbox (line 366)

  previous.(fixname(toolbox)) = status;

 

Error in ft_read_mri (line 45)

hasmri  = ft_hastoolbox('mri');     % from Darren Weber, see
http://eeg.sourceforge.net/

 

Thanks and all the best,

Jan

--

Jan Hirschmann

MSc. Neuroscience

Institute of Clinical Neuroscience and Medical Psychology

Heinrich Heine University Duesseldorf

Universitaetsstr.  1
40225  Duesseldorf

Tel: 0049 - (0)211 - 81 - 18415

 

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From max-philipp.stenner at med.ovgu.de  Wed Mar 21 19:53:28 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Wed, 21 Mar 2012 18:53:28 +0000
Subject: [FieldTrip] (no subject)
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830CB542@ESEN4.imed.uni-magdeburg.de>

Dear fieldtrip users/developers, 

I'd like to perform time-frequency analysis after computing the planar gradiometer representation of multi-session data and I am wondering whether the order in which the analysis steps are performed matters. The sequence I have used is

ft_megplanar
concatenate data across sessions
ft_average_sens, add the averaged (planar) sensor information to the datapool
ft_freqanalysis
ft_combineplanar

Does that make sense?

Thanks very much, 
best
Max
fieldtrip version: fieldtrip-20111130 on a Windows7 PC


From max-philipp.stenner at med.ovgu.de  Wed Mar 21 23:16:55 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Wed, 21 Mar 2012 22:16:55 +0000
Subject: [FieldTrip] (no subject)
In-Reply-To: <FBEFFA1F493D8944969D2F5AE78E58830CB542@ESEN4.imed.uni-magdeburg.de>
References: <FBEFFA1F493D8944969D2F5AE78E58830CB542@ESEN4.imed.uni-magdeburg.de>
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830CB553@ESEN4.imed.uni-magdeburg.de>

...just to specify the question: I am wondering whether ft_average_sens of data in planar sensor gradiometer representation is problematic

________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]&quot; im Auftrag von &quot;Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de]
Gesendet: Mittwoch, 21. März 2012 19:53
Bis: Email discussion list for the FieldTrip project
Betreff: [FieldTrip] (no subject)

Dear fieldtrip users/developers,

I'd like to perform time-frequency analysis after computing the planar gradiometer representation of multi-session data and I am wondering whether the order in which the analysis steps are performed matters. The sequence I have used is

ft_megplanar
concatenate data across sessions
ft_average_sens, add the averaged (planar) sensor information to the datapool
ft_freqanalysis
ft_combineplanar

Does that make sense?

Thanks very much,
best
Max
fieldtrip version: fieldtrip-20111130 on a Windows7 PC
_______________________________________________
fieldtrip mailing list
fieldtrip at donders.ru.nl
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From max-philipp.stenner at med.ovgu.de  Wed Mar 21 23:41:21 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Wed, 21 Mar 2012 22:41:21 +0000
Subject: [FieldTrip] (no subject)
In-Reply-To: <FBEFFA1F493D8944969D2F5AE78E58830CB553@ESEN4.imed.uni-magdeburg.de>
References: <FBEFFA1F493D8944969D2F5AE78E58830CB542@ESEN4.imed.uni-magdeburg.de>
	<FBEFFA1F493D8944969D2F5AE78E58830CB553@ESEN4.imed.uni-magdeburg.de>
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830CB561@ESEN4.imed.uni-magdeburg.de>

(i.e. before applying ft_combineplanar)
________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]&quot; im Auftrag von &quot;Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de]
Gesendet: Mittwoch, 21. März 2012 23:16
Bis: Email discussion list for the FieldTrip project
Betreff: Re: [FieldTrip] (no subject)

...just to specify the question: I am wondering whether ft_average_sens of data in planar sensor gradiometer representation is problematic

________________________________________
Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]&quot; im Auftrag von &quot;Stenner, Max-Philipp [max-philipp.stenner at med.ovgu.de]
Gesendet: Mittwoch, 21. März 2012 19:53
Bis: Email discussion list for the FieldTrip project
Betreff: [FieldTrip] (no subject)

Dear fieldtrip users/developers,

I'd like to perform time-frequency analysis after computing the planar gradiometer representation of multi-session data and I am wondering whether the order in which the analysis steps are performed matters. The sequence I have used is

ft_megplanar
concatenate data across sessions
ft_average_sens, add the averaged (planar) sensor information to the datapool
ft_freqanalysis
ft_combineplanar

Does that make sense?

Thanks very much,
best
Max
fieldtrip version: fieldtrip-20111130 on a Windows7 PC
_______________________________________________
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 bibi.raquel at gmail.com  Thu Mar 22 04:34:36 2012
From: bibi.raquel at gmail.com (Raquel Bibi)
Date: Wed, 21 Mar 2012 23:34:36 -0400
Subject: [FieldTrip] Combine Grand Average
In-Reply-To: <CAJSb8nPtg+d6dFPtWLgNXmasLFXHkOFeHEhrw7FNABMA1pE_fg@mail.gmail.com>
References: <CAJSb8nPtg+d6dFPtWLgNXmasLFXHkOFeHEhrw7FNABMA1pE_fg@mail.gmail.com>
Message-ID: <CA+Gwb028WOLjw9k9c-c3r6NfovKTG=ukuxroRG5mQPoQ+6XasA@mail.gmail.com>

Mark,
Can you calculate the weighted mean by hand?
(Data1.individual*no_of_trials(data1) +
Data2.individual*no_of_trials(data2)) / (no_trials(data1) +
no_of_trials(data2))

If so, no need to redo!



On Tue, Mar 20, 2012 at 4:37 AM, Mark Noordenbos
<mark.noordenbos at gmail.com>wrote:

> Hi Jörn, Steve and Eelke,
>
> Thanks for the suggestions for combining grand averages.
> Unfortunately, ft_appendtimelock did not work for the grand averages.
>
> Probably, the only proper way to this is to make completely new grand
> averages with all conditions included, instead of a grand average for each
> condition and combine them later.
>
> To quickly view the outcome of combining the grand averages of 2
> conditions a calculated the mean by hand:
>
> datatot.individual = (data1.individual + data2.individual)/2;
>
> Kind regards,
>
> Mark
>
>
> --
> Mark Noordenbos, MSc
>
> Radboud University Nijmegen
> Behavioural Science Institute
>
> P.O. Box 9104, Room A05.36
> 6500 HE Nijmegen
> The Netherlands
>
> Email: m.noordenbos at bsi.ru.nl
> Telephone: +31 24 3612070
> Fax:          +31 24 3616211
>
> http://www.ru.nl
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From jan.schoffelen at donders.ru.nl  Thu Mar 22 09:10:57 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 22 Mar 2012 09:10:57 +0100
Subject: [FieldTrip] error ft_read_mri
In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B03ADFF9E@Mail2-UKD.VMED.UKD>
References: <72E993C35FB11743B79FF9286E5B6D8B03ADFF9E@Mail2-UKD.VMED.UKD>
Message-ID: <F5816B77-88CB-4AA2-9B64-49E9BB83D3CB@donders.ru.nl>

Hi Jan

I cannot reproduce your problem. I'd check the following and try again:
-ensure that you have the latest version of FieldTrip
-ensure that there are no pointers to any spm directory on your matlab-path (apart perhaps from those that are distributed within fieldtrip, i.e. fieldtrip/external/spmXXX)

Cheers,

Jan

On Mar 21, 2012, at 4:36 PM, <Jan.Hirschmann at med.uni-duesseldorf.de> <Jan.Hirschmann at med.uni-duesseldorf.de> wrote:

> Dear fieldtrip programmers,
>  
> with the latest version of fieldtrip I am experiencing problems reading MRs:
>  
> a=ft_read_mri('/data/apps/spm/spm8/canonical/avg152T1.nii')
> Undefined function or variable "out".
>  
> Error in fixname (line 55)
> while(out(1) == '_'),   out = out(2:end); end;   % remove all underscore at the begin of the
> string
>  
> Error in ft_hastoolbox (line 366)
>   previous.(fixname(toolbox)) = status;
>  
> Error in ft_read_mri (line 45)
> hasmri  = ft_hastoolbox('mri');     % from Darren Weber, see http://eeg.sourceforge.net/
>  
> Thanks and all the best,
> Jan
> --
> Jan Hirschmann
> MSc. Neuroscience
> Institute of Clinical Neuroscience and Medical Psychology
> Heinrich Heine University Duesseldorf
> Universitaetsstr.  1
> 40225  Duesseldorf
> Tel: 0049 - (0)211 - 81 - 18415
>  
> _______________________________________________
> 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

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From marco.dahmane at gmail.com  Thu Mar 22 13:13:18 2012
From: marco.dahmane at gmail.com (Marco Dahmane)
Date: Thu, 22 Mar 2012 12:13:18 +0000
Subject: [FieldTrip] Trial-dependant baseline correction
Message-ID: <CAPPdCy__G9a7BL4HJsEbG4eVzYpA5k=pqxyXH5Tm-L=-P3uVrQ@mail.gmail.com>

Dear fellow Fieldtrippers,

I was having a small problem regarding baseline correction in FT.

My situation is rather simple : I have two types of trials, trials A and
trials B. Triggers A are always preceding triggers B, but the delay between
the two is NOT fixed.

I use triggers B to define my trials (for instance -0.5s to +0.5s).
Very straightforward.

However, I would like to use triggers A to define my baseline window. Say I
would like to use the one second preceding each trigger A as the baseline
for the following trial.

Until now the way I was going about it was rather tedious :
a) ft_preprocessing data as one big, long trial (filtering)
b) ft_definetrial to define long trials as starting from trigger A (origin)
to following trigger B (end)
*c) ft_preprocessing to baseline correct*
d) ft_redefinetrial with variable cfg.offset to set origin back to trigger B
e) ft_redefinetrial to take only window [ -0.5s ; +0.5s]

But I'm wondering whether that's not an overkill (especially since the
delay between triggers A and B can be quite long and make the preprocessing
really slow on my old machine).

Any advice is appreciated,

Best regards,
Marco
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From lavado at gmail.com  Thu Mar 22 15:24:42 2012
From: lavado at gmail.com (Ion Lavado)
Date: Thu, 22 Mar 2012 15:24:42 +0100
Subject: [FieldTrip] Sourceanalysis understanding problem
Message-ID: <CAMLwyK6Gi7d_EGxvsCfFGeYM_Pz2HQV8t_2sx8iEMRw9aLxSkA@mail.gmail.com>

Hello, I would like to ask you what does the "cfg.frequency" means in
ft_sourceanalysis. I want to plot a frequency range for example [14 30], do
i have to use cfg.frequency=22? why? It would be perfect if someone could
explain how to make the freqanalysis and the sourceanalysis for a frequency
range for example this one[14 30].

This is the code for my frequency analysis:
cfg = [];
cfg.method    = 'mtmfft';
cfg.output    = 'powandcsd';
cfg.channel   = {'MEG'};
cfg.tapsmofrq = 4;
cfg.foilim    = [14 30];
freq_post = ft_freqanalysis(cfg, words_post);

The i do the sourceanalysis:
cfg              = [];
cfg.frequency    = 22;
cfg.lambda=0;
cfg.method       = 'dics';
cfg.coordsys       = 'neuromag';
cfg.projectnoise = 'yes';
cfg.grad            = freq_pre.grad;
cfg.channel   = {'MEG'};
cfg.grid         = grid;
cfg.reducerank      = 2;
cfg.vol          = vol02;
vol02=ft_convert_units(vol02,'cm');
source_post11= ft_sourceanalysis(cfg, freq_post);


What i get i see that depends only in the cfg.frequency=22, if i change the
previous freqanalysis and use the 22 for the cfg.frequency i get the same
result. Hope someone can help me.

Thanks in advance.

Best,

Ion
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From lavado at gmail.com  Thu Mar 22 17:13:34 2012
From: lavado at gmail.com (Ion Lavado)
Date: Thu, 22 Mar 2012 17:13:34 +0100
Subject: [FieldTrip] is beamforming result correct?
Message-ID: <CAMLwyK4gzzrPbW3qGEfSs6sMz-NwxtsuXRE1J6DURM_Zg7pFbg@mail.gmail.com>

I think the result i got doing the beamforming source reconstruction is not
good as there is lot of activation at the bottom where the cerebellum is.
Can anyone confirm me it is incorrect? Possible mistake?

This is the code i used for the headmodel:

mri = ft_read_mri('/home/ilavado/ilavado/mutiT1/T1_02.mgz');
cfg = [];
cfg.interactive    = 'yes';
cfg.coordsys    = 'neuromag';
mri_real           = ft_volumerealign(cfg,mri);
[segmentedmri]   = ft_volumesegment(cfg, mri_real)
cfg = [];
cfg.sourceunits='cm';
cfg.coordsys       = 'neuromag';
vol02 = ft_prepare_singleshell(cfg, segmentedmri);
ft_plot_vol(vol02);
mri_real = rmfield(mri_real, 'pnt');

sourceDiff = source_post;
sourceDiff.avg.pow = (source_post.avg.pow - source_pre.avg.pow) ./
source_pre.avg.pow;
cfg            = []
cfg.downsample = 2;
sourceDiffInt  = ft_sourceinterpolate(cfg, sourceDiff , mri_real);
cfg = [];
cfg.coordsys      = 'ctf';
cfg.nonlinear     = 'no';
sourceDiffIntNorm = ft_volumenormalise(cfg, sourceDiffInt);

Thank you very much.

Best,

Ion
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From Jarmo.Kontinen at ruhr-uni-bochum.de  Thu Mar 22 17:14:46 2012
From: Jarmo.Kontinen at ruhr-uni-bochum.de (Jarmo Kontinen)
Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
Message-ID: <permail-201203221614466509e8c700002494-Jarmo.Kontinen@msgid.mail.ruhr-uni-bochum.de>

Dear all,
I am trying to import EEG subject averages into Field Trip. The files are
exported with the Brainvision Analyzer in binary form
:subject10_konPro2002.dat and subject10_konPro2002.vhdr.
I have a problem with turning the data into the Field Trip data-structure. I
am following instructions given on this forum on one similar post. What I have
tried is the following:

cfg=[];
cfg.trialdef.eventtype='average'
cfg.dataset='subject10_konPro2002.dat'

 cfg=ft_definetrial(cfg);

Warning: no trialfun was specified, using trialfun_general
> In ft_definetrial at 123
evaluating trialfunction 'trialfun_general'
reading the events from 'subject10_konPro2002.vhdr'
??? Error using ==> ft_definetrial at 176
no trials were defined, see FT_DEFINETRIAL for help

I am grateful for all the help.
Thanks,
Jarmo Kontinen


From Don.Rojas at ucdenver.edu  Thu Mar 22 20:22:47 2012
From: Don.Rojas at ucdenver.edu (Rojas, Don)
Date: Thu, 22 Mar 2012 13:22:47 -0600
Subject: [FieldTrip] is beamforming result correct?
In-Reply-To: <CAMLwyK4gzzrPbW3qGEfSs6sMz-NwxtsuXRE1J6DURM_Zg7pFbg@mail.gmail.com>
References: <CAMLwyK4gzzrPbW3qGEfSs6sMz-NwxtsuXRE1J6DURM_Zg7pFbg@mail.gmail.com>
Message-ID: <4C3A9E0C-C8FB-4B28-9563-8A7942C053B7@ucdenver.edu>

Ion,

I do not think we can say definitively if your result is incorrect or not with the information provided. Can you provide a summary of your task, preprocessing and source analysis steps? There are MEG papers using beamformers that reveal cerebellar activity that is task consistent. If you do not have any a priori reason to expect it, however, then perhaps you are correct.

Best,

Don
-----------------------
Don Rojas, Ph.D.
Associate Professor of Psychiatry
U. of Colorado Denver Anschutz Medical Campus
Director, UCD Magnetoencephalography Lab


On Mar 22, 2012, at 10:13 AM, Ion Lavado wrote:

> I think the result i got doing the beamforming source reconstruction is not good as there is lot of activation at the bottom where the cerebellum is. Can anyone confirm me it is incorrect? Possible mistake?
> 
> This is the code i used for the headmodel:
> 
> mri = ft_read_mri('/home/ilavado/ilavado/mutiT1/T1_02.mgz');
> cfg = [];
> cfg.interactive    = 'yes';
> cfg.coordsys    = 'neuromag';
> mri_real           = ft_volumerealign(cfg,mri); 
> [segmentedmri]   = ft_volumesegment(cfg, mri_real)
> cfg = [];
> cfg.sourceunits='cm';
> cfg.coordsys       = 'neuromag';
> vol02 = ft_prepare_singleshell(cfg, segmentedmri);
> ft_plot_vol(vol02);
> mri_real = rmfield(mri_real, 'pnt');
> 
> sourceDiff = source_post;
> sourceDiff.avg.pow = (source_post.avg.pow - source_pre.avg.pow) ./ source_pre.avg.pow;  
> cfg            = []
> cfg.downsample = 2;
> sourceDiffInt  = ft_sourceinterpolate(cfg, sourceDiff , mri_real);
> cfg = [];
> cfg.coordsys      = 'ctf';
> cfg.nonlinear     = 'no';
> sourceDiffIntNorm = ft_volumenormalise(cfg, sourceDiffInt);
> 
> Thank you very much. 
> 
> Best,
> 
> Ion
> <beam_result.jpg>_______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip






From e.maris at psych.ru.nl  Thu Mar 22 21:12:35 2012
From: e.maris at psych.ru.nl (Eric Maris)
Date: Thu, 22 Mar 2012 21:12:35 +0100 (CET)
Subject: [FieldTrip] statfun_depsamplesregrT
In-Reply-To: <CAAVVtzDY5stRD-XE2Pa5TjrO1L8AJXXSZToy7XhA72hK22bu+w@mail.gmail.com>
References: <CAAVVtzDY5stRD-XE2Pa5TjrO1L8AJXXSZToy7XhA72hK22bu+w@mail.gmail.com>
Message-ID: <035401cd0868$20b27640$621762c0$@maris@psych.ru.nl>

Dear Marcin,

 

 

The statfun_depsamplesregrT calculates a T-statistic for regression
coefficients that are calculated within each of the units-of-observation
(typically, participants) obtained by regressing the subject-specific data
(spatiotemporal, spatio-spectral, spatio-spectro-temporal) on some
predictor variable that varies over the different conditions in which this
participant has provided data (e.g., working-memory load, retention
interval, luminance, contrast, etc). If you doubt the assumed linear
relation between predictor variable and biological data, then you could
write your own statfun_depsamplesrankcorr. To use this test statistic for
cluster-based permutation inference, you need a threshold based on some
reference distribution (which can be parametric, but must not be). 

 

To get this statfun_depsamplesrankcorr running, you will probably have to
take a look in the Fieldtrip code to see how the statistics framework is
structured.

 

Best,

 

Eric Maris

 

 

From: Marcin [mailto:m.leszczynski.m at googlemail.com] 
Sent: woensdag 21 maart 2012 10:51
To: Email discussion list for the FieldTrip project
Subject: [FieldTrip] statfun_depsamplesregrT

 

Dear Fieldtripers,

Could anyone explain me what is being calculated with the
statfun_depsamplesregrT function, please.

David Groppe (thank you David) suggested in a previous thread on the list
that I might calculate permutation test based on rank correlation to
account for monotonic relationships within the permutation framework. I
was wondering if this is the kind of test that statfun_depsamplesregrT
function calculates.
http://mailman.science.ru.nl/pipermail/fieldtrip/2011-December/004578.html

Best,
Marcin

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From g.piantoni at nin.knaw.nl  Fri Mar 23 20:35:22 2012
From: g.piantoni at nin.knaw.nl (Gio Piantoni)
Date: Fri, 23 Mar 2012 20:35:22 +0100
Subject: [FieldTrip] Trial-dependant baseline correction
In-Reply-To: <CAPPdCy__G9a7BL4HJsEbG4eVzYpA5k=pqxyXH5Tm-L=-P3uVrQ@mail.gmail.com>
References: <CAPPdCy__G9a7BL4HJsEbG4eVzYpA5k=pqxyXH5Tm-L=-P3uVrQ@mail.gmail.com>
Message-ID: <CAHeOcru5O5O07Re92i3Eexkj++VHmabqqJ1g7_s9Ww0jFiVN0Q@mail.gmail.com>

Hi Marco,

I don't understand very well if the bottleneck is the number of steps
or the memory/time used in preprocessing (a).

I think that the simplest approach is to use:
1) ft_definetrial (as in your (b))
2) ft_preprocessing (read data and apply preproc options)
3) ft_redefinetrial to take the window [-0.5 0.5] and change the
origin (you can do that in one step if you pass cfg.trl with three
columns: [begin_sample end_sample offset] in sample points)

Otherwise, if you're concerned about memory problems, you could do a
ft_definetrial and preprocessing for A events, and the same for B
events. Then, in Matlab, you average A events and subtract the average
from the B trials.

I think preprocessing on your trials should not take too much memory though.

