From r.oostenveld at FCDONDERS.RU.NL  Wed Oct  1 10:50:03 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Wed, 1 Oct 2008 10:50:03 +0200
Subject: changed default reading functions for CTF
In-Reply-To: <1222808946.17803.63.camel@kurage.nimh.nih.gov>
Message-ID: <WED.1.OCT.2008.105003.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Tom,

On 30 Sep 2008, at 23:09, Tom Holroyd wrote:
> Two questions. 1) We record data with 3rd gradient turned on by
> default.
> That is, the MEG channels have already had the background noise
> subtracted. So our datasets contain only balanced data. No further
> processing is required. Does your code take care of this case?

Hmmm, good question... I cannot immediately answer confirmative. The
data that is read will be balanced, that won't be the problem. What I
don't immediately oversee is whether the leadfield computation will
match the balanced data. In the old case it was sure not to match the
data. In the new case the reading routine should take care of that.

I don't have any 3rd order data lying around right now, so would you
please check the following
   data = preprocessing(cfg)  % with your standard config
and then look into the field
   data.grad
There should be a
   data.grad.balance
structure and
   data.grad.balance.current
string. In your case current should be G3BR.

Subsequently please check the weighing of the gradiometer coils to
channels using
   imagesc(data.grad.tra)
You should more or less see two identity matrices concatenated with
some small non-zero numbers in the rightmost part of thaht figure.
This matrix is used in the forward computation: first the field at
every individual coil is computed (keeping the coil orientation in
mind), and then the "coils" are combined to form "channels". The two
identity matrices represent the bottom and top coil, and the small
numbers in the rightmost part represent the small corrections to the
forward model required to mimic the balancing (in which also a small
part of the dipole field is subtracted from the data).

Please let us know whether those two fields are as I expect them to
be. Perhaps you could also send me (not through this email list!) a
3rd gradient dataset (preverably averaged, i.e. small MB size) for
your system, so that I can use that for testing.  You can use ftp.fcdonders.nl/pub/incoming
  or something like yousendit.com.

> 2) Why is
> the code closed source?

We discussed the release of the code in the joined context of SPM8 and
Fieldtrip with the CTF support. See below for their statement

>> ---------- Forwarded message ----------
>> From: MEG Customer Support <support at megservice.com>
>> Date: Thu, Apr 24, 2008 at 1:00 AM
>> Subject: RE: MATLAB Import/Export Routines
>> To: David Bradbury <d.bradbury at fil.ion.ucl.ac.uk>, MEG Customer
>> Support <support at megservice.com>
>> Cc: litvak.vladimir at gmail.com
>>
>>
>> Dear David (& Vladimir),
>>
>> We're most glad to hear that the issue with the stim codes may have
>> been
>> resolved.  As you say please keep us informed if it is not.
>>
>> Thank you very much for your request regarding the VSM MatLab codes.
>> Because we consider them to be covered under the systems' general
>> non-disclosure agreements you are free to use these algorithms
>> internally (i.e. by all MEG users at UCL and F.C. Donders Centre)
>> without restriction however we would like to request that you only
>> distribute these functions external to your labs in a pre-compiled
>> form.
>> Thank you for your consideration in this matter.
>>
>> With best regards,
>>
>> Brent


So I have the m-files but am not allowed to distribute them, hence the
p-files in the fieldtrip/external/ctf directory (and in spm8/external/
ctf). I guess that you as CTF user should be able to get your own copy
of the m-files from CTF support.

best regards,
Robert





----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From r.oostenveld at FCDONDERS.RU.NL  Wed Oct  1 12:42:40 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Wed, 1 Oct 2008 12:42:40 +0200
Subject: problem reading old CTF data
In-Reply-To: <f7392e897f60b.48e27315@ru.nl>
Message-ID: <WED.1.OCT.2008.124240.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Barbara (CC fieldtrip list)

The problem that you have with your CTF dataset is due to a bug in the
dataset itself. Since other people might encounter the same problem,
I'll forward the information to the FT mailing list as well.

The dataset that you are trying to read has a bug in the
headcoordinates (*.hc) file. The 5th line in the file is
   stadard left ear coil position relative to dewar (cm):
but should be
   standard left ear coil position relative to dewar (cm):
Note the missing "n" in the buggy headcoordinates file.

In the previous reading routines (read_ctf_hc, see line 182) that bug
was known and the code explicitely tested for that bug. In the new
reading routines (i.e. the ones supplied to us by CTF to handle
synthetic gradients) that bug in the HC file causes a problem.

The only solution for now that I can think of is to edit the HC file
(in a text editor) and to fix the typo by adding the "n" to "stadard".

best regards,
Robert


On 30 Sep 2008, at 18:42, Barbara Haendel wrote:

> I'm not sure what happened but I can't read in my old files anymore
> (something which already had worked about two weeks go). I also
> can't make much sense out of the error message (see below). The
> problem seems to be that FT can't read the trial definition because
> cfg.trialdef.eventtype = '?'; does not give any event information
> anymore. Could it be that something has changed lately since it was
> already working before?
> It would be great if you could help me,
> Thanks,
> Barbara
>
> cfg=[];
>    cfg.dataset='AxLiPERCEPT390405.ds';
>    cfg.continuous = 'no';
>    cfg.trialdef.eventtype = 'trial';
>    cfg = definetrial(cfg);
> evaluating trialfunction 'trialfun_general'
>
> readCTFds: You are reading CTF data for use with a software-
> application tool
> 	that is not manufactured by VSM MedTech Ltd. and has not received
> marketing
> 	clearance for clinical applications.  If CTF MEG data are processed
> by this tool,
> 	they should not be later employed for clinical and/or diagnostic
> purposes.
>
> readCPersist: Stop strings (EndOfParameters) do not balance start
> strings (WS1_).
>              (No. of start strings)-(No. of stop strings)=1.
> ??? Index exceeds matrix dimensions.
>
> Error in ==> /home/common/matlab/fieldtrip/external/ctf/
> readCTFds.p>readHc at 599
>
> Error in ==> /home/common/matlab/fieldtrip/external/ctf/
> readCTFds.p>readCTFds at 203