HTH,
Gio

On Thu, Mar 22, 2012 at 13:13, Marco Dahmane <marco.dahmane at gmail.com> wrote:
> Dear fellow Fieldtrippers,
>
> I was having a small problem regarding baseline correction in FT.
>
> My situation is rather simple : I have two types of trials, trials A and
> trials B. Triggers A are always preceding triggers B, but the delay between
> the two is NOT fixed.
>
> I use triggers B to define my trials (for instance -0.5s to +0.5s).
> Very straightforward.
>
> However, I would like to use triggers A to define my baseline window. Say I
> would like to use the one second preceding each trigger A as the baseline
> for the following trial.
>
> Until now the way I was going about it was rather tedious :
> a) ft_preprocessing data as one big, long trial (filtering)
> b) ft_definetrial to define long trials as starting from trigger A (origin)
> to following trigger B (end)
> *c) ft_preprocessing to baseline correct*
> d) ft_redefinetrial with variable cfg.offset to set origin back to trigger B
> e) ft_redefinetrial to take only window [ -0.5s ; +0.5s]
>
> But I'm wondering whether that's not an overkill (especially since the delay
> between triggers A and B can be quite long and make the preprocessing really
> slow on my old machine).
>
> Any advice is appreciated,
>
> Best regards,
> Marco
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From politzerahless at gmail.com  Sun Mar 25 12:11:28 2012
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Sun, 25 Mar 2012 12:11:28 +0200
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
Message-ID: <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg@mail.gmail.com>

Hello Jarmo,

I haven't tried importing Brain Vision files into FieldTrip myself, but
based on the code you sent it looks like the problem may be that you're
missing cfg.trialdef.eventvalue (which is used to tell FieldTrip which
triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim . See
the example at
http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials.

If what you are trying to do is import all trials from all triggers in the
file, I think you have to define your own "trialfun" function to do that
(although I haven't tried this myself so I'm not sure).
http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
information.

Best,
Steve Politzer-Ahles
University of Kansas


Message: 1
> Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> Message-ID:
>        <
> permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de
> >
>
> Content-Type: text/plain; charset=us-ascii
>
> Dear all,
> I am trying to import EEG subject averages into Field Trip. The files are
> exported with the Brainvision Analyzer in binary form
> :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> I have a problem with turning the data into the Field Trip data-structure.
> I
> am following instructions given on this forum on one similar post. What I
> have
> tried is the following:
>
> cfg=[];
> cfg.trialdef.eventtype='average'
> cfg.dataset='subject10_konPro2002.dat'
>
>  cfg=ft_definetrial(cfg);
>
> Warning: no trialfun was specified, using trialfun_general
> > In ft_definetrial at 123
> evaluating trialfunction 'trialfun_general'
> reading the events from 'subject10_konPro2002.vhdr'
> ??? Error using ==> ft_definetrial at 176
> no trials were defined, see FT_DEFINETRIAL for help
>
> I am grateful for all the help.
> Thanks,
> Jarmo Kontinen
>
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From fredericroux at hotmail.de  Mon Mar 26 12:23:50 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Mon, 26 Mar 2012 12:23:50 +0200
Subject: [FieldTrip] SPM path and sourceanalysis on template brain
Message-ID: <DUB113-W76F2D058B3132334525D94B7450@phx.gbl>


Dear all,


I am getting the following error message with the fieldtrip-20120105 version,
and wanted to ask if anyone could tell me:

a) how to prevent it
b) what the consequences of ignoring it will be.

Also I wanted to get some feedback on the possibility of
using a template brain for source localization on data for which
MRI data is missing.

I have a recorded MEG data from n = 98 participants but only have
the MRs of 70 of them. Can I use a template MR to perform
source analysis on the missing data sets?

Looking forward to any kind of suggestions.
Have a nice day,

Fred


-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From ivano_triggiani at yahoo.it  Mon Mar 26 14:14:47 2012
From: ivano_triggiani at yahoo.it (Ivano Triggiani)
Date: Mon, 26 Mar 2012 13:14:47 +0100 (BST)
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
In-Reply-To: <mailman.1.1332756017.8892.fieldtrip@donders.ru.nl>
References: <mailman.1.1332756017.8892.fieldtrip@donders.ru.nl>
Message-ID: <1332764087.47250.YahooMailNeo@web132103.mail.ird.yahoo.com>

Dear Jarmo,

Filedtrip needs a definition of segments of interest. For example reading a trigger channel or something else to cut the EEG recording into trials. If I have understood what you want to do is to get an average of general EEG (for example resting state EEG closed eyes). But you have to indicate which average you want to obtain, for example you can tell fieldtrip to divide EEG into epochs of 3 seconds and then to make an average of all of them.
What you wrote is the request of an average, but you are not specifing of what.
Fof example you can write a trial function that provides a trl matrix, i.e.:
0 3 0

3 6 0
6 9 0
9 12 0
12 13 0
...

where first column is the start sample in seconds (you have to multiply it for sample rate), the second column is the end sample and the third is the offset (in this case is always zero), or look at 
http://fieldtrip.fcdonders.nl/tutorial/preprocessing#use_your_own_function_for_trial_selection

best wishes,
Ivano



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




"No man can wear one face to himself 
and another to the multitude,
without finally getting bewildered 
as to which one is true."


Nathaniel Hawthorne


________________________________
 Da: "fieldtrip-request at donders.ru.nl" <fieldtrip-request at donders.ru.nl>
A: fieldtrip at donders.ru.nl 
Inviato: Lunedì 26 Marzo 2012 12:00
Oggetto: fieldtrip Digest, Vol 16, Issue 33
 
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Today's Topics:

   1. Re: Problem with FT_DEFINETRIAL (Stephen Politzer-Ahles)


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

Message: 1
Date: Sun, 25 Mar 2012 12:11:28 +0200
From: Stephen Politzer-Ahles <politzerahless at gmail.com>
To: fieldtrip at donders.ru.nl
Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL
Message-ID:
    <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello Jarmo,

I haven't tried importing Brain Vision files into FieldTrip myself, but
based on the code you sent it looks like the problem may be that you're
missing cfg.trialdef.eventvalue (which is used to tell FieldTrip which
triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim . See
the example at
http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials.

If what you are trying to do is import all trials from all triggers in the
file, I think you have to define your own "trialfun" function to do that
(although I haven't tried this myself so I'm not sure).
http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
information.

Best,
Steve Politzer-Ahles
University of Kansas


Message: 1
> Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> Message-ID:
>        <
> permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de
> >
>
> Content-Type: text/plain; charset=us-ascii
>
> Dear all,
> I am trying to import EEG subject averages into Field Trip. The files are
> exported with the Brainvision Analyzer in binary form
> :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> I have a problem with turning the data into the Field Trip data-structure.
> I
> am following instructions given on this forum on one similar post. What I
> have
> tried is the following:
>
> cfg=[];
> cfg.trialdef.eventtype='average'
> cfg.dataset='subject10_konPro2002.dat'
>
>  cfg=ft_definetrial(cfg);
>
> Warning: no trialfun was specified, using trialfun_general
> > In ft_definetrial at 123
> evaluating trialfunction 'trialfun_general'
> reading the events from 'subject10_konPro2002.vhdr'
> ??? Error using ==> ft_definetrial at 176
> no trials were defined, see FT_DEFINETRIAL for help
>
> I am grateful for all the help.
> Thanks,
> Jarmo Kontinen
>
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------------------------------

_______________________________________________
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End of fieldtrip Digest, Vol 16, Issue 33
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From fredericroux at hotmail.de  Mon Mar 26 14:47:22 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Mon, 26 Mar 2012 14:47:22 +0200
Subject: [FieldTrip] beamforming with rank deficient covariance matrix
Message-ID: <DUB113-W8242FDFA7507E17608A292B7450@phx.gbl>



Dear all,

I have a question related to the rank of the covariance matrix
used for the beamformer.

I preprocessed my data using ICA to reject EOG and ECG component (typically
between 2-4 components). This however, leads to a reduction in the rank
of the covariance matrix and I get a warning using ft_sourceanalysis
saying that my covariance matrix is rank deficient because rank(COV) < Nchannels.

I would like to know, how much of a problem and how serious this can be.

The way I understand things, this should only cause trouble if the number
of active sources exceeds the number of linearly independent rows of the covariance matrix?
Is this assumption correct? 

Is there some step in the ft_sourceanalyis pipeline that assumes that the number of
sources is equal to the number of channels, and that could bias the computation
of the beamformer? I mean in that case I would have more sources than channels
and thus the beamformer would fail.

Would be great if someone could help me to figure this out.

Cheers,
Fred




-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From max-philipp.stenner at med.ovgu.de  Mon Mar 26 14:51:08 2012
From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp)
Date: Mon, 26 Mar 2012 12:51:08 +0000
Subject: [FieldTrip] ft_sourceanalysis
Message-ID: <FBEFFA1F493D8944969D2F5AE78E58830CB840@ESEN4.imed.uni-magdeburg.de>

Dear fieldtrip developers and users, 

I am computing single trial LCMV beamforming moments with ft_sourceanalysis and cfg.rawtrial = 'yes'. I chose cfg.rawtrial because my fieldtrip version (fieldtrip-lite-20111130) reports a bug when using cfg.singletrial.

Am I right that the single-trial covariance matrices will not affect the moments when using precomputed filters (precomputed on the basis of the covariance matrices from "keeptrial = no" timelockdata across all experimental conditions) on "keeptrial = yes" - timelock data (sorted according to conditions) with cfg.rawtrial = 'yes'?
(I am not interested in power (which is changed to NaN by lcmv_beamforming anyways) or noise).

Thanks very much 
Max

fieldtrip-lite-20111130 on a Windows7 PC


From Jarmo.Kontinen at ruhr-uni-bochum.de  Mon Mar 26 15:09:23 2012
From: Jarmo.Kontinen at ruhr-uni-bochum.de (Jarmo Kontinen)
Date: Mon, 26 Mar 2012 15:09:23 +0200 (CEST)
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
In-Reply-To: <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg@mail.gmail.com>
Message-ID: <permail-201203261309236509e8c70000654b-Jarmo.Kontinen@msgid.mail.ruhr-uni-bochum.de>


Dear Stephen,
Thanks for your reply. I  have added the  missing field you sugegsted, but FT
still gives the same error-message.

Maybe I was also unclear what I want to do in the first place. The data we
have is already preprocessed ( filtered, segmented etc.) with the Analyzer.
Also, we have averaged the ERP's for each subject and each experimental
condition over all the trials. I would like to import these averaged ERP's
into FT and do some statisitics on the data. The problem is that I do not know
how to get required data-structure to use the FT-functions.

Best,
Jarmo


Stephen Politzer-Ahles schrieb am 2012-03-25:
> Hello Jarmo,

> I haven't tried importing Brain Vision files into FieldTrip myself,
> but
> based on the code you sent it looks like the problem may be that
> you're
> missing cfg.trialdef.eventvalue (which is used to tell FieldTrip
> which
> triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim
> . See
> the example at
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials.

> If what you are trying to do is import all trials from all triggers
> in the
> file, I think you have to define your own "trialfun" function to do
> that
> (although I haven't tried this myself so I'm not sure).
> http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
> information.

> Best,
> Steve Politzer-Ahles
> University of Kansas


> Message: 1
> > Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> > From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> > To: <fieldtrip at donders.ru.nl>
> > Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> > Message-ID:
> >        <
> > permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de


> > Content-Type: text/plain; charset=us-ascii

> > Dear all,
> > I am trying to import EEG subject averages into Field Trip. The
> > files are
> > exported with the Brainvision Analyzer in binary form
> > :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> > I have a problem with turning the data into the Field Trip
> > data-structure.
> > I
> > am following instructions given on this forum on one similar post.
> > What I
> > have
> > tried is the following:

> > cfg=[];
> > cfg.trialdef.eventtype='average'
> > cfg.dataset='subject10_konPro2002.dat'

> >  cfg=ft_definetrial(cfg);

> > Warning: no trialfun was specified, using trialfun_general
> > > In ft_definetrial at 123
> > evaluating trialfunction 'trialfun_general'
> > reading the events from 'subject10_konPro2002.vhdr'
> > ??? Error using ==> ft_definetrial at 176
> > no trials were defined, see FT_DEFINETRIAL for help

> > I am grateful for all the help.
> > Thanks,
> > Jarmo Kontinen



From Maria.Pefkou at unige.ch  Mon Mar 26 18:01:00 2012
From: Maria.Pefkou at unige.ch (Maria Pefkou)
Date: Mon, 26 Mar 2012 18:01:00 +0200
Subject: [FieldTrip] Create BEM model for EEG source localisation
Message-ID: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>

Dear FieldTrip users,

I started using the toolbox fairly recently to analyse EEG data and I have
huge trouble making a BEM model, which I need for source localisation.
Following the online tutorial, I processed my subjects' individual
structural MRIs in FreeSurfer and MNE and managed to prepare the
triangulated mesh. However, my problem is the volume conduction model. I
can get a singleshell one, using the ft_prepare_singleshell function, but
as far as I understand it is excusively used for MEG data. I came to this
conclusion because when I try to compute the forward model, given that I
provide information about the electrodes position, I always get the
following error:

"unsupported volume conductor model for EEG".
I guess this is because the vol.type is 'nolte' and there is no such case
for EEG data, at least not in the ft_prepare_vol_sens.m function, which is
automatically called.

I have tried to prepare a BEM model using the ft_prepare_headmodel function
with cfg.method='bemcp' or cfg.method='dipoli' but I was unsuccessful.
The problem is that, after having tried various functions/options, I lost
the general picture and I'm running in circles... The question is: I have a
segmented mri, how can I get a BEM model out of this? I must be missing a
fundamental part of the procedure but I can't quite find out what it is.
Any suggestions/help would be very much appreciated.

Thank you in advance,
Maria Pefkou

------------------------------------------
Research Assistant
Functional Brain Mapping Lab
University of Geneva
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From Maria.Pefkou at unige.ch  Mon Mar 26 18:05:36 2012
From: Maria.Pefkou at unige.ch (Maria Pefkou)
Date: Mon, 26 Mar 2012 18:05:36 +0200
Subject: [FieldTrip] Create BEM model for EEG source localisation
In-Reply-To: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>
References: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>
Message-ID: <CAJ5HwaumWvg4CT5-3MPEO5=H=YWK5kkU-wY2xJR8Fithb7dsRA@mail.gmail.com>

I forgot to mention before that right now I'm running fieldtrip-20120325
under Ubuntu 10.04.

On 26 March 2012 18:01, Maria Pefkou <Maria.Pefkou at unige.ch> wrote:

> Dear FieldTrip users,
>
> I started using the toolbox fairly recently to analyse EEG data and I have
> huge trouble making a BEM model, which I need for source localisation.
> Following the online tutorial, I processed my subjects' individual
> structural MRIs in FreeSurfer and MNE and managed to prepare the
> triangulated mesh. However, my problem is the volume conduction model. I
> can get a singleshell one, using the ft_prepare_singleshell function, but
> as far as I understand it is excusively used for MEG data. I came to this
> conclusion because when I try to compute the forward model, given that I
> provide information about the electrodes position, I always get the
> following error:
>
> "unsupported volume conductor model for EEG".
> I guess this is because the vol.type is 'nolte' and there is no such case
> for EEG data, at least not in the ft_prepare_vol_sens.m function, which is
> automatically called.
>
> I have tried to prepare a BEM model using the ft_prepare_headmodel
> function with cfg.method='bemcp' or cfg.method='dipoli' but I was
> unsuccessful.
> The problem is that, after having tried various functions/options, I lost
> the general picture and I'm running in circles... The question is: I have a
> segmented mri, how can I get a BEM model out of this? I must be missing a
> fundamental part of the procedure but I can't quite find out what it is.
> Any suggestions/help would be very much appreciated.
>
> Thank you in advance,
> Maria Pefkou
>
> ------------------------------------------
> Research Assistant
> Functional Brain Mapping Lab
> University of Geneva
>
>
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From k.muesch at uke.uni-hamburg.de  Mon Mar 26 18:45:35 2012
From: k.muesch at uke.uni-hamburg.de (=?iso-8859-1?Q?Kathrin_M=FCsch?=)
Date: Mon, 26 Mar 2012 18:45:35 +0200
Subject: [FieldTrip] inconsistent results from dipolefitting and beamforming
Message-ID: <5D2500F2-F9AB-41B0-8BA1-25B18E08A5A5@uke.uni-hamburg.de>

Hi Fieldtrip users,

I am trying to apply a beamformer to simulated data to check whether my headmodels are correct. While ft_dipolefit localizes the dipole in the original position, the beamformer results in a source at a totally different position (see figure 1). I kept everything as similar as possible to the example scripts (forward simulation & dipole fit, forward simulation & beamformer) but used individual gradiometer positions, grid and volume of a single subject (CTF space) and plotted the source in a template grid (SPM space). If I run the dipolesimulation with the individual gradiometer structure and the template headmodel vol and template grid, the dipole and the source result in the same position, although the grad and vol are not in the same coordinate system (figure 2). And importantly, shouldn't the dipole be in the right hemisphere anyway with the coordinates 5/2/3? I appended the code below.

Could the different coordinate systems lead to the inconsistent results of dipolefitting and beamforming? Will the dipolesimulation be in the same coordinate system as the volume or gradiometer structure I feed in (CTF space, in my case)? How could I use the dipolesimulation, dipolefitting and beamforming to properly check my headmodels?

I tried so many things now but I couldn't find the error. Any help is very appreciated.

Best,
Kathrin



These are the variables I used:

vol = headmodel of individual subject in CTF space (cm)
data.grad = gradiometer structure of individual subject in CTF space (cm)
mnigrid = grid of individual subject in CTF space (cm)
template_grid = grid of template brain in SPM space (cm)
mri = spm8 template brain in SMP space


%% compute forward simulated data + apply diplole fit
cfg     = [];
cfg.vol = vol;
cfg.grad = data.grad;
cfg.channel = 'MEG';
cfg.dip.pos = [5 2 3]; % pos of dipole in cm
cfg.dip.mom = [1 0 0]';
cfg.dip.frequency = 10;
cfg.ntrials = 20;
cfg.relnoise = 10;
raw = ft_dipolesimulation(cfg);
 
% compute the data covariance matrix, which will capture the activity of
% the simulated dipole
cfg = [];
cfg.covariance = 'yes';
avg = ft_timelockanalysis(cfg, raw);
 
% apply dipolefit
cfg = [];
cfg.vol = vol;
cfg.grad = data.grad;
cfg.dip.pos = [0 0 0];
cfg.gridsearch = 'no';
dip = ft_dipolefitting(cfg, avg);
 
cfg = [];
cfg.location = dip.dip.pos *10;
figure, ft_sourceplot(cfg,mri)

 
% do the beamformer source reconstuction on a 1 cm grid
cfg = [];
cfg.channel = 'MEG';
cfg.vol = vol;
cfg.grad = data.grad;
cfg.grid  = mnigrid;
cfg.method = 'lcmv';
cfg.projectnoise = 'yes'; 
source = ft_sourceanalysis(cfg, avg);

% compute the neural activity index, i.e. projected power divided by
% projected noise
cfg = [];
cfg.powmethod = 'none'; % keep the power as estimated from the data covariance, i.e. the induced power
source = ft_sourcedescriptives(cfg, source);
 
interp = ft_sourceinterpolate([], source, mri);
 
cfg = [];
cfg.method = 'ortho';
cfg.interactive = 'yes';
cfg.funparameter = 'nai';
cfg.funcolorlim = [1.5 4];  % the voxel in the center of the volume conductor messes up the autoscaling
figure, ft_sourceplot(cfg, interp);
 






_____________________________________
Kathrin Müsch

Dept. of Neurophysiology and Pathophysiology
University Medical Center Hamburg-Eppendorf
Martinistr. 52
20246 Hamburg
Germany
Phone: +49-40-7410-54680
Fax: +49-40-7410-57752
E-Mail: k.muesch at uke.uni-hamburg.de
_____________________________________


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

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg

Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus 
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From smoratti at psi.ucm.es  Mon Mar 26 16:13:00 2012
From: smoratti at psi.ucm.es (Stephan Moratti)
Date: Mon, 26 Mar 2012 16:13:00 +0200
Subject: [FieldTrip] beamforming with rank deficient covariance matrix
In-Reply-To: <DUB113-W8242FDFA7507E17608A292B7450@phx.gbl>
References: <DUB113-W8242FDFA7507E17608A292B7450@phx.gbl>
Message-ID: <9BF0E297-D3D1-41F4-A2BF-D9940E50E51C@psi.ucm.es>

Dear Fred,

In case of reduced rank people usually do regularization specifying  a lambda value (cfg.lcmv.lambda ='5%').

Best,

Stephan

El 26/03/2012, a las 14:47, Frederic Roux escribió:

> 
> Dear all,
> 
> I have a question related to the rank of the covariance matrix
> used for the beamformer.
> 
> I preprocessed my data using ICA to reject EOG and ECG component (typically
> between 2-4 components). This however, leads to a reduction in the rank
> of the covariance matrix and I get a warning using ft_sourceanalysis
> saying that my covariance matrix is rank deficient because rank(COV) < Nchannels.
> 
> I would like to know, how much of a problem and how serious this can be.
> 
> The way I understand things, this should only cause trouble if the number
> of active sources exceeds the number of linearly independent rows of the covariance matrix?
> Is this assumption correct? 
> 
> Is there some step in the ft_sourceanalyis pipeline that assumes that the number of
> sources is equal to the number of channels, and that could bias the computation
> of the beamformer? I mean in that case I would have more sources than channels
> and thus the beamformer would fail.
> 
> Would be great if someone could help me to figure this out.
> 
> Cheers,
> Fred
> 
> 
> 
> 
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


________________________________________________________
Stephan Moratti, PhD

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

Universidad Complutense de Madrid
Facultad de Psicología
Departamento de Psicología Básica I
Campus de Somosaguas
28223 Pozuelo de Alarcón (Madrid)
Spain

and

Center for Biomedical Technology
Laboratory for Cognitive and Computational Neuroscience
Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)
Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982


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From jan.schoffelen at donders.ru.nl  Mon Mar 26 21:42:19 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Mon, 26 Mar 2012 21:42:19 +0200
Subject: [FieldTrip] Create BEM model for EEG source localisation
In-Reply-To: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>
References: <CAJ5Hwas6s5C=-PDv+6KGAsNPjAr14-HUwogaTs2ZJQtYcos==A@mail.gmail.com>
Message-ID: <29B44597-C214-468C-A291-ABCDEEA6E099@donders.ru.nl>

Hi Maria,

You could have a look at:

http://fieldtrip.fcdonders.nl/tutorial/headmodel

and

http://fieldtrip.fcdonders.nl/example/create_bem_headmodel_for_eeg

Hopefully this will give you some inspiration.

Best,

Jan-Mathijs

On Mar 26, 2012, at 6:01 PM, Maria Pefkou wrote:

> Dear FieldTrip users,
> 
> I started using the toolbox fairly recently to analyse EEG data and I have huge trouble making a BEM model, which I need for source localisation.
> Following the online tutorial, I processed my subjects' individual structural MRIs in FreeSurfer and MNE and managed to prepare the triangulated mesh. However, my problem is the volume conduction model. I can get a singleshell one, using the ft_prepare_singleshell function, but as far as I understand it is excusively used for MEG data. I came to this conclusion because when I try to compute the forward model, given that I provide information about the electrodes position, I always get the following error: 
> 
> "unsupported volume conductor model for EEG".
> I guess this is because the vol.type is 'nolte' and there is no such case for EEG data, at least not in the ft_prepare_vol_sens.m function, which is automatically called.
> 
> I have tried to prepare a BEM model using the ft_prepare_headmodel function with cfg.method='bemcp' or cfg.method='dipoli' but I was unsuccessful.
> The problem is that, after having tried various functions/options, I lost the general picture and I'm running in circles... The question is: I have a segmented mri, how can I get a BEM model out of this? I must be missing a fundamental part of the procedure but I can't quite find out what it is.
> Any suggestions/help would be very much appreciated.
> 
> Thank you in advance,
> Maria Pefkou
> 
> ------------------------------------------
> Research Assistant
> Functional Brain Mapping Lab
> University of Geneva
> 
> _______________________________________________
> 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




From jan.schoffelen at donders.ru.nl  Mon Mar 26 21:52:11 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Mon, 26 Mar 2012 21:52:11 +0200
Subject: [FieldTrip] inconsistent results from dipolefitting and
	beamforming
In-Reply-To: <5D2500F2-F9AB-41B0-8BA1-25B18E08A5A5@uke.uni-hamburg.de>
References: <5D2500F2-F9AB-41B0-8BA1-25B18E08A5A5@uke.uni-hamburg.de>
Message-ID: <E931E86A-3F5A-4998-A098-3DC9091C72CF@donders.ru.nl>

Dear Kathrin,

Note that you cannot just mix geometrical objects which are defined in different coordinate systems within a simulation / source reconstruction.
The code cannot make the distinction about the coordinate systems, and assumes that all geometrical objects that go into a function are defined within the same coordinate system (i.e. x,y,z position mean the same in all objects). This also goes for the mri used for the interpolation. You should use an MRI volume that has a transformation matrix attached to it that transforms from voxel space into CTF coordinate system, rather than into MNI space. The result of a faulty interpolation would lead among others to the x and y axis being exchanged. I think you should look into this direction for a solution. 
By the way, (5,2,3) is indeed in the right hemisphere, but how it shows up on the screen depends on whether the anatomy is shown in radiological or neurological convention.

Best,

Jan-Mathijs

On Mar 26, 2012, at 6:45 PM, Kathrin Müsch wrote:

> Hi Fieldtrip users,
> 
> I am trying to apply a beamformer to simulated data to check whether my headmodels are correct. While ft_dipolefit localizes the dipole in the original position, the beamformer results in a source at a totally different position (see figure 1). I kept everything as similar as possible to the example scripts (forward simulation & dipole fit, forward simulation & beamformer) but used individual gradiometer positions, grid and volume of a single subject (CTF space) and plotted the source in a template grid (SPM space). If I run the dipolesimulation with the individual gradiometer structure and the template headmodel vol and template grid, the dipole and the source result in the same position, although the grad and vol are not in the same coordinate system (figure 2). And importantly, shouldn't the dipole be in the right hemisphere anyway with the coordinates 5/2/3? I appended the code below.
> 
> Could the different coordinate systems lead to the inconsistent results of dipolefitting and beamforming? Will the dipolesimulation be in the same coordinate system as the volume or gradiometer structure I feed in (CTF space, in my case)? How could I use the dipolesimulation, dipolefitting and beamforming to properly check my headmodels?
> 
> I tried so many things now but I couldn't find the error. Any help is very appreciated.
> 
> Best,
> Kathrin
> 
> 
> 
> These are the variables I used:
> 
> vol = headmodel of individual subject in CTF space (cm)
> data.grad = gradiometer structure of individual subject in CTF space (cm)
> mnigrid = grid of individual subject in CTF space (cm)
> template_grid = grid of template brain in SPM space (cm)
> mri = spm8 template brain in SMP space
> 
> 
> %% compute forward simulated data + apply diplole fit
> cfg     = [];
> cfg.vol = vol;
> cfg.grad = data.grad;
> cfg.channel = 'MEG';
> cfg.dip.pos = [5 2 3]; % pos of dipole in cm
> cfg.dip.mom = [1 0 0]';
> cfg.dip.frequency = 10;
> cfg.ntrials = 20;
> cfg.relnoise = 10;
> raw = ft_dipolesimulation(cfg);
>  
> % compute the data covariance matrix, which will capture the activity of
> % the simulated dipole
> cfg = [];
> cfg.covariance = 'yes';
> avg = ft_timelockanalysis(cfg, raw);
>  
> % apply dipolefit
> cfg = [];
> cfg.vol = vol;
> cfg.grad = data.grad;
> cfg.dip.pos = [0 0 0];
> cfg.gridsearch = 'no';
> dip = ft_dipolefitting(cfg, avg);
>  
> cfg = [];
> cfg.location = dip.dip.pos *10;
> figure, ft_sourceplot(cfg,mri)
> 
>  
> % do the beamformer source reconstuction on a 1 cm grid
> cfg = [];
> cfg.channel = 'MEG';
> cfg.vol = vol;
> cfg.grad = data.grad;
> cfg.grid  = mnigrid;
> cfg.method = 'lcmv';
> cfg.projectnoise = 'yes'; 
> source = ft_sourceanalysis(cfg, avg);
> 
> % compute the neural activity index, i.e. projected power divided by
> % projected noise
> cfg = [];
> cfg.powmethod = 'none'; % keep the power as estimated from the data covariance, i.e. the induced power
> source = ft_sourcedescriptives(cfg, source);
>  
> interp = ft_sourceinterpolate([], source, mri);
>  
> cfg = [];
> cfg.method = 'ortho';
> cfg.interactive = 'yes';
> cfg.funparameter = 'nai';
> cfg.funcolorlim = [1.5 4];  % the voxel in the center of the volume conductor messes up the autoscaling
> figure, ft_sourceplot(cfg, interp);
>  
> 
> <individual.png>
> 
> 
> <template.png>
> 
> 
> _____________________________________
> Kathrin Müsch
> 
> Dept. of Neurophysiology and Pathophysiology
> University Medical Center Hamburg-Eppendorf
> Martinistr. 52
> 20246 Hamburg
> Germany
> Phone: +49-40-7410-54680
> Fax: +49-40-7410-57752
> E-Mail: k.muesch at uke.uni-hamburg.de
> _____________________________________
> 
> 
> --
> Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG):
> 
> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg
> 
> Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus
> _______________________________________________
> 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

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From wljj09 at gmail.com  Mon Mar 26 22:06:52 2012
From: wljj09 at gmail.com (Jing Wang)
Date: Mon, 26 Mar 2012 22:06:52 +0200
Subject: [FieldTrip] about ft_appendspike
Message-ID: <CABKH8xZdF2QZsL_WXR2iiSw8GjYnjMBLvaeJ5bmD5n=X9Dh7Xw@mail.gmail.com>

Dear fieldtrip developers and users,

I am trying to append spikes to local field potential with ft_appendspike.

The local field potential data have five channels, but the spikes data have
12 channels. They have some trials. According to the ft_appenddata, the
channels will be concatenated within each trial when the input datasets
have different channels.

However, my purpose is to append the first 2 channel of spike data on the
first channel of local field potential data. And to append the third
channel of spike data on the second channel of local field potential data,
and so on. How can I do with ft_appendspike?

Thank you very much! I am grateful for all the help!

Jing
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From lavado at gmail.com  Tue Mar 27 11:19:12 2012
From: lavado at gmail.com (Ion Lavado)
Date: Tue, 27 Mar 2012 11:19:12 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band, concept problem
Message-ID: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>

Hello, i'm having problems trying the beamformer analysis with a frequency
band of interest. I would like to have for example an interval like [8 14]
Hz. My concept problem is about the cfg.frequency and
cfg.tapsmofrq  values. (it must be a escalar, but i want a frequency band).

%FREQ ANALYSIS
cfg = [];
cfg.method    = 'mtmfft';
cfg.output    = 'powandcsd';
cfg.tapsmofrq = 5;
cfg.foilim    = [8 14];
freq_words_alpha = ft_freqanalysis(cfg, words);


%SOURCE ANALYSIS
cfg              = [];
cfg.frequency    = 11;
cfg.lambda=0;
cfg.method       = 'dics';
cfg.coordsys       = 'neuromag';
cfg.projectnoise = 'yes';
cfg.grad            =  freq_words_alpha.grad;
cfg.channel   = {'MEG'};
cfg.grid         = grid;
cfg.reducerank      = 2;
cfg.vol          = vol02;
vol02=ft_convert_units(vol02,'cm');
source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );


I use a cfg.frequency of 11 but i don't have really clear what i'm doing as
a get the same result using cfg.frequency=11 but a freqanalysis in [10 12].
I would be very grateful if someone could solve my doubt.

Best wishes,

Mikel
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From fredericroux at hotmail.de  Tue Mar 27 12:14:45 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Tue, 27 Mar 2012 12:14:45 +0200
Subject: [FieldTrip] question to the fieldtrip developers - multiple spm
 versions in fieldtrip
Message-ID: <DUB113-W12B64F64480B0A75AB493EB74A0@phx.gbl>



Dear all,

I would like to ask again if the fact of getting a warning
that different spm versions will confuse fieldtrip
can have consequences in the ft_sourceanalysis pipeline.

I am using version 2012-01-05 which has SPM2 and SPM8
in the external folder.

It would be great if someone from the development-team could tell me

a) why this is a problem
b) how to circumvent it


I renamed the spm.m file into spm.m.bak in the SPM2 folder so that
only the spm.m file from the SPM8 folder is used. However, it would
be great if someone could tell me if this is a workaround or not.


Best regards,
Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From smoratti at psi.ucm.es  Tue Mar 27 12:38:19 2012
From: smoratti at psi.ucm.es (Stephan Moratti)
Date: Tue, 27 Mar 2012 12:38:19 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band,
	concept problem
In-Reply-To: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
References: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
Message-ID: <EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>

Dear Mikel,

I understand that you should do a mtmfft with a center frequency of interest (in your case cfg.foil = [11 11]) and then you do a frequency smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you need a time window big enough to allow such a smoothing. The CSD should represent a frequency window of 8 to 14 Hz then. Then you put the result of the mtmfft into the dics beamformer.

Best,

Stephan
 
El 27/03/2012, a las 11:19, Ion Lavado escribió:

> Hello, i'm having problems trying the beamformer analysis with a frequency band of interest. I would like to have for example an interval like [8 14] Hz. My concept problem is about the cfg.frequency and cfg.tapsmofrq  values. (it must be a escalar, but i want a frequency band). 
> 
> %FREQ ANALYSIS
> cfg = [];
> cfg.method    = 'mtmfft';
> cfg.output    = 'powandcsd';
> cfg.tapsmofrq = 5;
> cfg.foilim    = [8 14];
> freq_words_alpha = ft_freqanalysis(cfg, words);
> 
> 
> %SOURCE ANALYSIS
> cfg              = []; 
> cfg.frequency    = 11;  
> cfg.lambda=0;
> cfg.method       = 'dics';
> cfg.coordsys       = 'neuromag';
> cfg.projectnoise = 'yes';
> cfg.grad            =  freq_words_alpha.grad;
> cfg.channel   = {'MEG'}; 
> cfg.grid         = grid; 
> cfg.reducerank      = 2;
> cfg.vol          = vol02;
> vol02=ft_convert_units(vol02,'cm');
> source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
> 
> 
> I use a cfg.frequency of 11 but i don't have really clear what i'm doing as a get the same result using cfg.frequency=11 but a freqanalysis in [10 12]. I would be very grateful if someone could solve my doubt.
> 
> Best wishes,
> 
> Mikel
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


________________________________________________________
Stephan Moratti, PhD

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

Universidad Complutense de Madrid
Facultad de Psicología
Departamento de Psicología Básica I
Campus de Somosaguas
28223 Pozuelo de Alarcón (Madrid)
Spain

and

Center for Biomedical Technology
Laboratory for Cognitive and Computational Neuroscience
Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)
Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982


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From lavado at gmail.com  Tue Mar 27 12:46:35 2012
From: lavado at gmail.com (Ion Lavado)
Date: Tue, 27 Mar 2012 12:46:35 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band,
	concept problem
In-Reply-To: <EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>
References: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
	<EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>
Message-ID: <CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>

Thank you Stephan, just one thing, why i need a time window big enough? so
i'm just studying the frequency.

Best,

Mikel

2012/3/27 Stephan Moratti <smoratti at psi.ucm.es>

> Dear Mikel,
>
> I understand that you should do a mtmfft with a center frequency of
> interest (in your case cfg.foil = [11 11]) and then you do a frequency
> smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you need a time window big
> enough to allow such a smoothing. The CSD should represent a frequency
> window of 8 to 14 Hz then. Then you put the result of the mtmfft into the
> dics beamformer.
>
> Best,
>
> Stephan
>
> El 27/03/2012, a las 11:19, Ion Lavado escribió:
>
> Hello, i'm having problems trying the beamformer analysis with a frequency
> band of interest. I would like to have for example an interval like [8 14]
> Hz. My concept problem is about the cfg.frequency and
> cfg.tapsmofrq  values. (it must be a escalar, but i want a frequency band).
>
> %FREQ ANALYSIS
> cfg = [];
> cfg.method    = 'mtmfft';
> cfg.output    = 'powandcsd';
> cfg.tapsmofrq = 5;
> cfg.foilim    = [8 14];
> freq_words_alpha = ft_freqanalysis(cfg, words);
>
>
> %SOURCE ANALYSIS
> cfg              = [];
> cfg.frequency    = 11;
> cfg.lambda=0;
> cfg.method       = 'dics';
> cfg.coordsys       = 'neuromag';
> cfg.projectnoise = 'yes';
> cfg.grad            =  freq_words_alpha.grad;
> cfg.channel   = {'MEG'};
> cfg.grid         = grid;
> cfg.reducerank      = 2;
> cfg.vol          = vol02;
> vol02=ft_convert_units(vol02,'cm');
> source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
>
>
> I use a cfg.frequency of 11 but i don't have really clear what i'm doing
> as a get the same result using cfg.frequency=11 but a freqanalysis in [10
> 12]. I would be very grateful if someone could solve my doubt.
>
> Best wishes,
>
> Mikel
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> ________________________________________________________
> Stephan Moratti, PhD
>
> see also: http://web.me.com/smoratti/
>
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
> and
>
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
>
>
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
>
>
>
> _______________________________________________
> 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 Mar 27 13:14:56 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 27 Mar 2012 13:14:56 +0200
Subject: [FieldTrip] SPM path and sourceanalysis on template brain
In-Reply-To: <DUB113-W76F2D058B3132334525D94B7450@phx.gbl>
References: <DUB113-W76F2D058B3132334525D94B7450@phx.gbl>
Message-ID: <4F71A130.7070705@donders.ru.nl>

Dear Frederic,

I meant to send this mail already yesterday - but at least you cleared 
up the issue I had with your first mail ;)
Original mail:

Although you forgot to actually paste the error message into the mail 
you sent, I assume that you get a warning that mentions something like 
"Multiple occurences of SPM have been found on your path". If this is 
the error, you are using 
addpath(genpath('WhereeverFieldTripIsStoredOnYourMachine')), but should 
just do addpath('WhereeverFieldTripIsStoredOnYourMachine') and then call 
ft_defaults. Otherwise, your source reconstruction might be a result of 
different version of SPM, which might lead to faulty behaviour, because 
functions of different versions are not designed to be compatible with 
each other.

Best,
Jörn

On 3/26/2012 12:23 PM, Frederic Roux wrote:
> Dear all,
>
>
> I am getting the following error message with the fieldtrip-20120105 
> version,
> and wanted to ask if anyone could tell me:
>
> a) how to prevent it
> b) what the consequences of ignoring it will be.
>
> Also I wanted to get some feedback on the possibility of
> using a template brain for source localization on data for which
> MRI data is missing.
>
> I have a recorded MEG data from n = 98 participants but only have
> the MRs of 70 of them. Can I use a template MR to perform
> source analysis on the missing data sets?
>
> Looking forward to any kind of suggestions.
> Have a nice day,
>
> Fred
>
>
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
>
>
>
>
> _______________________________________________
> 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

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 Jarmo.Kontinen at ruhr-uni-bochum.de  Tue Mar 27 13:24:43 2012
From: Jarmo.Kontinen at ruhr-uni-bochum.de (Jarmo Kontinen)
Date: Tue, 27 Mar 2012 13:24:43 +0200 (CEST)
Subject: [FieldTrip] Problem with FT_DEFINETRIAL
In-Reply-To: <1332764087.47250.YahooMailNeo@web132103.mail.ird.yahoo.com>
Message-ID: <permail-201203271124436509e8c7000033ba-Jarmo.Kontinen@msgid.mail.ruhr-uni-bochum.de>


Dear Ivano,
I had some problem with email, so if I am replying to you twice, I apologize.

 I was maybe a  bit unclear maybe in my first post. My files already contain
 averaged data.
Problem is to get the right data-structure to use the existing FT-functions to
do analysis on the data.

Best,
Jarmo

Ivano Triggiani schrieb am 2012-03-26:
> Dear Jarmo,

> Filedtrip needs a definition of segments of interest. For example
> reading a trigger channel or something else to cut the EEG recording
> into trials. If I have understood what you want to do is to get an
> average of general EEG (for example resting state EEG closed eyes).
> But you have to indicate which average you want to obtain, for
> example you can tell fieldtrip to divide EEG into epochs of 3 seconds
> and then to make an average of all of them.
> What you wrote is the request of an average, but you are not
> specifing of what.
> Fof example you can write a trial function that provides a trl
> matrix, i.e.:
> 0 3 0

> 3 6 0
> 6 9 0
> 9 12 0
> 12 13 0
> ...

> where first column is the start sample in seconds (you have to
> multiply it for sample rate), the second column is the end sample and
> the third is the offset (in this case is always zero), or look at
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#use_your_own_function_for_trial_selection

> best wishes,
> Ivano



> ------------------------------------------------------------------------




> "No man can wear one face to himself
> and another to the multitude,
> without finally getting bewildered
> as to which one is true."


> Nathaniel Hawthorne


> ________________________________
>  Da: "fieldtrip-request at donders.ru.nl"
>  <fieldtrip-request at donders.ru.nl>
> A: fieldtrip at donders.ru.nl
> Inviato: Lunedì 26 Marzo 2012 12:00
> Oggetto: fieldtrip Digest, Vol 16, Issue 33

> Send fieldtrip mailing list submissions to
>     fieldtrip at donders.ru.nl

> To subscribe or unsubscribe via the World Wide Web, visit
>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>     fieldtrip-request at donders.ru.nl

> You can reach the person managing the list at
>     fieldtrip-owner at donders.ru.nl

> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."


> Today's Topics:

>    1. Re: Problem with FT_DEFINETRIAL (Stephen Politzer-Ahles)


> ----------------------------------------------------------------------

> Message: 1
> Date: Sun, 25 Mar 2012 12:11:28 +0200
> From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> To: fieldtrip at donders.ru.nl
> Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL
> Message-ID:
>    
> <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"

> Hello Jarmo,

> I haven't tried importing Brain Vision files into FieldTrip myself,
> but
> based on the code you sent it looks like the problem may be that
> you're
> missing cfg.trialdef.eventvalue (which is used to tell FieldTrip
> which
> triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim
> . See
> the example at
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials.

> If what you are trying to do is import all trials from all triggers
> in the
> file, I think you have to define your own "trialfun" function to do
> that
> (although I haven't tried this myself so I'm not sure).
> http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
> information.

> Best,
> Steve Politzer-Ahles
> University of Kansas


> Message: 1
> > Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> > From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> > To: <fieldtrip at donders.ru.nl>
> > Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> > Message-ID:
> >        <
> > permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de


> > Content-Type: text/plain; charset=us-ascii

> > Dear all,
> > I am trying to import EEG subject averages into Field Trip. The
> > files are
> > exported with the Brainvision Analyzer in binary form
> > :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> > I have a problem with turning the data into the Field Trip
> > data-structure.
> > I
> > am following instructions given on this forum on one similar post.
> > What I
> > have
> > tried is the following:

> > cfg=[];
> > cfg.trialdef.eventtype='average'
> > cfg.dataset='subject10_konPro2002.dat'

> >  cfg=ft_definetrial(cfg);

> > Warning: no trialfun was specified, using trialfun_general
> > > In ft_definetrial at 123
> > evaluating trialfunction 'trialfun_general'
> > reading the events from 'subject10_konPro2002.vhdr'
> > ??? Error using ==> ft_definetrial at 176
> > no trials were defined, see FT_DEFINETRIAL for help

> > I am grateful for all the help.
> > Thanks,
> > Jarmo Kontinen

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> 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 Mar 27 13:27:27 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 27 Mar 2012 13:27:27 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band,
	concept problem
In-Reply-To: <CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>
References: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
	<EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>
	<CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>
Message-ID: <4F71A41F.4080807@donders.ru.nl>

Hi Ion,

A frequency is by definition at least a peak and a trough(up flank and 
down flank), making it one cycle (think of sinusoid here). Thus, you 
could say that one needs at least one cycle of a certain frequency such 
that it is eligible to talk about a 'frequency'. Just in case you don't 
know it already, you might want to look things up as Rayleigh frequency, 
Nyquist frequency, and I would suggest that you read (or start reading) 
the digitial signal processing book: http://www.dspguide.com/

Note that a true oscillation is usually considered to last at least 
three cycles (of course, opinions differ her - I go with four). The 
length of the window of interest reflects the number of cycles that can 
be estimated. For source reconstruction, make sure cfg.toilim is as long 
as the number of cycles you want to estimate, e.g. when using cfg.foi = 
10, then cfg.toilim(2)-cfg.toilim(1) should be at least 400ms when you 
want an estimate of 4 cycles.

Hope it helps!
Best,
Jörn



On 3/27/2012 12:46 PM, Ion Lavado wrote:
> Thank you Stephan, just one thing, why i need a time window big 
> enough? so i'm just studying the frequency.
>
> Best,
>
> Mikel
>
> 2012/3/27 Stephan Moratti <smoratti at psi.ucm.es 
> <mailto:smoratti at psi.ucm.es>>
>
>     Dear Mikel,
>
>     I understand that you should do a mtmfft with a center frequency
>     of interest (in your case cfg.foil = [11 11]) and then you do a
>     frequency smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you
>     need a time window big enough to allow such a smoothing. The CSD
>     should represent a frequency window of 8 to 14 Hz then. Then you
>     put the result of the mtmfft into the dics beamformer.
>
>     Best,
>
>     Stephan
>
>     El 27/03/2012, a las 11:19, Ion Lavado escribió:
>
>>     Hello, i'm having problems trying the beamformer analysis with a
>>     frequency band of interest. I would like to have for example an
>>     interval like [8 14] Hz. My concept problem is about the
>>     cfg.frequency and cfg.tapsmofrq  values. (it must be a escalar,
>>     but i want a frequency band).
>>
>>     %FREQ ANALYSIS
>>     cfg = [];
>>     cfg.method    = 'mtmfft';
>>     cfg.output    = 'powandcsd';
>>     cfg.tapsmofrq = 5;
>>     cfg.foilim    = [8 14];
>>     freq_words_alpha = ft_freqanalysis(cfg, words);
>>
>>
>>     %SOURCE ANALYSIS
>>     cfg              = [];
>>     cfg.frequency    = 11;
>>     cfg.lambda=0;
>>     cfg.method       = 'dics';
>>     cfg.coordsys       = 'neuromag';
>>     cfg.projectnoise = 'yes';
>>     cfg.grad            =  freq_words_alpha.grad;
>>     cfg.channel   = {'MEG'};
>>     cfg.grid         = grid;
>>     cfg.reducerank      = 2;
>>     cfg.vol          = vol02;
>>     vol02=ft_convert_units(vol02,'cm');
>>     source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
>>
>>
>>     I use a cfg.frequency of 11 but i don't have really clear what
>>     i'm doing as a get the same result using cfg.frequency=11 but a
>>     freqanalysis in [10 12]. I would be very grateful if someone
>>     could solve my doubt.
>>
>>     Best wishes,
>>
>>     Mikel
>>     _______________________________________________
>>     fieldtrip mailing list
>>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>     ________________________________________________________
>     Stephan Moratti, PhD
>
>     see also: http://web.me.com/smoratti/
>
>     Universidad Complutense de Madrid
>     Facultad de Psicología
>     Departamento de Psicología Básica I
>     Campus de Somosaguas
>     28223 Pozuelo de Alarcón (Madrid)
>     Spain
>
>     and
>
>     Center for Biomedical Technology
>     Laboratory for Cognitive and Computational Neuroscience
>     Parque Científico y Tecnológico de la Universidad Politecnica de
>     Madrid
>     Campus Montegancedo
>     28223 Pozuelo de Alarcón (Madrid)
>     Spain
>
>
>     email: smoratti at psi.ucm.es <mailto:smoratti at psi.ucm.es>
>     Tel.: +34 679219982 <tel:%2B34%20679219982>
>
>
>
>     _______________________________________________
>     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

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 Ulrich.Pomper at charite.de  Tue Mar 27 15:00:32 2012
From: Ulrich.Pomper at charite.de (Pomper, Ulrich)
Date: Tue, 27 Mar 2012 15:00:32 +0200
Subject: [FieldTrip] one-sample cluster test
Message-ID: <4F71B9F0.8080106@charite.de>

Dear list members,

this topic was discussed some time in 2008, but it seems to me no 
conclusion was found.

I would like to find source activity that differs significantly from 
zero. I could run a one sample t-test for every voxel and end up having 
a huge MC problem, or (preferably) use some kind of cluster based 
permutation statistics. However, the option for a one sample cluster 
test is not implemented in FT.

Would it be correct to test the data from my experimental condition 
against a set of data containing all zeros using a cluster based 
permutation test?

Any help is very much appreciated!
Best, Ulrich



From mark.noordenbos at gmail.com  Tue Mar 27 15:35:00 2012
From: mark.noordenbos at gmail.com (Mark Noordenbos)
Date: Tue, 27 Mar 2012 15:35:00 +0200
Subject: [FieldTrip] one-sample cluster test
Message-ID: <CAJSb8nMMcxO0xxW8+6z1rAswYReKKPxq+3Rc0Htaz-dyoXELJA@mail.gmail.com>

Hi Ulrich,

There is a function 'statfun_actvsblT' to test your activity against the
baseline. However, this function only accepts input with dimord
'chan_freq_time'.
Maybe, you can create your own function based on 'statfun_actvsblT' to test
the activity against zero.

Kind regards,
Mark

Op 27 maart 2012 15:00 schreef <fieldtrip-request at donders.ru.nl> het
volgende:

> Send fieldtrip mailing list submissions to
>        fieldtrip at donders.ru.nl
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
>        fieldtrip-request at donders.ru.nl
>
> You can reach the person managing the list at
>        fieldtrip-owner at donders.ru.nl
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
>
>
> Today's Topics:
>
>   1. Re: Problem with FT_DEFINETRIAL (Jarmo Kontinen)
>   2. Re: Beamforming analysis in frequency band,       concept problem
>      (J?rn M. Horschig)
>   3. one-sample cluster test (Pomper, Ulrich)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 27 Mar 2012 13:24:43 +0200 (CEST)
> From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> To: Ivano Triggiani <ivano_triggiani at yahoo.it>, Email discussion list
>        for the FieldTrip project <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL
> Message-ID:
>        <
> permail-201203271124436509e8c7000033ba-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de
> >
>
> Content-Type: text/plain; charset=iso-8859-1
>
>
> Dear Ivano,
> I had some problem with email, so if I am replying to you twice, I
> apologize.
>
>  I was maybe a  bit unclear maybe in my first post. My files already
> contain
>  averaged data.
> Problem is to get the right data-structure to use the existing
> FT-functions to
> do analysis on the data.
>
> Best,
> Jarmo
>
> Ivano Triggiani schrieb am 2012-03-26:
> > Dear Jarmo,
>
> > Filedtrip needs a definition of segments of interest. For example
> > reading a trigger channel or something else to cut the EEG recording
> > into trials. If I have understood what you want to do is to get an
> > average of general EEG (for example resting state EEG closed eyes).
> > But you have to indicate which average you want to obtain, for
> > example you can tell fieldtrip to divide EEG into epochs of 3 seconds
> > and then to make an average of all of them.
> > What you wrote is the request of an average, but you are not
> > specifing of what.
> > Fof example you can write a trial function that provides a trl
> > matrix, i.e.:
> > 0 3 0
>
> > 3 6 0
> > 6 9 0
> > 9 12 0
> > 12 13 0
> > ...
>
> > where first column is the start sample in seconds (you have to
> > multiply it for sample rate), the second column is the end sample and
> > the third is the offset (in this case is always zero), or look at
> >
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#use_your_own_function_for_trial_selection
>
> > best wishes,
> > Ivano
>
>
>
> > ------------------------------------------------------------------------
>
>
>
>
> > "No man can wear one face to himself
> > and another to the multitude,
> > without finally getting bewildered
> > as to which one is true."
>
>
> > Nathaniel Hawthorne
>
>
> > ________________________________
> >  Da: "fieldtrip-request at donders.ru.nl"
> >  <fieldtrip-request at donders.ru.nl>
> > A: fieldtrip at donders.ru.nl
> > Inviato: Luned? 26 Marzo 2012 12:00
> > Oggetto: fieldtrip Digest, Vol 16, Issue 33
>
> > Send fieldtrip mailing list submissions to
> > ??? fieldtrip at donders.ru.nl
>
> > To subscribe or unsubscribe via the World Wide Web, visit
> > ??? http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > ??? fieldtrip-request at donders.ru.nl
>
> > You can reach the person managing the list at
> > ??? fieldtrip-owner at donders.ru.nl
>
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
>
>
> > Today's Topics:
>
> > ?  1. Re: Problem with FT_DEFINETRIAL (Stephen Politzer-Ahles)
>
>
> > ----------------------------------------------------------------------
>
> > Message: 1
> > Date: Sun, 25 Mar 2012 12:11:28 +0200
> > From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> > To: fieldtrip at donders.ru.nl
> > Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL
> > Message-ID:
> > ???
> > <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
>
> > Hello Jarmo,
>
> > I haven't tried importing Brain Vision files into FieldTrip myself,
> > but
> > based on the code you sent it looks like the problem may be that
> > you're
> > missing cfg.trialdef.eventvalue (which is used to tell FieldTrip
> > which
> > triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim
> > . See
> > the example at
> >
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials
> .
>
> > If what you are trying to do is import all trials from all triggers
> > in the
> > file, I think you have to define your own "trialfun" function to do
> > that
> > (although I haven't tried this myself so I'm not sure).
> > http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
> > information.
>
> > Best,
> > Steve Politzer-Ahles
> > University of Kansas
>
>
> > Message: 1
> > > Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> > > From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> > > To: <fieldtrip at donders.ru.nl>
> > > Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> > > Message-ID:
> > >? ? ? ? <
> > >
> permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de
>
>
> > > Content-Type: text/plain; charset=us-ascii
>
> > > Dear all,
> > > I am trying to import EEG subject averages into Field Trip. The
> > > files are
> > > exported with the Brainvision Analyzer in binary form
> > > :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> > > I have a problem with turning the data into the Field Trip
> > > data-structure.
> > > I
> > > am following instructions given on this forum on one similar post.
> > > What I
> > > have
> > > tried is the following:
>
> > > cfg=[];
> > > cfg.trialdef.eventtype='average'
> > > cfg.dataset='subject10_konPro2002.dat'
>
> > >? cfg=ft_definetrial(cfg);
>
> > > Warning: no trialfun was specified, using trialfun_general
> > > > In ft_definetrial at 123
> > > evaluating trialfunction 'trialfun_general'
> > > reading the events from 'subject10_konPro2002.vhdr'
> > > ??? Error using ==> ft_definetrial at 176
> > > no trials were defined, see FT_DEFINETRIAL for help
>
> > > I am grateful for all the help.
> > > Thanks,
> > > Jarmo Kontinen
>
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >  <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120325/df4ce70a/attachment-0001.html
> >
>
> > ------------------------------
>
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> > End of fieldtrip Digest, Vol 16, Issue 33
> > *****************************************
>
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 27 Mar 2012 13:27:27 +0200
> From: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> To: fieldtrip at donders.ru.nl
> Subject: Re: [FieldTrip] Beamforming analysis in frequency band,
>        concept problem
> Message-ID: <4F71A41F.4080807 at donders.ru.nl>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Ion,
>
> A frequency is by definition at least a peak and a trough(up flank and
> down flank), making it one cycle (think of sinusoid here). Thus, you
> could say that one needs at least one cycle of a certain frequency such
> that it is eligible to talk about a 'frequency'. Just in case you don't
> know it already, you might want to look things up as Rayleigh frequency,
> Nyquist frequency, and I would suggest that you read (or start reading)
> the digitial signal processing book: http://www.dspguide.com/
>
> Note that a true oscillation is usually considered to last at least
> three cycles (of course, opinions differ her - I go with four). The
> length of the window of interest reflects the number of cycles that can
> be estimated. For source reconstruction, make sure cfg.toilim is as long
> as the number of cycles you want to estimate, e.g. when using cfg.foi =
> 10, then cfg.toilim(2)-cfg.toilim(1) should be at least 400ms when you
> want an estimate of 4 cycles.
>
> Hope it helps!
> Best,
> J?rn
>
>
>
> On 3/27/2012 12:46 PM, Ion Lavado wrote:
> > Thank you Stephan, just one thing, why i need a time window big
> > enough? so i'm just studying the frequency.
> >
> > Best,
> >
> > Mikel
> >
> > 2012/3/27 Stephan Moratti <smoratti at psi.ucm.es
> > <mailto:smoratti at psi.ucm.es>>
> >
> >     Dear Mikel,
> >
> >     I understand that you should do a mtmfft with a center frequency
> >     of interest (in your case cfg.foil = [11 11]) and then you do a
> >     frequency smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you
> >     need a time window big enough to allow such a smoothing. The CSD
> >     should represent a frequency window of 8 to 14 Hz then. Then you
> >     put the result of the mtmfft into the dics beamformer.
> >
> >     Best,
> >
> >     Stephan
> >
> >     El 27/03/2012, a las 11:19, Ion Lavado escribi?:
> >
> >>     Hello, i'm having problems trying the beamformer analysis with a
> >>     frequency band of interest. I would like to have for example an
> >>     interval like [8 14] Hz. My concept problem is about the
> >>     cfg.frequency and cfg.tapsmofrq  values. (it must be a escalar,
> >>     but i want a frequency band).
> >>
> >>     %FREQ ANALYSIS
> >>     cfg = [];
> >>     cfg.method    = 'mtmfft';
> >>     cfg.output    = 'powandcsd';
> >>     cfg.tapsmofrq = 5;
> >>     cfg.foilim    = [8 14];
> >>     freq_words_alpha = ft_freqanalysis(cfg, words);
> >>
> >>
> >>     %SOURCE ANALYSIS
> >>     cfg              = [];
> >>     cfg.frequency    = 11;
> >>     cfg.lambda=0;
> >>     cfg.method       = 'dics';
> >>     cfg.coordsys       = 'neuromag';
> >>     cfg.projectnoise = 'yes';
> >>     cfg.grad            =  freq_words_alpha.grad;
> >>     cfg.channel   = {'MEG'};
> >>     cfg.grid         = grid;
> >>     cfg.reducerank      = 2;
> >>     cfg.vol          = vol02;
> >>     vol02=ft_convert_units(vol02,'cm');
> >>     source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
> >>
> >>
> >>     I use a cfg.frequency of 11 but i don't have really clear what
> >>     i'm doing as a get the same result using cfg.frequency=11 but a
> >>     freqanalysis in [10 12]. I would be very grateful if someone
> >>     could solve my doubt.
> >>
> >>     Best wishes,
> >>
> >>     Mikel
> >>     _______________________________________________
> >>     fieldtrip mailing list
> >>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
> >>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
> >     ________________________________________________________
> >     Stephan Moratti, PhD
> >
> >     see also: http://web.me.com/smoratti/
> >
> >     Universidad Complutense de Madrid
> >     Facultad de Psicolog?a
> >     Departamento de Psicolog?a B?sica I
> >     Campus de Somosaguas
> >     28223 Pozuelo de Alarc?n (Madrid)
> >     Spain
> >
> >     and
> >
> >     Center for Biomedical Technology
> >     Laboratory for Cognitive and Computational Neuroscience
> >     Parque Cient?fico y Tecnol?gico de la Universidad Politecnica de
> >     Madrid
> >     Campus Montegancedo
> >     28223 Pozuelo de Alarc?n (Madrid)
> >     Spain
> >
> >
> >     email: smoratti at psi.ucm.es <mailto:smoratti at psi.ucm.es>
> >     Tel.: +34 679219982 <tel:%2B34%20679219982>
> >
> >
> >
> >     _______________________________________________
> >     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
>
>
> --
> J?rn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
>
> 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
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120327/6c8a4090/attachment-0001.html
> >
>
> ------------------------------
>
> Message: 3
> Date: Tue, 27 Mar 2012 15:00:32 +0200
> From: "Pomper, Ulrich" <Ulrich.Pomper at charite.de>
> To: Email discussion list for the FieldTrip project
>        <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] one-sample cluster test
> Message-ID: <4F71B9F0.8080106 at charite.de>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear list members,
>
> this topic was discussed some time in 2008, but it seems to me no
> conclusion was found.
>
> I would like to find source activity that differs significantly from
> zero. I could run a one sample t-test for every voxel and end up having
> a huge MC problem, or (preferably) use some kind of cluster based
> permutation statistics. However, the option for a one sample cluster
> test is not implemented in FT.
>
> Would it be correct to test the data from my experimental condition
> against a set of data containing all zeros using a cluster based
> permutation test?
>
> Any help is very much appreciated!
> Best, Ulrich
>
>
>
> ------------------------------
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> End of fieldtrip Digest, Vol 16, Issue 39
> *****************************************
>
>
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From jm.horschig at donders.ru.nl  Tue Mar 27 15:48:07 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Tue, 27 Mar 2012 15:48:07 +0200
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <4F71B9F0.8080106@charite.de>
References: <4F71B9F0.8080106@charite.de>
Message-ID: <4F71C517.9010906@donders.ru.nl>

Dear Ulrich,


First of all, you might want to use the Neural Activity Index (NAI), as 
also described in the tutorial:
http://fieldtrip.fcdonders.nl/tutorial/beamformer#source_analysiswithout_contrasting_condition

Then, to answer your question, I am tempted to say that this would be an 
invalid approach when dealing with power, so in frequency-space. Power 
obviously has a lower bound, so that the average of any random 
collection of power values will never be 0. Though, what you are 
suggesting is the same as a regular t-test, isn't it?
In case you are dealing e.g. with am LCMV beamformer, I am not quite 
sure, but the null-hypothesis you suggested (amplitude==0)  sounds fair.

In any case, building a surrogate distribution same mean and variance 
than your data might be a better way to deal with your problem. That 
should be easily doable in Matlab without any need to implement this in 
FieldTrip. And note that the MC problem is always present, but a 
cluster-based correction (similar to Bonferroni, but correcting by the 
number of voxels in the cluster not by the number of all voxels) sounds 
legitimate to me. Afair, that's how it's done in FT.

Best,
Jörn




On 3/27/2012 3:00 PM, Pomper, Ulrich wrote:
> Dear list members,
>
> this topic was discussed some time in 2008, but it seems to me no
> conclusion was found.
>
> I would like to find source activity that differs significantly from
> zero. I could run a one sample t-test for every voxel and end up having
> a huge MC problem, or (preferably) use some kind of cluster based
> permutation statistics. However, the option for a one sample cluster
> test is not implemented in FT.
>
> Would it be correct to test the data from my experimental condition
> against a set of data containing all zeros using a cluster based
> permutation test?
>
> Any help is very much appreciated!
> Best, Ulrich
>
> _______________________________________________
> 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

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 tessa.vanleeuwen at fcdonders.ru.nl  Tue Mar 27 18:27:25 2012
From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen)
Date: Tue, 27 Mar 2012 18:27:25 +0200 (CEST)
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <189719464.70211.1332863376495.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <1710162166.70656.1332865645305.JavaMail.root@draco.zimbra.ru.nl>

Dear Fieldtrip experts,

I have noticed enhanced coherence (sensor level) in my data after applying ICA during preprocessing, removing only 1 EOG component. Of course the (mainly quantitatively) enhanced coherence could be due to the removal of (artifact induced) noise from the data. But this increase also occured when applying ICA to previously cleaned data, implying changes induced by ICA somehow affect coherence.

One of the aims of our project is to compute coherence/connectivity measures at the source level. Since connectivity measures are often difficult to interpret as they are, I would like to ask whether anyone has experience with connectivity analyses after preprocessing that involved ICA. Are people aware of possible influences of ICA on connectivity measures and is there a way to deal with this? Or would it be advisable NOT to use ICA when later looking at coherence/connectivity at the source level? 

We initially aim to compare across conditions (data that have been preprocessed together and from which the same ICA component has been removed). But we also have different experimental groups for which we would like to qualitatively compare active networks during our task.

Thank you in advance for any input, it is highly appreciated.

Best wishes,
Tessa


---

Tessa van Leeuwen, PhD
postdoctoral researcher

Department of Neurophysiology
Max Planck Institute for Brain Research


From toncho11 at gmail.com  Tue Mar 27 19:13:18 2012
From: toncho11 at gmail.com (Anton Andreev)
Date: Tue, 27 Mar 2012 19:13:18 +0200
Subject: [FieldTrip] Time stamp per sample
Message-ID: <CAG3TGCN+1ZV7zaAbGKvm8j3M1arg8pQXRgrfSLaof2hVp7G-vg@mail.gmail.com>

Hi,

I have a question about the fieldtrip buffer.
Does the protocol provides information about the time every sample has been
taken?

I would like to produce a chunk of data for 300ms or 1 second for example.
I can build such chunk if I simply sort out samples that are in the time
range of 1 second starting with the time stamp of the first one. Then again
for 1 second and ....

Thanks,
Anton
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From eelke.spaak at donders.ru.nl  Tue Mar 27 20:20:28 2012
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Tue, 27 Mar 2012 20:20:28 +0200
Subject: [FieldTrip] question regarding FieldTrip
In-Reply-To: <CAGhHk+itOwLA7rv42X1tbLH=-wYBYwincRSRUdHFM+AvaMAiJw@mail.gmail.com>
References: <CAGhHk+itOwLA7rv42X1tbLH=-wYBYwincRSRUdHFM+AvaMAiJw@mail.gmail.com>
Message-ID: <CABPNLUp9EpsGqqv6pgQPnPrjn09FE1oqcwtO2QUVLrVZn4XQ2Q@mail.gmail.com>

Dear Ilya,

You probably intended to post to the FieldTrip mailing list, so I am
also forwarding my reply to the list. If you are not registered on the
list, please do so (http://fieldtrip.fcdonders.nl/discussion_list).

Your question suggests to me that you are not using FieldTrip-style
data structures. All FT functions are designed to work with such
structures, so you should convert your data to an FT data structure
first. You can have a look at these FAQs on the Wiki for suggestions:
http://fieldtrip.fcdonders.nl/faq/how_are_the_various_data_structures_defined
and http://fieldtrip.fcdonders.nl/faq/how_can_i_import_my_own_dataformat
. Also, you should probably have a look at the tutorial documentation
(http://fieldtrip.fcdonders.nl/tutorial), specifically the one on
time-frequency analysis.

Hope this helps,
Best,

Eelke

On 27 March 2012 19:13, ilya monosov <ilya.monosov at gmail.com> wrote:
> Hello,
> i have a quick question. thank you so much in advance. if i have a matrix of
> single trial lfps (10 by 10,000) .. meaning that i have 10 trials that are
> 10,000 msec long,
> and i want to get single trial frequency power matrixes for each trial and
> also the average (and perhaps do stats, but most likely not as i am doing
> this to just get
> a quick impression of LFP frequency behavior in locations where i recorded
> single neurons), what commands would i use for FieldTrip?
>
> i have tried but i am getting strange errors that lead me to believe that my
> input format is wrong.
>
> Thank you very much
> ilya


From batrod at gmail.com  Tue Mar 27 18:36:54 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Tue, 27 Mar 2012 11:36:54 -0500
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <1710162166.70656.1332865645305.JavaMail.root@draco.zimbra.ru.nl>
References: <189719464.70211.1332863376495.JavaMail.root@draco.zimbra.ru.nl>
	<1710162166.70656.1332865645305.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <CAPy7a9C0Av7RaH7QTsvErDBU-rf-Buu2x0EvfF5+mk=wGn=XnA@mail.gmail.com>

Dear Tessa,
would it be possible to give some precision about your analyzes.

1) After your first "cleaning", do you test coherence on particular
components or your entire data minus the "EOG" component?

2) When you say that you redo ICA on cleaned data (of course, an ICA
analysis made on a result of a previous ICA analysis with components
removed is a bad idea), do you remove another component or do you  test
your coherence on particular components?

Rodolphe

On Tue, Mar 27, 2012 at 11:27 AM, Tessa van Leeuwen <
tessa.vanleeuwen at fcdonders.ru.nl> wrote:

> Dear Fieldtrip experts,
>
> I have noticed enhanced coherence (sensor level) in my data after applying
> ICA during preprocessing, removing only 1 EOG component. Of course the
> (mainly quantitatively) enhanced coherence could be due to the removal of
> (artifact induced) noise from the data. But this increase also occured when
> applying ICA to previously cleaned data, implying changes induced by ICA
> somehow affect coherence.
>
> One of the aims of our project is to compute coherence/connectivity
> measures at the source level. Since connectivity measures are often
> difficult to interpret as they are, I would like to ask whether anyone has
> experience with connectivity analyses after preprocessing that involved
> ICA. Are people aware of possible influences of ICA on connectivity
> measures and is there a way to deal with this? Or would it be advisable NOT
> to use ICA when later looking at coherence/connectivity at the source level?
>
> We initially aim to compare across conditions (data that have been
> preprocessed together and from which the same ICA component has been
> removed). But we also have different experimental groups for which we would
> like to qualitatively compare active networks during our task.
>
> Thank you in advance for any input, it is highly appreciated.
>
> Best wishes,
> Tessa
>
>
> ---
>
> Tessa van Leeuwen, PhD
> postdoctoral researcher
>
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From batrod at gmail.com  Tue Mar 27 19:36:36 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Tue, 27 Mar 2012 12:36:36 -0500
Subject: [FieldTrip] optimum number of cycles
Message-ID: <CAPy7a9B64dcStbT9eEOZ4BR-HXq4WbkQ8LmzeqYxKNrnAooQqw@mail.gmail.com>

Dear filedtrippers, i had a question regarding the time-frequency analysis,
such as the one that can be found on the tutorial :
http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis

In the fixed-widow example, using a hanning taper, it is said that a fixed
widow of 500 ms can estimate power of different frequency bands like 2 Hz,
4Hz, etc...
However, for 2 Hz it means only 1 cycle.

In the frequency-dependent window length, 7 cycles per frequency bands are
used.

My questions are, is it ok to estimate a power with one cycle? What could
be the optimum number of cycles? Is ot ok to compare the power of different
frequency bands that have been estimated using a different number of cycles?

Thanks a lot,

Rodolphe.
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From smoratti at psi.ucm.es  Tue Mar 27 22:33:36 2012
From: smoratti at psi.ucm.es (smoratti at psi.ucm.es)
Date: Tue, 27 Mar 2012 22:33:36 +0200
Subject: [FieldTrip] Beamforming analysis in frequency band,
	concept problem
In-Reply-To: <CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>
References: <CAMLwyK7hHAKhHGoE=K_gvanh10LHOSkbrUYgBQL7smoKZL9=Uw@mail.gmail.com>
	<EB46A810-47A8-462F-A497-5C06C4058B14@psi.ucm.es>
	<CAMLwyK7xrbbd6_2=0MiJyXQ2OGjESnLn6TnK1R7Tqzanywk9gA@mail.gmail.com>
Message-ID: <E0D49E5B-2248-466C-A88D-0ECFB2E57851@psi.ucm.es>

Hi Mikel,

I think Jörn gave you already the answer. You need enough time points to accurately estimate the oscillations of a frequency. For example in wavelet analysis (morlet) people use at least 5 cycles.

Best,

Stephan

________________________________________________________
Stephan Moratti, PhD

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

Universidad Complutense de Madrid
Facultad de Psicología
Departamento de Psicología Básica I
Campus de Somosaguas
28223 Pozuelo de Alarcón (Madrid)
Spain

and

Center for Biomedical Technology
Laboratory for Cognitive and Computational Neuroscience
Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
Campus Montegancedo
28223 Pozuelo de Alarcón (Madrid)
Spain


email: smoratti at psi.ucm.es
Tel.:    +34 679219982

El 27/03/2012, a las 12:46, Ion Lavado escribió:

> Thank you Stephan, just one thing, why i need a time window big enough? so i'm just studying the frequency.
> 
> Best,
> 
> Mikel
> 
> 2012/3/27 Stephan Moratti <smoratti at psi.ucm.es>
> Dear Mikel,
> 
> I understand that you should do a mtmfft with a center frequency of interest (in your case cfg.foil = [11 11]) and then you do a frequency smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you need a time window big enough to allow such a smoothing. The CSD should represent a frequency window of 8 to 14 Hz then. Then you put the result of the mtmfft into the dics beamformer.
> 
> Best,
> 
> Stephan
>  
> El 27/03/2012, a las 11:19, Ion Lavado escribió:
> 
>> Hello, i'm having problems trying the beamformer analysis with a frequency band of interest. I would like to have for example an interval like [8 14] Hz. My concept problem is about the cfg.frequency and cfg.tapsmofrq  values. (it must be a escalar, but i want a frequency band). 
>> 
>> %FREQ ANALYSIS
>> cfg = [];
>> cfg.method    = 'mtmfft';
>> cfg.output    = 'powandcsd';
>> cfg.tapsmofrq = 5;
>> cfg.foilim    = [8 14];
>> freq_words_alpha = ft_freqanalysis(cfg, words);
>> 
>> 
>> %SOURCE ANALYSIS
>> cfg              = []; 
>> cfg.frequency    = 11;  
>> cfg.lambda=0;
>> cfg.method       = 'dics';
>> cfg.coordsys       = 'neuromag';
>> cfg.projectnoise = 'yes';
>> cfg.grad            =  freq_words_alpha.grad;
>> cfg.channel   = {'MEG'}; 
>> cfg.grid         = grid; 
>> cfg.reducerank      = 2;
>> cfg.vol          = vol02;
>> vol02=ft_convert_units(vol02,'cm');
>> source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
>> 
>> 
>> I use a cfg.frequency of 11 but i don't have really clear what i'm doing as a get the same result using cfg.frequency=11 but a freqanalysis in [10 12]. I would be very grateful if someone could solve my doubt.
>> 
>> Best wishes,
>> 
>> Mikel
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> ________________________________________________________
> Stephan Moratti, PhD
> 
> see also: http://web.me.com/smoratti/
> 
> Universidad Complutense de Madrid
> Facultad de Psicología
> Departamento de Psicología Básica I
> Campus de Somosaguas
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> and
> 
> Center for Biomedical Technology
> Laboratory for Cognitive and Computational Neuroscience
> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
> Campus Montegancedo
> 28223 Pozuelo de Alarcón (Madrid)
> Spain
> 
> 
> email: smoratti at psi.ucm.es
> Tel.:    +34 679219982
> 
> 
> 
> _______________________________________________
> 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 tessa.vanleeuwen at fcdonders.ru.nl  Tue Mar 27 23:34:33 2012
From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen)
Date: Tue, 27 Mar 2012 23:34:33 +0200 (CEST)
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <CAPy7a9C0Av7RaH7QTsvErDBU-rf-Buu2x0EvfF5+mk=wGn=XnA@mail.gmail.com>
Message-ID: <1832235848.73257.1332884073180.JavaMail.root@draco.zimbra.ru.nl>

Dear Rodolphe, Thank you for your response, I tried to clarify below. > 1) After your first "cleaning", do you test coherence on particular
> components or your entire data minus the "EOG" component?
I tested the coherence on the entire dataset after removal of the EOG component. > 2) When you say that you redo ICA on cleaned data (of course, an ICA
> analysis made on a result of a previous ICA analysis with components
> removed is a bad idea), do you remove another component or do you test
> your coherence on particular components?
Sorry, I could have been more clear about this. I initially compared two versions of the same dataset: one in which all trials containing a blink were removed from the dataset after manual inspection; another version in which only trials with a blink during the actual stimulus period were removed manually and the rest of the trials, including trials with blinks outside the stimulus window, were 'cleaned' with ICA, i.e. the EOG component was removed. Eye-balling coherence in occipital channels, this was increased in the ICA-cleaned version. To check whether the increase in coherence could have been explained by an increased number of retained trials in the ICA-cleaned-version, I also applied the unmixing matrix obtained from the ICA to the manually cleaned version of the data, i.e., in which only smaller eye-movements or unidentified EOG artifacts would have been remaining after manual inspection. Now of course I could have been over-removing non-existent noise in this case, but also here the same difference in coherence appeared, now with the same number of trials in both condition. When I look at the time-frequency representations from both versions, these look highly similar, only small intensity differences can be seen. I only used a small amount of data to test this and these results might therefore not be completely reliable. But I know other people have experienced similar problems with altered coherence and I was wondering whether any effect of ICA-preprocessing on coherence/connectivity measures was generally known on the list and in the literature. Perhaps the removal of common noise with ICA can already explain the differences? Best wishes, Tessa > Rodolphe
> On Tue, Mar 27, 2012 at 11:27 AM, Tessa van Leeuwen <
> tessa.vanleeuwen at fcdonders.ru.nl > wrote:
> > Dear Fieldtrip experts,
> > I have noticed enhanced coherence (sensor level) in my data after
> > applying ICA during preprocessing, removing only 1 EOG component. Of
> > course the (mainly quantitatively) enhanced coherence could be due
> > to
> > the removal of (artifact induced) noise from the data. But this
> > increase also occured when applying ICA to previously cleaned data,
> > implying changes induced by ICA somehow affect coherence.
> > One of the aims of our project is to compute coherence/connectivity
> > measures at the source level. Since connectivity measures are often
> > difficult to interpret as they are, I would like to ask whether
> > anyone
> > has experience with connectivity analyses after preprocessing that
> > involved ICA. Are people aware of possible influences of ICA on
> > connectivity measures and is there a way to deal with this? Or would
> > it be advisable NOT to use ICA when later looking at
> > coherence/connectivity at the source level?
> > We initially aim to compare across conditions (data that have been
> > preprocessed together and from which the same ICA component has been
> > removed). But we also have different experimental groups for which
> > we
> > would like to qualitatively compare active networks during our task.
> > Thank you in advance for any input, it is highly appreciated.
> > Best wishes,
> > Tessa
> > ---
> > Tessa van Leeuwen, PhD
> > postdoctoral researcher
> > Department of Neurophysiology
> > Max Planck Institute for Brain Research
> > _______________________________________________
> > 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 yoni.levy at inserm.fr  Wed Mar 28 00:40:25 2012
From: yoni.levy at inserm.fr (yoni.levy at inserm.fr)
Date: Wed, 28 Mar 2012 00:40:25 +0200
Subject: [FieldTrip] actvsblT test statistic when running ft_freqstatistics
Message-ID: <20120328004025.8z450t1fk04wc8gk@imp.inserm.fr>

I am running the ft_freqstatistics using the actvsblT option, so as to  
statistically test activation period with baseline activity. For this,  
I followed the "Within trial experiments" tutorial in fieldtrip  
(http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq#within_trial_experiments).
The tutorial emphasizes that one should select equal length time  
windows. However, the number of trials in both conditions (activation  
and baseline) remains unequal. Therefore, when I run ft_freqstatistics  
with the design mentioned in the tutorial (inserting only the number  
of trials of the activation condition), I receive the following error  
message:
"the number of observations in the design does not match the number of  
observations in the data"

Is there an error in the turorial, or is the script intended to create  
two frequency output-files, with different total number of trials.

Thanks in advance,
Yoni


----------------------------------------------------------------
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From batrod at gmail.com  Wed Mar 28 02:20:42 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Tue, 27 Mar 2012 19:20:42 -0500
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <1832235848.73257.1332884073180.JavaMail.root@draco.zimbra.ru.nl>
References: <CAPy7a9C0Av7RaH7QTsvErDBU-rf-Buu2x0EvfF5+mk=wGn=XnA@mail.gmail.com>
	<1832235848.73257.1332884073180.JavaMail.root@draco.zimbra.ru.nl>
Message-ID: <CAPy7a9CkPgza79Tg7fFykksYQhsfgVRkK63Hq4Q=uN+iO6Y4kQ@mail.gmail.com>

Dear Tessa,

ok this is more clear now.
ICA is a wonderful tool which can easily become your worst enemy in data
analyzing.

By removing yourself certains epochs with blinks before doing an ICA, its
is possible that you remove relevant data that can be used by your ICA
algorithm to better separate components.  Certain people would argue that
even filtering your data before ICA can be a bad idea.
Therefore, when you apply the ICA on your "cleaned" data, there is more
chance that the component that will reflect the most what is left from
blinks will also contains more relevant data.
This data removal could potentially decrease your data variability
therefore increase your coherence.
Also, the number of epochs you keep after your cleaning (which should be
different from ICA compared to visual removal) could potentially explain
such a difference.

Hope this helps,

Rodolphe


On Tue, Mar 27, 2012 at 4:34 PM, Tessa van Leeuwen <
tessa.vanleeuwen at fcdonders.ru.nl> wrote:

> Dear Rodolphe,
>
> Thank you for your response, I tried to clarify below.
>
>
> 1) After your first "cleaning", do you test coherence on particular
> components or your entire data minus the "EOG" component?
>
> I tested the coherence on the entire dataset after removal of the EOG
> component.
>
> 2) When you say that you redo ICA on cleaned data (of course, an ICA
> analysis made on a result of a previous ICA analysis with components
> removed is a bad idea), do you remove another component or do you  test
> your coherence on particular components?
>
> Sorry, I could have been more clear about this. I initially compared two
> versions of the same dataset: one in which all trials containing a blink
> were removed from the dataset after manual inspection; another version in
> which only trials with a blink during the actual stimulus period were
> removed manually and the rest of the trials, including trials with blinks
> outside the stimulus window, were 'cleaned' with ICA, i.e. the EOG
> component was removed. Eye-balling coherence in occipital channels, this
> was increased in the ICA-cleaned version.
>
> To check whether the increase in coherence could have been explained by an
> increased number of retained trials in the ICA-cleaned-version, I also
> applied the unmixing matrix obtained from the ICA to the manually cleaned
> version of the data, i.e., in which only smaller eye-movements or
> unidentified EOG artifacts would have been remaining after manual
> inspection. Now of course I could have been over-removing non-existent
> noise in this case, but also here the same difference in coherence
> appeared, now with the same number of trials in both condition. When I look
> at the time-frequency representations from both versions, these look highly
> similar, only small intensity differences can be seen.
>
> I only used a small amount of data to test this and these results might
> therefore not be completely reliable. But I know other people have
> experienced similar problems with altered coherence and I was wondering
> whether any effect of ICA-preprocessing on coherence/connectivity measures
> was generally known on the list and in the literature. Perhaps the removal
> of common noise with ICA can already explain the differences?
>
> Best wishes,
> Tessa
>
>
> Rodolphe
>
> On Tue, Mar 27, 2012 at 11:27 AM, Tessa van Leeuwen <
> tessa.vanleeuwen at fcdonders.ru.nl> wrote:
>
>> Dear Fieldtrip experts,
>>
>> I have noticed enhanced coherence (sensor level) in my data after
>> applying ICA during preprocessing, removing only 1 EOG component. Of course
>> the (mainly quantitatively) enhanced coherence could be due to the removal
>> of (artifact induced) noise from the data. But this increase also occured
>> when applying ICA to previously cleaned data, implying changes induced by
>> ICA somehow affect coherence.
>>
>> One of the aims of our project is to compute coherence/connectivity
>> measures at the source level. Since connectivity measures are often
>> difficult to interpret as they are, I would like to ask whether anyone has
>> experience with connectivity analyses after preprocessing that involved
>> ICA. Are people aware of possible influences of ICA on connectivity
>> measures and is there a way to deal with this? Or would it be advisable NOT
>> to use ICA when later looking at coherence/connectivity at the source level?
>>
>> We initially aim to compare across conditions (data that have been
>> preprocessed together and from which the same ICA component has been
>> removed). But we also have different experimental groups for which we would
>> like to qualitatively compare active networks during our task.
>>
>> Thank you in advance for any input, it is highly appreciated.
>>
>> Best wishes,
>> Tessa
>>
>>
>> ---
>>
>> Tessa van Leeuwen, PhD
>> postdoctoral researcher
>>
>> Department of Neurophysiology
>> Max Planck Institute for Brain Research
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From sysoevao at psychiatry.wustl.edu  Wed Mar 28 04:01:22 2012
From: sysoevao at psychiatry.wustl.edu (Sysoeva, Olga Vladimirovna)
Date: Wed, 28 Mar 2012 02:01:22 +0000
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <CAPy7a9CkPgza79Tg7fFykksYQhsfgVRkK63Hq4Q=uN+iO6Y4kQ@mail.gmail.com>
References: <CAPy7a9C0Av7RaH7QTsvErDBU-rf-Buu2x0EvfF5+mk=wGn=XnA@mail.gmail.com>
	<1832235848.73257.1332884073180.JavaMail.root@draco.zimbra.ru.nl>,
	<CAPy7a9CkPgza79Tg7fFykksYQhsfgVRkK63Hq4Q=uN+iO6Y4kQ@mail.gmail.com>
Message-ID: <41C83D63782BE149B1B984A58E866D8FE82D@CITEMB2D.cits.wustl.edu>

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From politzerahless at gmail.com  Wed Mar 28 06:58:34 2012
From: politzerahless at gmail.com (Stephen Politzer-Ahles)
Date: Tue, 27 Mar 2012 23:58:34 -0500
Subject: [FieldTrip] question to the fieldtrip developers - multiple spm
 versions in fieldtrip
Message-ID: <CAJT2k_-jbUesSdb1b3Y6TaTQwx7P8oFw6nMGoVz-Qjw=VAX26Q@mail.gmail.com>

Hi Frederic,

As far as I know, those SPM errors are a consequence of adding all the
subdirectories of FieldTrip to your MATLAB path; see
http://fieldtrip.fcdonders.nl/faq/should_i_add_fieldtrip_with_all_subdirectories_to_my_matlab_path.
If you add just the main Fieldtrip directory instead of all
subdirectories, you shouldn't get the error. I haven't tried
ft_sourceanalysis myself so I'm not sure if this issue has any consequences
when running that.

Best,
Steve

----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 27 Mar 2012 12:14:45 +0200
> From: Frederic Roux <fredericroux at hotmail.de>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] question to the fieldtrip developers - multiple
>        spm versions in fieldtrip
> Message-ID: <DUB113-W12B64F64480B0A75AB493EB74A0 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
> Dear all,
>
> I would like to ask again if the fact of getting a warning
> that different spm versions will confuse fieldtrip
> can have consequences in the ft_sourceanalysis pipeline.
>
> I am using version 2012-01-05 which has SPM2 and SPM8
> in the external folder.
>
> It would be great if someone from the development-team could tell me
>
> a) why this is a problem
> b) how to circumvent it
>
>
> I renamed the spm.m file into spm.m.bak in the SPM2 folder so that
> only the spm.m file from the SPM8 folder is used. However, it would
> be great if someone could tell me if this is a workaround or not.
>
>
> Best regards,
> Fred
>
> --
> Fr?d?ric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
>
>
>
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From m.leszczynski.m at googlemail.com  Wed Mar 28 08:22:23 2012
From: m.leszczynski.m at googlemail.com (Marcin)
Date: Wed, 28 Mar 2012 08:22:23 +0200
Subject: [FieldTrip] statfun_depsamplesregrT
In-Reply-To: <4f6b87bf.86600e0a.3f3a.ffff8106SMTPIN_ADDED@mx.google.com>
References: <CAAVVtzDY5stRD-XE2Pa5TjrO1L8AJXXSZToy7XhA72hK22bu+w@mail.gmail.com>
	<4f6b87bf.86600e0a.3f3a.ffff8106SMTPIN_ADDED@mx.google.com>
Message-ID: <CAAVVtzAJe6zEuu-wR_6MX8c7bSekX+k0v=H43TAnGRMt2yz=2g@mail.gmail.com>

Dear Dr. Maris,

thanks for your reply.
If I get you right you say that whether I use the statfun_depsamplesregrT
or use/write statfun_depsamplesrankcorr depends on assumed (apriori)
relation between the predictor variable (experimental condition) and the
data. If I assume linearity (i.e. in the case of WM load:  ERP/TF(1) <
ERP/TF(2) < ERP/TF(3) < ERP/TF(4)) I might use the statfun_depsamplesregrT.
If I doubt linearity (i.e.WM load ERP/TF(1) < ERP/TF(2) <= ERP/TF(3) <
ERP/TF(4)) I should use the statfun_depsamplesrankcorr. Is this correct?

I am not sure if I underestood your point about reference distribution. Are
you saying that for the cluster-based permutation inference I need to
threshold on a reference distribution which might be either parametric or
non-parametric? If this is the case. What does it depend on whether I use
parametric or non parametric reference distribution?

Thank you again for your time and your help.

Best,
Marcin

W dniu 22 marca 2012 21:12 użytkownik Eric Maris <e.maris at psych.ru.nl>napisał:

> Dear Marcin,****
>
> ** **
>
> ** **
>
> The statfun_depsamplesregrT calculates a T-statistic for regression
> coefficients that are calculated within each of the units-of-observation
> (typically, participants) obtained by regressing the subject-specific data
> (spatiotemporal, spatio-spectral, spatio-spectro-temporal) on some
> predictor variable that varies over the different conditions in which this
> participant has provided data (e.g., working-memory load, retention
> interval, luminance, contrast, etc). If you doubt the assumed linear
> relation between predictor variable and biological data, then you could
> write your own statfun_depsamplesrankcorr. To use this test statistic for
> cluster-based permutation inference, you need a threshold based on some
> reference distribution (which can be parametric, but must not be). ****
>
> ** **
>
> To get this statfun_depsamplesrankcorr running, you will probably have to
> take a look in the Fieldtrip code to see how the statistics framework is
> structured.****
>
> ** **
>
> Best,****
>
> ** **
>
> Eric Maris****
>
> ** **
>
> ** **
>
> *From:* Marcin [mailto:m.leszczynski.m at googlemail.com]
> *Sent:* woensdag 21 maart 2012 10:51
> *To:* Email discussion list for the FieldTrip project
> *Subject:* [FieldTrip] statfun_depsamplesregrT****
>
> ** **
>
> Dear Fieldtripers,
>
> Could anyone explain me what is being calculated with the
> statfun_depsamplesregrT function, please.
>
> David Groppe (thank you David) suggested in a previous thread on the list
> that I might calculate permutation test based on rank correlation to
> account for monotonic relationships within the permutation framework. I was
> wondering if this is the kind of test that statfun_depsamplesregrT function
> calculates.
> http://mailman.science.ru.nl/pipermail/fieldtrip/2011-December/004578.html
>
> Best,
> Marcin****
>
> _______________________________________________
> 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  Wed Mar 28 09:32:30 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 28 Mar 2012 09:32:30 +0200
Subject: [FieldTrip] optimum number of cycles
In-Reply-To: <CAPy7a9B64dcStbT9eEOZ4BR-HXq4WbkQ8LmzeqYxKNrnAooQqw@mail.gmail.com>
References: <CAPy7a9B64dcStbT9eEOZ4BR-HXq4WbkQ8LmzeqYxKNrnAooQqw@mail.gmail.com>
Message-ID: <4F72BE8E.7020603@donders.ru.nl>

Hi Rodolphe,

I don't think that your questions have a 'best' answer, but see below 
for my opinion.

> In the fixed-widow example, using a hanning taper, it is said that a 
> fixed widow of 500 ms can estimate power of different frequency bands 
> like 2 Hz, 4Hz, etc...
> However, for 2 Hz it means only 1 cycle.
>
> In the frequency-dependent window length, 7 cycles per frequency bands 
> are used.
>
> My questions are, is it ok to estimate a power with one cycle?

I would say no, but it depends on what trade-off between precision in 
time and frequency space you want to achieve. Of course it can be done, 
but the estimate is much more unreliable than when taking more cycles.

>  What could be the optimum number of cycles?

It depends on your question and frequency band. I would use at least 
three to five cycles for the most prominent frequencies(theta, alpha, 
beta), maybe two for very low frequencies (delta and below) and at least 
six or seven for higher frequencies (>40Hz). Some people use a fixed 
window length for the gamma-range and frequency smoothing around 10Hz, 
independent of the exact frequency (see e.g. the Neuron paper by Siegel 
et al., 2008, they use 250ms and 12Hz smoothing)

> Is ot ok to compare the power of different frequency bands that have 
> been estimated using a different number of cycles?

Yes and no, because different frequency bands have different 
characteristics, and are influenced differently by the 1/f noise. Taking 
more cycles for a higher frequency band and less for lower sounds 
logical, given that a signal low SNR requires more smoothing to reliably 
estimate the frequency content. However, frequencies bands are due to 
this 1/f noise different in power, e.g. alpha band activity will always 
have more power than gamma band activity.

>
> Thanks a lot,

You're welcome.

Best,
Jörn

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

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 jm.horschig at donders.ru.nl  Wed Mar 28 09:41:29 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Wed, 28 Mar 2012 09:41:29 +0200
Subject: [FieldTrip] Time stamp per sample
In-Reply-To: <CAG3TGCN+1ZV7zaAbGKvm8j3M1arg8pQXRgrfSLaof2hVp7G-vg@mail.gmail.com>
References: <CAG3TGCN+1ZV7zaAbGKvm8j3M1arg8pQXRgrfSLaof2hVp7G-vg@mail.gmail.com>
Message-ID: <4F72C0A9.7040604@donders.ru.nl>

Hi Anton,

This depends on the decimation rate that you specify, see here:
http://fieldtrip.fcdonders.nl/development/realtime/ctf?s[]=acq2ftx#downsampling_channel_selection_applying_gains

You can use ft_read_header(buffer) to read out the sampling frequency 
and then call ft_read_data to read the data. Here, you can specify a 
begin and an endsample, which define the length of the data the function 
returns. Prior, you can call ft_read_event to get the time stamp of the 
trigger value of interest. If you are interested in continuously reading 
data in without relying on certain events, you can don't need to call 
ft_read_event.

In FieldTrip, there are some example functions that you can look at, 
/e.g. //ft_realtime_asynchronous/ or/ft_realtime_synchronous/, see also 
here:
http://fieldtrip.fcdonders.nl/tutorial/realtime

 From what you wrote I get that the asynchronous type is what you aim for.

Best,
Jörn



On 3/27/2012 7:13 PM, Anton Andreev wrote:
> Hi,
>
> I have a question about the fieldtrip buffer.
> Does the protocol provides information about the time every sample has 
> been taken?
>
> I would like to produce a chunk of data for 300ms or 1 second for 
> example.
> I can build such chunk if I simply sort out samples that are in the 
> time range of 1 second starting with the time stamp of the first one. 
> Then again for 1 second and ....
>
> Thanks,
> Anton
>
>
> _______________________________________________
> 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

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 tessa.vanleeuwen at fcdonders.ru.nl  Wed Mar 28 10:59:58 2012
From: tessa.vanleeuwen at fcdonders.ru.nl (Tessa van Leeuwen)
Date: Wed, 28 Mar 2012 10:59:58 +0200 (CEST)
Subject: [FieldTrip] coherence/connectivity measures after applying ICA
In-Reply-To: <41C83D63782BE149B1B984A58E866D8FE82D@CITEMB2D.cits.wustl.edu>
Message-ID: <2130657903.77844.1332925198031.JavaMail.root@draco.zimbra.ru.nl>

Dear Olga, Thank you very much for your reply, this is very useful information! Because my trials are short I do not have sufficient data to let ICA compute all 275 possible components from my 275 channels - I use component reduction and estimate 80 components. This could then very well be the reason why coherence is altered after ICA. It makes sense that the interpolation would destroy any original phase relationships that are there. Thanks! Best wishes, Tessa ----- Original Message -----
> From: "Olga Vladimirovna Sysoeva" <sysoevao at psychiatry.wustl.edu>
> To: "Email discussion list for the FieldTrip project"
> <fieldtrip at donders.ru.nl>
> Sent: Wednesday, March 28, 2012 4:01:22 AM
> Subject: Re: [FieldTrip] coherence/connectivity measures after
> applying ICA
> Hi, Tessa,
> I do not have much experience for myself with coherence, but I'm very
> interested in the question you raised. Here is what I've seen in
> R.Thatcher's tutorial on Adulteration of Phase Relations when using
> Independent Components Analysis/Blind Identification and other
> Regression Methods to “Correct for Artifact
> http://www.appliedneuroscience.com/Tutorial%20on%20ICA%20Phase%20Adulteration.pdf
> .
> "Let us consider the rejection of eye movement artifact (EOG) using
> the ICA method which is the mathematical basis for Blind Source
> analysis. The ICA method decomposes a time series into a set of
> globally independent time series. Mathematically ICA can invert the
> equation and exactly reproduce the original time series based on the
> mathematical components. In this case the originally measured time or
> phase differences between each electrode are preserved and the
> cross-spectrum is unaltered.
> However, everything changes when the ICA or PCA or Blind Source, etc.
> methods are used to remove artifact by reconstructing 19 channels
> based on a smaller set of components, e.g., 17 or 18 channels and then
> deleting or omitting the EOG “components” to reconstruct 19 channels.
> This is because a regression process (interpolation) is used to
> minimize the deviation of the original 19 channel time series from the
> 17 or 18 “components” by which the remainder is used as weights to
> produce a second time series that has altered all of the phase
> relations in the original time series. The regression uses the average
> of the entire time series and therefore “smoothes” time or phase at
> each time point. Averaging a time series and computing deviations
> (whether information min-max, equimax, or simple linear regression)
> and then using the result to weight each time point by averages
> thereby smoothes each data point’s phase relations at each moment of
> time, distorting coherence, and destroys the time and phase relations
> present in the original time series."
> Hope it can help...
> Best Regards,
> Olga
> Olga Sysoeva,
> Research Associate, PhD
> Washington University School of Medicine
> Campus Box 8134
> 660 South Euclid Ave
> Saint Louis, MO 63110-9909
> From: fieldtrip-bounces at donders.ru.nl
> [fieldtrip-bounces at donders.ru.nl] on behalf of Rodolphe Nenert
> [batrod at gmail.com]
> Sent: Tuesday, March 27, 2012 7:20 PM
> To: Email discussion list for the FieldTrip project
> Subject: Re: [FieldTrip] coherence/connectivity measures after
> applying ICA
> Dear Tessa,
> ok this is more clear now.
> ICA is a wonderful tool which can easily become your worst enemy in
> data analyzing.
> By removing yourself certains epochs with blinks before doing an ICA,
> its is possible that you remove relevant data that can be used by your
> ICA algorithm to better separate components. Certain people would
> argue that even filtering your data before ICA can be a bad idea.
> Therefore, when you apply the ICA on your "cleaned" data, there is
> more chance that the component that will reflect the most what is left
> from blinks will also contains more relevant data.
> This data removal could potentially decrease your data variability
> therefore increase your coherence.
> Also, the number of epochs you keep after your cleaning (which should
> be different from ICA compared to visual removal) could potentially
> explain such a difference.
> Hope this helps,
> Rodolphe
> On Tue, Mar 27, 2012 at 4:34 PM, Tessa van Leeuwen <
> tessa.vanleeuwen at fcdonders.ru.nl > wrote:
> > Dear Rodolphe,
> > Thank you for your response, I tried to clarify below.
> > > 1) After your first "cleaning", do you test coherence on
> > > particular
> > > components or your entire data minus the "EOG" component?
> > I tested the coherence on the entire dataset after removal of the
> > EOG
> > component.
> > > 2) When you say that you redo ICA on cleaned data (of course, an
> > > ICA
> > > analysis made on a result of a previous ICA analysis with
> > > components
> > > removed is a bad idea), do you remove another component or do you
> > > test
> > > your coherence on particular components?
> > Sorry, I could have been more clear about this. I initially compared
> > two versions of the same dataset: one in which all trials containing
> > a
> > blink were removed from the dataset after manual inspection; another
> > version in which only trials with a blink during the actual stimulus
> > period were removed manually and the rest of the trials, including
> > trials with blinks outside the stimulus window, were 'cleaned' with
> > ICA, i.e. the EOG component was removed. Eye-balling coherence in
> > occipital channels, this was increased in the ICA-cleaned version.
> > To check whether the increase in coherence could have been explained
> > by an increased number of retained trials in the
> > ICA-cleaned-version,
> > I also applied the unmixing matrix obtained from the ICA to the
> > manually cleaned version of the data, i.e., in which only smaller
> > eye-movements or unidentified EOG artifacts would have been
> > remaining
> > after manual inspection. Now of course I could have been
> > over-removing
> > non-existent noise in this case, but also here the same difference
> > in
> > coherence appeared, now with the same number of trials in both
> > condition. When I look at the time-frequency representations from
> > both
> > versions, these look highly similar, only small intensity
> > differences
> > can be seen.
> > I only used a small amount of data to test this and these results
> > might therefore not be completely reliable. But I know other people
> > have experienced similar problems with altered coherence and I was
> > wondering whether any effect of ICA-preprocessing on
> > coherence/connectivity measures was generally known on the list and
> > in
> > the literature. Perhaps the removal of common noise with ICA can
> > already explain the differences?
> > Best wishes,
> > Tessa
> > > Rodolphe
> > > On Tue, Mar 27, 2012 at 11:27 AM, Tessa van Leeuwen <
> > > tessa.vanleeuwen at fcdonders.ru.nl > wrote:
> > > > Dear Fieldtrip experts,
> > > > I have noticed enhanced coherence (sensor level) in my data
> > > > after
> > > > applying ICA during preprocessing, removing only 1 EOG
> > > > component.
> > > > Of
> > > > course the (mainly quantitatively) enhanced coherence could be
> > > > due
> > > > to
> > > > the removal of (artifact induced) noise from the data. But this
> > > > increase also occured when applying ICA to previously cleaned
> > > > data,
> > > > implying changes induced by ICA somehow affect coherence.
> > > > One of the aims of our project is to compute
> > > > coherence/connectivity
> > > > measures at the source level. Since connectivity measures are
> > > > often
> > > > difficult to interpret as they are, I would like to ask whether
> > > > anyone
> > > > has experience with connectivity analyses after preprocessing
> > > > that
> > > > involved ICA. Are people aware of possible influences of ICA on
> > > > connectivity measures and is there a way to deal with this? Or
> > > > would
> > > > it be advisable NOT to use ICA when later looking at
> > > > coherence/connectivity at the source level?
> > > > We initially aim to compare across conditions (data that have
> > > > been
> > > > preprocessed together and from which the same ICA component has
> > > > been
> > > > removed). But we also have different experimental groups for
> > > > which
> > > > we
> > > > would like to qualitatively compare active networks during our
> > > > task.
> > > > Thank you in advance for any input, it is highly appreciated.
> > > > Best wishes,
> > > > Tessa
> > > > ---
> > > > Tessa van Leeuwen, PhD
> > > > postdoctoral researcher
> > > > Department of Neurophysiology
> > > > Max Planck Institute for Brain Research
> > > > _______________________________________________
> > > > 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
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If
> you are not the intended recipient, be advised that any unauthorized
> use, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If
> you are not the intended recipient, be advised that any unauthorized
> use, disclosure, copying or the taking of any action in reliance on
> the contents of this information is strictly prohibited. If you have
> received this email in error, please immediately notify the sender via
> telephone or return mail.
> _______________________________________________
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From dieter.devlaminck at inria.fr  Wed Mar 28 11:26:15 2012
From: dieter.devlaminck at inria.fr (Dieter Devlaminck)
Date: Wed, 28 Mar 2012 11:26:15 +0200 (CEST)
Subject: [FieldTrip] warning: the trial definition in the configuration is
 inconsistent with the actual data
In-Reply-To: <763718776.653827.1332926546901.JavaMail.root@zmbs2.inria.fr>
Message-ID: <1286872503.653958.1332926775888.JavaMail.root@zmbs2.inria.fr>


Dear All, 

When I try to invoke the 'ft_topoplotER(cfg,GA_FC)' command, I get the following warning 

Warning: the trial definition in the configuration is inconsistent with the actual data 

This happens both with the tutorial data as with my own data and is apparently caused by the fact that in the data structure there is a field 'previous' which in turn contains a field 'trl' which contains information on all triggers found in my original data. As I only take the average of the trials corresponding to certain target stimuli with ft_timelockanalysis (using 'cfg.trials = find(data.cfg.trl(:,end));') and then try to make a plot of that, fieldtrip finds an inconsistency in the dimensions and then does some kind of reconstruction, stating the following 

Warning: reconstructing sampleinfo by assuming that the trials are consecutive segments of a continuous recording 

This worries me a bit as I do not know exactly what it is doing although the tutorial plot seemed to be the same as the one on the website. What can I do to avoid this warning? 

I use fieldtrip version 20120308 and matlab R2010b on fedora 14. 

Thanks in advance, 
Best regards, 
Dieter Devlaminck 
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From eelke.spaak at donders.ru.nl  Wed Mar 28 11:39:05 2012
From: eelke.spaak at donders.ru.nl (Eelke Spaak)
Date: Wed, 28 Mar 2012 11:39:05 +0200
Subject: [FieldTrip] warning: the trial definition in the configuration
 is inconsistent with the actual data
In-Reply-To: <1286872503.653958.1332926775888.JavaMail.root@zmbs2.inria.fr>
References: <763718776.653827.1332926546901.JavaMail.root@zmbs2.inria.fr>
	<1286872503.653958.1332926775888.JavaMail.root@zmbs2.inria.fr>
Message-ID: <CABPNLUozQGCeGXm3DkH5eVrG5155RsBncFpjCfTwfTbPnSSmOg@mail.gmail.com>

Dear Dieter,

You have correctly tracked down the cause of the warning: the actual
data is inconsistent with a trl-matrix found somewhere in your
data.cfg (.previous) tree.

The reason you are getting these warnings is that certain FieldTrip
functions (apparently including ft_topoplotER and/or some of its
dependencies) require a data.sampleinfo field in your data structure
that is consistent with the actual data. In general, data.sampleinfo
is an Nx2 matrix containing, for each trial in the data, the indices
of the begin and end sample of that trial, with respect to the
original data set (on disk). If such a consistent data.sampleinfo does
not exist, as is the case with your data, fieldtrip will simply
reconstruct this sampleinfo by using 1 as the begin sample of trial 1,
and k as its end sample, where k is the number of samples in trial 1.
Trial 2 will be numbered from k+1 to k+n, where n is trial 2's length,
etc. This allows all FT functions depending on sampleinfo to function
adequately. Thus, given that you understand where the warning comes
from (as is the case), you should not worry about it and can safely
ignore it.

Do keep in mind, though (also for other people on the list, who might
find this post in the future), that you cannot interpret the
reconstructed sampleinfo in terms of the original recording anymore.
This is not an issue with the plotting functions (since you do not
directly use the manipulated data anyway), but might become relevant
when you e.g. use ft_databrowser or ft_artifact_zvalue, which can
return segments of interest in your data, specified in begin and end
samples.

Best,
Eelke

On 28 March 2012 11:26, Dieter Devlaminck <dieter.devlaminck at inria.fr> wrote:
> Dear All,
>
> When I try to invoke the 'ft_topoplotER(cfg,GA_FC)' command, I get the
> following warning
>
> Warning: the trial definition in the configuration is inconsistent with the
> actual data
>
> This happens both with the tutorial data as with my own data and is
> apparently caused by the fact that in the data structure there is a field
> 'previous' which in turn contains a field 'trl' which contains information
> on all triggers found in my original data. As I only take the average of the
> trials corresponding to certain target stimuli with ft_timelockanalysis
> (using 'cfg.trials = find(data.cfg.trl(:,end));') and then try to make a
> plot of that, fieldtrip finds an inconsistency in the dimensions and then
> does some kind of reconstruction, stating the following
>
> Warning: reconstructing sampleinfo by assuming that the trials are
> consecutive segments of a continuous recording
>
> This worries me a bit as I do not know exactly what it is doing although the
> tutorial plot seemed to be the same as the one on the website. What can I do
> to avoid this warning?
>
> I use fieldtrip version 20120308 and matlab R2010b on fedora 14.
>
> Thanks in advance,
> Best regards,
> Dieter Devlaminck
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


From dieter.devlaminck at inria.fr  Wed Mar 28 13:07:34 2012
From: dieter.devlaminck at inria.fr (Dieter Devlaminck)
Date: Wed, 28 Mar 2012 13:07:34 +0200 (CEST)
Subject: [FieldTrip] warning: the trial definition in the configuration
 is inconsistent with the actual data
In-Reply-To: <CABPNLUozQGCeGXm3DkH5eVrG5155RsBncFpjCfTwfTbPnSSmOg@mail.gmail.com>
Message-ID: <1504836263.656522.1332932854634.JavaMail.root@zmbs2.inria.fr>

Dear Eelke,

Thank you for answering so quickly.

> Do keep in mind, though (also for other people on the list, who might
> find this post in the future), that you cannot interpret the
> reconstructed sampleinfo in terms of the original recording anymore.
> This is not an issue with the plotting functions (since you do not
> directly use the manipulated data anyway), but might become relevant
> when you e.g. use ft_databrowser or ft_artifact_zvalue, which can
> return segments of interest in your data, specified in begin and end
> samples.

Indeed, this is the main reason why I asked this question, as it might have repercussions when calling other methods.

Is there a reason why the sampleinfo field disappears when calling the ft_timelockanalysis method? The field is still present in my data after calling the ft_redefinetrial method. I assume the normal operation is that the sampleinfo field is still present as it is normally used by subsequent methods?

A second thing I noticed is that now that I read my file with ft_preprocessing as one continuous trial and then partition my data into trials with ft_definetrials and ft_redefinetrials that the trialinfo (where I set some custom labels with my own trialfun) field has disappeared. If I first call ft_definetrials and the ft_preprocessing the trialinfo field is still there.

Best regards,
Dieter Devlaminck

----- Oorspronkelijk bericht -----
> Van: "Eelke Spaak" <eelke.spaak at donders.ru.nl>
> Aan: "Email discussion list for the FieldTrip project" <fieldtrip at donders.ru.nl>
> Verzonden: Woensdag 28 maart 2012 11:39:05
> Onderwerp: Re: [FieldTrip] warning: the trial definition in the configuration is inconsistent with the actual data
> Dear Dieter,
> 
> You have correctly tracked down the cause of the warning: the actual
> data is inconsistent with a trl-matrix found somewhere in your
> data.cfg (.previous) tree.
> 
> The reason you are getting these warnings is that certain FieldTrip
> functions (apparently including ft_topoplotER and/or some of its
> dependencies) require a data.sampleinfo field in your data structure
> that is consistent with the actual data. In general, data.sampleinfo
> is an Nx2 matrix containing, for each trial in the data, the indices
> of the begin and end sample of that trial, with respect to the
> original data set (on disk). If such a consistent data.sampleinfo does
> not exist, as is the case with your data, fieldtrip will simply
> reconstruct this sampleinfo by using 1 as the begin sample of trial 1,
> and k as its end sample, where k is the number of samples in trial 1.
> Trial 2 will be numbered from k+1 to k+n, where n is trial 2's length,
> etc. This allows all FT functions depending on sampleinfo to function
> adequately. Thus, given that you understand where the warning comes
> from (as is the case), you should not worry about it and can safely
> ignore it.
> 
> Do keep in mind, though (also for other people on the list, who might
> find this post in the future), that you cannot interpret the
> reconstructed sampleinfo in terms of the original recording anymore.
> This is not an issue with the plotting functions (since you do not
> directly use the manipulated data anyway), but might become relevant
> when you e.g. use ft_databrowser or ft_artifact_zvalue, which can
> return segments of interest in your data, specified in begin and end
> samples.
> 
> Best,
> Eelke
> 
> On 28 March 2012 11:26, Dieter Devlaminck <dieter.devlaminck at inria.fr>
> wrote:
> > Dear All,
> >
> > When I try to invoke the 'ft_topoplotER(cfg,GA_FC)' command, I get
> > the
> > following warning
> >
> > Warning: the trial definition in the configuration is inconsistent
> > with the
> > actual data
> >
> > This happens both with the tutorial data as with my own data and is
> > apparently caused by the fact that in the data structure there is a
> > field
> > 'previous' which in turn contains a field 'trl' which contains
> > information
> > on all triggers found in my original data. As I only take the
> > average of the
> > trials corresponding to certain target stimuli with
> > ft_timelockanalysis
> > (using 'cfg.trials = find(data.cfg.trl(:,end));') and then try to
> > make a
> > plot of that, fieldtrip finds an inconsistency in the dimensions and
> > then
> > does some kind of reconstruction, stating the following
> >
> > Warning: reconstructing sampleinfo by assuming that the trials are
> > consecutive segments of a continuous recording
> >
> > This worries me a bit as I do not know exactly what it is doing
> > although the
> > tutorial plot seemed to be the same as the one on the website. What
> > can I do
> > to avoid this warning?
> >
> > I use fieldtrip version 20120308 and matlab R2010b on fedora 14.
> >
> > Thanks in advance,
> > Best regards,
> > Dieter Devlaminck
> >
> > _______________________________________________
> > 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 akiko.ikkai at gmail.com  Thu Mar 29 00:22:46 2012
From: akiko.ikkai at gmail.com (Akiko Ikkai)
Date: Wed, 28 Mar 2012 18:22:46 -0400
Subject: [FieldTrip] beamformer results smaller than brain
Message-ID: <CAKwx6Qc-TBiKARXJmJewk2Ob-CMZpTyXijCJ71iuOYGkH0ZbQA@mail.gmail.com>

Hi Fieldtrip users,

I'm hoping that someone could give me advice on segmentation and beamformer
on EEG data. I have EEG data set based on 128 channel cap. Thanks to the
help I got in mid-Feb, I'm now able to create a decent
segmentation (seg_results image attached) and volume conduction model.
However, when I run beamformer based on these models, resulting beamforming
image is often smaller than the brain (beamformer_result attached).
Particularly posterior parietal and occipital map is NaN.

I have tried going back to segmentation and expanded brain by
using imdilate after ft_volumesegment such as:

newbrain = imdilate(seg2.brain,strel_bol(1)); % seg2.brain is original
brain tissue from segmentation

seg2.brain = newbrain;
seg2.seg = seg2.scalp + seg2.skull*3 + seg2.brain*6;

and run ft_prepare_mesh_new on seg2. Of course, I have to make sure there
is no intersect between different tissue types, so using imdilate has
limitation.

Could someone explain why this shrinkage might be happening, and how I
could fix it?

Thanks in advance! Akiko

-- 
Akiko Ikkai, Ph.D.
Postdoctoral Fellow
Department of Psychological and Brain Sciences
Johns Hopkins University
Ames Hall, 3400 N. Charles St.
Baltimore, MD 21218
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From a.stolk at fcdonders.ru.nl  Thu Mar 29 10:19:47 2012
From: a.stolk at fcdonders.ru.nl (Stolk, A.)
Date: Thu, 29 Mar 2012 10:19:47 +0200 (CEST)
Subject: [FieldTrip] beamformer results smaller than brain
In-Reply-To: <CAKwx6Qc-TBiKARXJmJewk2Ob-CMZpTyXijCJ71iuOYGkH0ZbQA@mail.gmail.com>
Message-ID: <1939595059.215032.1333009187080.JavaMail.root@sculptor.zimbra.ru.nl>

Hi Akiko, I'm not sure whether this is causing it, but w hat size inwardshift did you use when preparing your sourcemodel? Also check this page on our wiki: http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space Best, Arjen ----- Oorspronkelijk bericht -----
> Van: "Akiko Ikkai" <akiko.ikkai at gmail.com>
> Aan: fieldtrip at donders.ru.nl
> Verzonden: Donderdag 29 maart 2012 00:22:46
> Onderwerp: [FieldTrip] beamformer results smaller than brain
> Hi Fieldtrip users,
> I'm hoping that someone could give me advice on segmentation and
> beamformer on EEG data. I have EEG data set based on 128 channel cap.
> Thanks to the help I got in mid-Feb, I'm now able to create a decent
> segmentation (seg_results image attached) and volume conduction model.
> However, when I run beamformer based on these models, resulting
> beamforming image is often smaller than the brain (beamformer_result
> attached). Particularly posterior parietal and occipital map is NaN. 
> I have tried going back to segmentation and expanded brain by
> using imdilate after ft_volumesegment such as:
> newbrain = imdilate(seg2.brain,strel_bol(1)); % seg2.brain is original
> brain tissue from segmentation
> seg2.brain = newbrain;
> seg2.seg = seg2.scalp + seg2.skull*3 + seg2.brain*6;
> and run ft_prepare_mesh_new on seg2. Of course, I have to make sure
> there is no intersect between different tissue types, so using
> imdilate has limitation. 
> Could someone explain why this shrinkage might be happening, and how I
> could fix it? 
> Thanks in advance! Akiko
> --
> Akiko Ikkai, Ph.D.
> Postdoctoral Fellow
> Department of Psychological and Brain Sciences
> Johns Hopkins University
> Ames Hall, 3400 N. Charles St.
> Baltimore, MD 21218
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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From g.piantoni at nin.knaw.nl  Thu Mar 29 11:13:19 2012
From: g.piantoni at nin.knaw.nl (Gio Piantoni)
Date: Thu, 29 Mar 2012 11:13:19 +0200
Subject: [FieldTrip] beamformer results smaller than brain
In-Reply-To: <CAKwx6Qc-TBiKARXJmJewk2Ob-CMZpTyXijCJ71iuOYGkH0ZbQA@mail.gmail.com>
References: <CAKwx6Qc-TBiKARXJmJewk2Ob-CMZpTyXijCJ71iuOYGkH0ZbQA@mail.gmail.com>
Message-ID: <CAHeOcruuVvKPDwhwXfozS8s6VciGf8T_stFcjYLMjOEvVOJiMg@mail.gmail.com>

Hi Akiko,

Your headmodel looks pretty good and your beamformer plot seems to
cover most of the gray matter.

However, it's good to check the location of your dipoles in respect to
your headmodel. For example, you can plot the .pos field of your
leadfield. Something like:

ft_plot_mesh(bnd(3), 'facealpha', .5)
hold on
plot3(lead.pos(:,1), lead.pos(:,2), lead.pos(:,3), '.')

It might well be that your grid is too coarse and some dipoles just
happen to be over the edge of the brain. Remember that your
"beamformer_result.png" is just an interpolation of the values of this
dipole grid.

You can either try to make your grid more refined (but remember that
your computation time will significantly increase). Or you can
manipulate the way dipoles are considered inside or outside the brain
with "inwardshift" for ft_prepare_leadfield (although I'd advise
against using a negative value as some dipoles might really end up
outside of your brain mesh, with some numerical instabilities).
Another option (the easiest) is to nudge your grid by, say, a few
millimeters, so that the parietal dipoles will be just inside the
brain mesh.

HTH,

Gio

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

+31 20 5665492
gio at gpiantoni.com
www.gpiantoni.com

On Thu, Mar 29, 2012 at 00:22, Akiko Ikkai <akiko.ikkai at gmail.com> wrote:
> Hi Fieldtrip users,
>
> I'm hoping that someone could give me advice on segmentation and beamformer
> on EEG data. I have EEG data set based on 128 channel cap. Thanks to the
> help I got in mid-Feb, I'm now able to create a decent
> segmentation (seg_results image attached) and volume conduction model.
> However, when I run beamformer based on these models, resulting beamforming
> image is often smaller than the brain (beamformer_result attached).
> Particularly posterior parietal and occipital map is NaN.
>
> I have tried going back to segmentation and expanded brain by using imdilate
> after ft_volumesegment such as:
>
> newbrain = imdilate(seg2.brain,strel_bol(1)); % seg2.brain is original brain
> tissue from segmentation
>
> seg2.brain = newbrain;
>
> seg2.seg = seg2.scalp + seg2.skull*3 + seg2.brain*6;
>
> and run ft_prepare_mesh_new on seg2. Of course, I have to make sure there is
> no intersect between different tissue types, so using imdilate has
> limitation.
>
> Could someone explain why this shrinkage might be happening, and how I could
> fix it?
>
> Thanks in advance! Akiko
>
> --
> Akiko Ikkai, Ph.D.
> Postdoctoral Fellow
> Department of Psychological and Brain Sciences
> Johns Hopkins University
> Ames Hall, 3400 N. Charles St.
> Baltimore, MD 21218
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip



From fredericroux at hotmail.de  Thu Mar 29 12:37:59 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 12:37:59 +0200
Subject: [FieldTrip] segmented volume not aligned with individual mri
Message-ID: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>


Dear all,

I am trying to create mni-aligned grids in individual head-space
and have followed the code provided in the corresponding example-script 
on the fieldtrip site to the line.

However when I plot the segmented volume it looks as if something
is going wrong. I am attaching the plots of the gray and white matter,
as well as of the csf.

I tried flipping the dimensions as suggested in the example script, however
this had zero effect.

My code looks like this.

addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
ft_defaults;

mri = ft_read_mri([path2files,'ID_V2.mri']);

cfg = [];
cfg.coordsys = 'ctf';
cfg.downsample = 2;
seg = ft_volumesegment(cfg,mri);

seg.transform = mri.transform;
seg.anatomy = mri.anatomy;

figure;
cfg = [];
ft_sourceplot(cfg,seg);
figure;
cfg = [];
cfg.funparameter = 'gray';

ft_sourceplot(cfg,seg);

figure;

cfg = [];

cfg.funparameter = 'white';


ft_sourceplot(cfg,seg);


figure;

cfg = [];

cfg.funparameter = 'csf';


ft_sourceplot(cfg,seg);



Anybody an idea why this is happening?
Any help would be highly appreciated.

Fred
-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From ali at cs.ru.nl  Thu Mar 29 12:46:54 2012
From: ali at cs.ru.nl (Ali Bahramisharif)
Date: Thu, 29 Mar 2012 12:46:54 +0200
Subject: [FieldTrip] segmented volume not aligned with individual mri
In-Reply-To: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>
References: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>
Message-ID: <165141044b7f16d8ba3fa0bc824d2c59.squirrel@squirrel.science.ru.nl>

Dear Fred,

Why do you enforce:

seg.transform = mri.transform;

after segmentation? I do not do it, and it looks fine!

Cheers,
Ali

>
> Dear all,
>
> I am trying to create mni-aligned grids in individual head-space
> and have followed the code provided in the corresponding example-script
> on the fieldtrip site to the line.
>
> However when I plot the segmented volume it looks as if something
> is going wrong. I am attaching the plots of the gray and white matter,
> as well as of the csf.
>
> I tried flipping the dimensions as suggested in the example script,
> however
> this had zero effect.
>
> My code looks like this.
>
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
> ft_defaults;
>
> mri = ft_read_mri([path2files,'ID_V2.mri']);
>
> cfg = [];
> cfg.coordsys = 'ctf';
> cfg.downsample = 2;
> seg = ft_volumesegment(cfg,mri);
>
> seg.transform = mri.transform;
> seg.anatomy = mri.anatomy;
>
> figure;
> cfg = [];
> ft_sourceplot(cfg,seg);
> figure;
> cfg = [];
> cfg.funparameter = 'gray';
>
> ft_sourceplot(cfg,seg);
>
> figure;
>
> cfg = [];
>
> cfg.funparameter = 'white';
>
>
> ft_sourceplot(cfg,seg);
>
>
> figure;
>
> cfg = [];
>
> cfg.funparameter = 'csf';
>
>
> ft_sourceplot(cfg,seg);
>
>
>
> Anybody an idea why this is happening?
> Any help would be highly appreciated.
>
> Fred
> --
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
>
>
>  		 	   		  _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Address:
        HG02.517
        Intelligent Systems
        Radboud University Nijmegen
        Heyendaalseweg 135
        6525 AJ Nijmegen
        The Netherlands

http://www.cs.ru.nl/~ali
Tel.:   +31 (0)24 36 52634



From jan.schoffelen at donders.ru.nl  Thu Mar 29 13:22:40 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 29 Mar 2012 13:22:40 +0200
Subject: [FieldTrip] segmented volume not aligned with individual mri
In-Reply-To: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>
References: <DUB113-W36C66241D78DAA3D687650B7480@phx.gbl>
Message-ID: <9CDB7D6C-A8FC-4000-A234-3CD5913EBD12@donders.ru.nl>

Hi Fred,

You specify the seg to be downsampled. Therefore, I guess that the seg.dim and the mri.dim don't match anymore. Nor will the dimensions of the mri.anatomy match those of the seg.gray/white/csf. Also, as Ali suggests, the transformation matrices cannot be exchanged anymore.
I suspect that if you do: cfg = []; cfg.downsample = 2; mri2=ft_volumedownsample(cfg, mri); seg.anatomy = mri2.anatomy (and leave out seg.transform = mri.transform) that things will look a bit better.

JM

On Mar 29, 2012, at 12:37 PM, Frederic Roux wrote:

> Dear all,
> 
> I am trying to create mni-aligned grids in individual head-space
> and have followed the code provided in the corresponding example-script 
> on the fieldtrip site to the line.
> 
> However when I plot the segmented volume it looks as if something
> is going wrong. I am attaching the plots of the gray and white matter,
> as well as of the csf.
> 
> I tried flipping the dimensions as suggested in the example script, however
> this had zero effect.
> 
> My code looks like this.
> 
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
> ft_defaults;
> 
> mri = ft_read_mri([path2files,'ID_V2.mri']);
> 
> cfg = [];
> cfg.coordsys = 'ctf';
> cfg.downsample = 2;
> seg = ft_volumesegment(cfg,mri);
> 
> seg.transform = mri.transform;
> seg.anatomy = mri.anatomy;
> 
> figure;
> cfg = [];
> ft_sourceplot(cfg,seg);
> figure;
> cfg = [];
> cfg.funparameter = 'gray';
> ft_sourceplot(cfg,seg);
> figure;
> cfg = [];
> cfg.funparameter = 'white';
> ft_sourceplot(cfg,seg);
> figure;
> cfg = [];
> cfg.funparameter = 'csf';
> ft_sourceplot(cfg,seg);
> 
> Anybody an idea why this is happening?
> Any help would be highly appreciated.
> 
> Fred
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 
> <segmented_1.jpg>_______________________________________________
> 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

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From fredericroux at hotmail.de  Thu Mar 29 16:05:18 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 16:05:18 +0200
Subject: [FieldTrip] segmentation and individual grids
Message-ID: <DUB113-W1130856191D4A2E13FDACDCB7480@phx.gbl>


Dear Ali, Dear JM,

thanks a lot for your help.

According to your suggestions I have modified
my code as following:

mri = ft_read_mir('MRI_FILE_V2.mri');

cfg = [];
cfg.downsample = 2;
cfg.coordsys = 'ctf';

mri = ft_volume_downsample(cfg,mri);

cfg = [];
cfg.coordsys = 'ctf';
seg = ft_volumesegment(cfg,mri);
seg.anatomy = mri.anatomy;

Now the comparison of the segmented volumes and the MRI look fine,
but it seems that there is still a problem when I compute the individual grids (see attached figure).

I am also attaching the code I am using.

Would be great if you could help me to get this working.

Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From jan.schoffelen at donders.ru.nl  Thu Mar 29 16:17:00 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Thu, 29 Mar 2012 16:17:00 +0200
Subject: [FieldTrip] Fwd: segmentation and individual grids
References: <DUB113-W1130856191D4A2E13FDACDCB7480@phx.gbl>
Message-ID: <E9FA494C-82EA-4CCE-8951-1B020914FB2B@donders.ru.nl>

Hi Fred,

I forwarded your question to the list, so that other people get the opportunity to answer, and/or benefit from the answer ;-).

JM


Begin forwarded message:

> From: Frederic Roux <fredericroux at hotmail.de>
> Date: March 29, 2012 4:05:18 PM GMT+02:00
> To: <fieldtrip at donders.ru.nl>, <jan.schoffelen at donders.ru.nl>, <ali at cs.ru.nl>
> Subject: segmentation and individual grids
> Reply-To: <fredericrouxw at gmail.com>
> 
> Dear Ali, Dear JM,
> 
> thanks a lot for your help.
> 
> According to your suggestions I have modified
> my code as following:
> 
> mri = ft_read_mir('MRI_FILE_V2.mri');
> 
> cfg = [];
> cfg.downsample = 2;
> cfg.coordsys = 'ctf';
> 
> mri = ft_volume_downsample(cfg,mri);
> 
> cfg = [];
> cfg.coordsys = 'ctf';
> seg = ft_volumesegment(cfg,mri);
> seg.anatomy = mri.anatomy;
> 
> Now the comparison of the segmented volumes and the MRI look fine,
> but it seems that there is still a problem when I compute the individual grids (see attached figure).
> 
> I am also attaching the code I am using.
> 
> Would be great if you could help me to get this working.
> 
> Fred
> 
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 

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

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From fredericroux at hotmail.de  Thu Mar 29 17:45:52 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 17:45:52 +0200
Subject: [FieldTrip] alignment channel array, head model & individual grid
Message-ID: <DUB113-W104C6E0B399243CBB06024BB7480@phx.gbl>


Dear all,

I have trouble finding the right alignment for my head models and individual grids
with the MEG channel array.

The code I use is the following:

addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/fieltdrip_private/');
ft_defaults;

spm2path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm2/';
spm8path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm8/';

rmpath(spm2path,spm8path);


mri = ft_read_mri('ID_V2.mri');

cfg = [];
cfg.coordsys = 'ctf';
seg = ft_volumesegment(cfg,mri);

cfg = [];
hdm = ft_prepare_singleshell(cfg,seg);

cfg = [];
cfg.template = '/data/common/SPM8current/spm8/canonical/single_subj_T1.nii';
cfg.coordsys = 'ctf';
cfg.nonlinear = 'no';

norm = ft_volumenormalise(cfg,mri);

load template_grid.mat % template created from the SPM8 single_subj_T1.nii template located in the canonical folder of SPM8

grid = [];
grid.pos = warp_apply(inv(norm.cfg.final), template_grid.pos, 'homogenous')/10;
grid.inside = template_gird.inside;
grid.outside = template_grid.outside;

transfrom_ctf2spm = norm.cfg.final;

figure;
hold on;
ft_plot_sens(ft_read_sens('ID.ds'));
ft_plot_vol(hdm);
ft_plot_mesh(grid.pos(grid.inside,:));


Would be great if you could help me to figure out what is going wrong here.

Best,
Fred


-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From fredericroux at hotmail.de  Thu Mar 29 18:39:01 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 18:39:01 +0200
Subject: [FieldTrip] alignment channel array, head model & individual grid
Message-ID: <DUB113-W824234F69AD703490B557DB7480@phx.gbl>


I forgot to the mention that the left plot shows the headmodel and the channel array
whereas the rigth plot shows the grid and the channel array.

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From fredericroux at hotmail.de  Thu Mar 29 19:03:02 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Thu, 29 Mar 2012 19:03:02 +0200
Subject: [FieldTrip] fieldtrip Digest, Vol 16, Issue 51
In-Reply-To: <mailman.715.1333035969.902.fieldtrip@donders.ru.nl>
References: <mailman.715.1333035969.902.fieldtrip@donders.ru.nl>
Message-ID: <DUB113-W63BCB0620F89F65ED05E6DB7480@phx.gbl>


Hi Julian,

thank you for response. That did indeed solve the problem.
I had commented out the section where everything is converted
from mm to cm.

Now the grid is at least on the same scale as the head model.
However, when I compare the template grid (Figure1) with
the individual grid (Figure6) it seems as if there is still a difference.

Is this normal and a consequence of the warping or should the
plot look different?

Best, Fred

-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225




> From: fieldtrip-request at donders.ru.nl
> Subject: fieldtrip Digest, Vol 16, Issue 51
> To: fieldtrip at donders.ru.nl
> Date: Thu, 29 Mar 2012 17:46:09 +0200
> 
> Send fieldtrip mailing list submissions to
> 	fieldtrip at donders.ru.nl
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> or, via email, send a message with subject or body 'help' to
> 	fieldtrip-request at donders.ru.nl
> 
> You can reach the person managing the list at
> 	fieldtrip-owner at donders.ru.nl
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of fieldtrip digest..."
> 
> 
> Today's Topics:
> 
>    1. alignment channel array, head model & individual grid
>       (Frederic Roux)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 29 Mar 2012 17:45:52 +0200
> From: Frederic Roux <fredericroux at hotmail.de>
> To: <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] alignment channel array, head model & individual
> 	grid
> Message-ID: <DUB113-W104C6E0B399243CBB06024BB7480 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 
> Dear all,
> 
> I have trouble finding the right alignment for my head models and individual grids
> with the MEG channel array.
> 
> The code I use is the following:
> 
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/');
> addpath('/data/common/FieldtripCurrent/fieldtrip-20120105/fieltdrip_private/');
> ft_defaults;
> 
> spm2path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm2/';
> spm8path = '/data/common/FieldtripCurrent/fieldtrip-20120105/external/spm8/';
> 
> rmpath(spm2path,spm8path);
> 
> 
> mri = ft_read_mri('ID_V2.mri');
> 
> cfg = [];
> cfg.coordsys = 'ctf';
> seg = ft_volumesegment(cfg,mri);
> 
> cfg = [];
> hdm = ft_prepare_singleshell(cfg,seg);
> 
> cfg = [];
> cfg.template = '/data/common/SPM8current/spm8/canonical/single_subj_T1.nii';
> cfg.coordsys = 'ctf';
> cfg.nonlinear = 'no';
> 
> norm = ft_volumenormalise(cfg,mri);
> 
> load template_grid.mat % template created from the SPM8 single_subj_T1.nii template located in the canonical folder of SPM8
> 
> grid = [];
> grid.pos = warp_apply(inv(norm.cfg.final), template_grid.pos, 'homogenous')/10;
> grid.inside = template_gird.inside;
> grid.outside = template_grid.outside;
> 
> transfrom_ctf2spm = norm.cfg.final;
> 
> figure;
> hold on;
> ft_plot_sens(ft_read_sens('ID.ds'));
> ft_plot_vol(hdm);
> ft_plot_mesh(grid.pos(grid.inside,:));
> 
> 
> Would be great if you could help me to figure out what is going wrong here.
> 
> Best,
> Fred
> 
> 
> -- 
> Fr?d?ric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 
>  		 	   		  
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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 16, Issue 51
> *****************************************
 		 	   		  
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From Ulrich.Pomper at charite.de  Fri Mar 30 10:37:06 2012
From: Ulrich.Pomper at charite.de (Pomper, Ulrich)
Date: Fri, 30 Mar 2012 10:37:06 +0200
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <203022dc538e40168d5b72ded3195dcc@EXCCAHT-1.mail.uke.ads>
References: <4F71B9F0.8080106@charite.de>
	<203022dc538e40168d5b72ded3195dcc@EXCCAHT-1.mail.uke.ads>
Message-ID: <4F7570B2.5040707@charite.de>

Thanks Mark + Jörn for the replies!
I'll have a look at the NAI.

On 27.03.2012 15:48, "Jörn M. Horschig" wrote:

Dear Ulrich,


First of all, you might want to use the Neural Activity Index (NAI), as
also described in the tutorial:
http://fieldtrip.fcdonders.nl/tutorial/beamformer#source_analysiswithout_contrasting_condition

Then, to answer your question, I am tempted to say that this would be an
invalid approach when dealing with power, so in frequency-space. Power
obviously has a lower bound, so that the average of any random
collection of power values will never be 0.

That sounds plausible for raw power data, but actually, I want to compare whether my power change to baseline activity is different from zero (maybe that wasn't evident in my first post). I think that's a correct approach.




Though, what you are
suggesting is the same as a regular t-test, isn't it?
In case you are dealing e.g. with am LCMV beamformer, I am not quite
sure, but the null-hypothesis you suggested (amplitude==0)  sounds fair.

In any case, building a surrogate distribution same mean and variance
than your data might be a better way to deal with your problem. That
should be easily doable in Matlab without any need to implement this in
FieldTrip. And note that the MC problem is always present, but a
cluster-based correction (similar to Bonferroni, but correcting by the
number of voxels in the cluster not by the number of all voxels) sounds
legitimate to me. Afair, that's how it's done in FT.

Are you sure? I am not aware of any correction to the alpha level that is done by the cluster-based correction in FT. Afaik all it does is look for a certain number of significant voxels that are close in time, freq and space.
Best, Ulrich

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From yoni.levy at inserm.fr  Fri Mar 30 10:40:25 2012
From: yoni.levy at inserm.fr (yoni.levy at inserm.fr)
Date: Fri, 30 Mar 2012 10:40:25 +0200
Subject: [FieldTrip] actvsblT test statistic when running ft_freqstatistic
Message-ID: <20120330104025.kbc1vye188wwcoc8@imp.inserm.fr>

Dear All,

Would anyone know how to run ft_freqstatistics using the actvsblT?

I intend to statistically test activation period with baseline  
activity. For this, I followed the "Within trial experiments" tutorial  
in fieldtrip
(http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq#within_trial_experiments).
The tutorial emphasizes that one should select equal length time
windows. However, the number of trials in both conditions (activation
and baseline) remains unequal. Therefore, when I run ft_freqstatistics
with the design mentioned in the tutorial (inserting only the number
of trials of the activation condition), I receive the following error
message:
"the number of observations in the design does not match the number of
observations in the data"

Is there an error in the turorial, or is the script intended to create
two frequency output-files, with different total number of trials.

Any advice would be appreciated,

Thanks,

Yoni

----
Yoni Levy, Ph.D.,
INSERM U825,
Address: Pavillon BAUDOT / CHU Purpan,
Place du Docteur Joseph Baylac,
31024 TOULOUSE cédex 3, FRANCE.
E-Mail : yoni.levy at inserm.fr

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





From Ulrich.Pomper at charite.de  Fri Mar 30 10:56:52 2012
From: Ulrich.Pomper at charite.de (Pomper, Ulrich)
Date: Fri, 30 Mar 2012 10:56:52 +0200
Subject: [FieldTrip] =?utf-8?q?Postdoctoral_Position_-_Charit=C3=A9_Berlin?=
In-Reply-To: <8B8CE00B-155C-41D9-9F50-16EA83EB9314@charite.de>
References: <8B8CE00B-155C-41D9-9F50-16EA83EB9314@charite.de>
Message-ID: <4F757554.10703@charite.de>

The Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin invites applications for a Post-doctoral position.

A Starting Grant of the European Research Council (ERC) will fund the position. The main objective of this ERC research program is to examine neural and neurochemical markers of multisensory integration and to test a new hypothesis that considers dynamic interplay of synchronized neural populations as a key to multisensory processes. The studies within this program include healthy subjects and patients with schizophrenia, as an example of a mental disorder with deficits in multisensory integration. Multisensory processes will be examined in a series of experiments requiring both bottom-up and top-down processing.

Applicants should have a background in psychology, medicine, biology, physics, engineering, or neuroscience. Experience in human EEG/MEG studies, Matlab programming skills, as well as German language skills for interacting with patients are prerequisites for the position. An interest in neurophysiological studies including clinical populations is expected.

Applicants are asked to submit their CV, a motivation letter, 2 names of referees, and documentation of relevant qualifications (e.g., copies of diplomas and/or transcripts of grades) until April 15, 2012, electronically to:

Daniel Senkowski, Department of Psychiatry and Psychotherapy, Charité, University Medicine Berlin, 10115 Berlin, Germany, Phone: +49-30-2311-2738, Fax: +49-30-2311-2209, www.danielsenkowski.com<http://www.danielsenkowski.com/>, daniel.senkowski at charite.de<mailto:daniel.senkowski at charite.de>






---------------------------------------------------------------
Daniel Senkowski, Ph.D

Head of the Multisensory Integration research group
Department of Psychiatry and Psychotherapy
Charité, University Medicine Berlin
St. Hedwig Hospital, Große Hamburger Str. 5-11
10115 Berlin, Germany
Phone: +49-30-2311-2738
Fax:      +49-30-2311-2209
http://psy-ccm.charite.de/en/research/neuroimaging/multisensory_integration

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From jm.horschig at donders.ru.nl  Fri Mar 30 15:38:43 2012
From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=)
Date: Fri, 30 Mar 2012 15:38:43 +0200
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <4F7570B2.5040707@charite.de>
References: <4F71B9F0.8080106@charite.de>
	<203022dc538e40168d5b72ded3195dcc@EXCCAHT-1.mail.uke.ads>
	<4F7570B2.5040707@charite.de>
Message-ID: <4F75B763.9010906@donders.ru.nl>

Hi Ulrich,

>
> Are you sure? I am not aware of any correction to the alpha level that 
> is done by the cluster-based correction in FT. Afaik all it does is 
> look for a certain number of significant voxels that are close in 
> time, freq and space.

Oh indeed, I was mixing things up there. I couldn't find anything 
mentioned like this neither in the code nor in the Maris&Oostenveld 
paper. Then it was probably something I remembered from another 
test/tool, or I was mixing thoughts of mine with a simplistic 
explanation of random field theory. In any way, my apologies for the 
confusion.

Best,
Jörn


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

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 samarakm at mail.uc.edu  Fri Mar 30 21:04:42 2012
From: samarakm at mail.uc.edu (Samarasinghe, Kasun (samarakm))
Date: Fri, 30 Mar 2012 19:04:42 +0000
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <4F71B9F0.8080106@charite.de>
References: <4F71B9F0.8080106@charite.de>
Message-ID: <158540F0F1AD27479479077742EA83C515EA8C66@CH1PRD0102MB148.prod.exchangelabs.com>

Dear Fieldtrip members,

I am trying to construct a generic head model by following the tutorial "Build a geometrical description of the volume conduction model of the head". For some reason, I cannot download the zipped MRI file in the location : '"ftp://ftp.fcdonders.nl/pub/fieldtrip/". Any help regarding the correct location of this file would be appreciated.

Thank you,
Kasun

--------------------------------------------
Kasun M Samarasinghe
Doctoral Student
Electrical Engineering - Systems Track
University of Cincinnati








From samarakm at mail.uc.edu  Fri Mar 30 21:09:50 2012
From: samarakm at mail.uc.edu (Samarasinghe, Kasun (samarakm))
Date: Fri, 30 Mar 2012 19:09:50 +0000
Subject: [FieldTrip] Failure to access the MRI file in the Tutorial section
Message-ID: <158540F0F1AD27479479077742EA83C515EA8C74@CH1PRD0102MB148.prod.exchangelabs.com>

Dear Fieldtrip members,

I am trying to construct a generic head model by following the tutorial "Build a geometrical description of the volume conduction model of the head". For some reason, I cannot download the zipped MRI file in the location : '"ftp://ftp.fcdonders.nl/pub/fieldtrip/". Any help regarding the correct location of this file would be appreciated.

Please disregard my previous email since it had the wrong title.

Thank you,
Kasun

--------------------------------------------
Kasun M Samarasinghe
Doctoral Student
Electrical Engineering - Systems Track
University of Cincinnati



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From batrod at gmail.com  Fri Mar 30 21:24:56 2012
From: batrod at gmail.com (Rodolphe Nenert)
Date: Fri, 30 Mar 2012 14:24:56 -0500
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <158540F0F1AD27479479077742EA83C515EA8C66@CH1PRD0102MB148.prod.exchangelabs.com>
References: <4F71B9F0.8080106@charite.de>
	<158540F0F1AD27479479077742EA83C515EA8C66@CH1PRD0102MB148.prod.exchangelabs.com>
Message-ID: <CAPy7a9CfQRDROZ6U_ksCddV8pMVyGdB--Uxhr1y3k6Lz3kKsoQ@mail.gmail.com>

Hi Kasun,

what software do you use to access this adress?
I know Chrome has issue with ftp, but Firefox handle that well. (I just
remade a test).

Rodolphe

On Fri, Mar 30, 2012 at 2:04 PM, Samarasinghe, Kasun (samarakm) <
samarakm at mail.uc.edu> wrote:

> Dear Fieldtrip members,
>
> I am trying to construct a generic head model by following the tutorial
> "Build a geometrical description of the volume conduction model of the
> head". For some reason, I cannot download the zipped MRI file in the
> location : '"ftp://ftp.fcdonders.nl/pub/fieldtrip/". Any help regarding
> the correct location of this file would be appreciated.
>
> Thank you,
> Kasun
>
> --------------------------------------------
> Kasun M Samarasinghe
> Doctoral Student
> Electrical Engineering - Systems Track
> University of Cincinnati
>
>
>
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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From samarakm at mail.uc.edu  Fri Mar 30 21:42:27 2012
From: samarakm at mail.uc.edu (Samarasinghe, Kasun (samarakm))
Date: Fri, 30 Mar 2012 19:42:27 +0000
Subject: [FieldTrip] one-sample cluster test
In-Reply-To: <CAPy7a9CfQRDROZ6U_ksCddV8pMVyGdB--Uxhr1y3k6Lz3kKsoQ@mail.gmail.com>
References: <4F71B9F0.8080106@charite.de>
	<158540F0F1AD27479479077742EA83C515EA8C66@CH1PRD0102MB148.prod.exchangelabs.com>,
	<CAPy7a9CfQRDROZ6U_ksCddV8pMVyGdB--Uxhr1y3k6Lz3kKsoQ@mail.gmail.com>
Message-ID: <158540F0F1AD27479479077742EA83C515EA8C98@CH1PRD0102MB148.prod.exchangelabs.com>



Hi Rodolphe,



Yes, I can access using Firefox now, and thank you for your prompt response. I was using Chrome earlier, and yes it seems to have issues with the server.



Thank you again,

Kasun

--------------------------------------------
Kasun M Samarasinghe
Doctoral Student
Electrical Engineering - Systems Track
University of Cincinnati

________________________________
From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Rodolphe Nenert [batrod at gmail.com]
Sent: Friday, March 30, 2012 3:24 PM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] one-sample cluster test

Hi Kasun,

what software do you use to access this adress?
I know Chrome has issue with ftp, but Firefox handle that well. (I just remade a test).

Rodolphe

On Fri, Mar 30, 2012 at 2:04 PM, Samarasinghe, Kasun (samarakm) <samarakm at mail.uc.edu<mailto:samarakm at mail.uc.edu>> wrote:
Dear Fieldtrip members,

I am trying to construct a generic head model by following the tutorial "Build a geometrical description of the volume conduction model of the head". For some reason, I cannot download the zipped MRI file in the location : '"ftp://ftp.fcdonders.nl/pub/fieldtrip/". Any help regarding the correct location of this file would be appreciated.

Thank you,
Kasun

--------------------------------------------
Kasun M Samarasinghe
Doctoral Student
Electrical Engineering - Systems Track
University of Cincinnati






_______________________________________________
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 fredericroux at hotmail.de  Sat Mar 31 13:10:31 2012
From: fredericroux at hotmail.de (Frederic Roux)
Date: Sat, 31 Mar 2012 13:10:31 +0200
Subject: [FieldTrip] restrict source reconstruction to gray matter
Message-ID: <DUB113-W1405024A1BD2BE5FF28CE14B74E0@phx.gbl>



Dear all,

I read that it is possible to restrict source reconstruction to gray matter.
Can anyone give me a hint on where can I find example code on how to do it?

I was searching for it on the fieldtrip-webstite but couldn't find anything.

Any help would as always be highly appreciated.

Fred



-- 
Frédéric Roux, PhD student
Department of Neurophysiology
Max Planck Institute for Brain Research
D-60529 Frankfurt am Main
Frederic.Roux at brain.mpg.de
+49(0)69630183225


 		 	   		  
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From jan.schoffelen at donders.ru.nl  Sat Mar 31 13:30:02 2012
From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen)
Date: Sat, 31 Mar 2012 13:30:02 +0200
Subject: [FieldTrip] restrict source reconstruction to gray matter
In-Reply-To: <DUB113-W1405024A1BD2BE5FF28CE14B74E0@phx.gbl>
References: <DUB113-W1405024A1BD2BE5FF28CE14B74E0@phx.gbl>
Message-ID: <A6ECCF8A-A40D-40CA-B560-578267AEABFC@donders.ru.nl>

Hi Fred,

I am not aware of any example code on the FT-website, but I would do something like this:

mri = ft_read_mri('...');
seg = ft_volumesegment([],mri);

cfg = [];
cfg.parameter = 'gray';
cfg.smooth = 10; % or some other value
cfg.downsample = 5; % downsample with a factor of 5
seg = ft_volumedownsample(cfg, seg);

% create a dipole grid
[X,Y,Z] = ndgrid(1:seg.dim(1), 1:seg.dim(2), 1:seg.dim(3));

grid = [];
grid.pos = warp_apply(seg.transform, [X(:) Y(:) Z(:)]); clear X Y Z
grid.dim = seg.dim;
grid.inside = find(seg.gray>0.5); % the threshold value needs to be verified, you can play with the value
grid.outside = find(seg.gray<=0.5);

grid = ft_convert_units(grid, 'cm'); % I assume that the sensors are defined in cm.

Just give it a shot. I would appreciate it very much if you could try this code and maybe optimize it. When you have done that, we could make a piece of documentation on the FT-website, i.e. I will create a page (because I don't think you could do that), and you'll write the documentation ;-). Sounds like a win-win situation to me. How does it sound to you?

Best wishes,

Jan-Mathijs


On Mar 31, 2012, at 1:10 PM, Frederic Roux wrote:

> 
> Dear all,
> 
> I read that it is possible to restrict source reconstruction to gray matter.
> Can anyone give me a hint on where can I find example code on how to do it?
> 
> I was searching for it on the fieldtrip-webstite but couldn't find anything.
> 
> Any help would as always be highly appreciated.
> 
> Fred
> 
> 
> 
> -- 
> Frédéric Roux, PhD student
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> D-60529 Frankfurt am Main
> Frederic.Roux at brain.mpg.de
> +49(0)69630183225
> 
> 
> _______________________________________________
> 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

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