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From michael.wibral at WEB.DE  Thu Oct  2 16:02:18 2008
From: michael.wibral at WEB.DE (Michael Wibral)
Date: Thu, 2 Oct 2008 16:02:18 +0200
Subject: Missing dim filed after source analysis.
Message-ID: <THU.2.OCT.2008.160218.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Listuser,

I am having a little problem with the beamformer (dics) tutorial. If I run first sourceanalysis on 'data' like this:

SourceDataSingleTrial=sourceanalysis(cfg, data)

applying precomputed filters to single trials (as in the tutorial) and then feed SourceDataSingleTrial to sourcestatistics like this:

SourceStats=sourceanalysis(cfg,SourceDataSingleTrial )

Then sourcestatistics complains about a missing filed 'dim'. I can fix this problem by creating the field SourceStats.dim by hand, giving the voxel conuts in each dimension [voxX voxY voxZ] and the code runs. However, the function might also need the number of trials or the like ???

Any idea what could be the reason for sourceanalysis not producing the dim field?

Michael

----------------------------------
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From r.oostenveld at FCDONDERS.RU.NL  Thu Oct  2 17:39:32 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 2 Oct 2008 17:39:32 +0200
Subject: Missing dim filed after source analysis.
In-Reply-To: <794538785@web.de>
Message-ID: <THU.2.OCT.2008.173932.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Michael,

On 2 Oct 2008, at 16:02, Michael Wibral wrote:
> I am having a little problem with the beamformer (dics) tutorial. If
> I run first sourceanalysis on 'data' like this:
>
> SourceDataSingleTrial=sourceanalysis(cfg, data)
>
> applying precomputed filters to single trials (as in the tutorial)
> and then feed SourceDataSingleTrial to sourcestatistics like this:
>
> SourceStats=sourceanalysis(cfg,SourceDataSingleTrial )
>
> Then sourcestatistics complains about a missing filed 'dim'.

Are you working wih the latest copy of fieldtirp? If not, please see
whether that fixes the problem.

> I can fix this problem by creating the field SourceStats.dim by hand,

I presume you mean that you add dim to SourceDataSingleTrial and not
to SourceStats?

> giving the voxel conuts in each dimension [voxX voxY voxZ] and the
> code runs. However, the function might also need the number of
> trials or the like ???

The number of trials is determined in the code as
length(SourceDataSingleTrial.trial) and equals size(cfg.design,2).

> Any idea what could be the reason for sourceanalysis not producing
> the dim field?

We recently started cleaning up the representation of source data. In
the FT code there was a possible confusion about sources being
represented as a "random set of points", where each point is specified
by its position, or represented as a nicely arranged 3D volume. In the
latter case you can also specify the position of each voxel, but the
latter case is more conveniently represented using a homogenous
transformation matrix in combination with voxel indices.

This cleanup was realized in the "checkdata" function, which ensures
that the input to each FT function is as what the function expects.
The checkdata function manages backward compatibility of data
structures (i.e. still allowing to work with data that was sitting in
a mat file for a long time, and not requiring to compute the data
every time) and it tries to convert data between different
representations (i.e. volume->source_positions and the other way
around if the positions are arranged in a 3D grid).

I'll try to reproduce the problem and get back to you. For the moment
you can just add the dim field, that won't break anything.

best regards,
Robert

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From wibral at BIC.UNI-FRANKFURT.DE  Thu Oct  2 17:41:58 2008
From: wibral at BIC.UNI-FRANKFURT.DE (Michael Wibral)
Date: Thu, 2 Oct 2008 17:41:58 +0200
Subject: fix pow=pow' still necessary
Message-ID: <THU.2.OCT.2008.174158.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Listusers,

a question related to my last one. In the beamformer tutorial, the pow matrix gets transposed for each trial when going form sourceanalysis to sourcestatistics. Is that still necessary at the moment (i.e. FT20081001)?

Best Regards,
Michael

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From r.oostenveld at FCDONDERS.RU.NL  Thu Oct  2 18:07:33 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 2 Oct 2008 18:07:33 +0200
Subject: fix pow=pow' still necessary
In-Reply-To: <794649790@web.de>
Message-ID: <THU.2.OCT.2008.180733.0200.FIELDTRIP@NIC.SURFNET.NL>

On 2 Oct 2008, at 17:41, Michael Wibral wrote:

> Dear Listusers,
>
> a question related to my last one. In the beamformer tutorial, the
> pow matrix gets transposed for each trial when going form
> sourceanalysis to sourcestatistics. Is that still necessary at the
> moment (i.e. FT20081001)?

Hmm, I though that I had removed the transposing of the pow just a few
days ago on the wiki, because that is indeed not needed any more in
recent versions. Could you check the wiki once more (maybe you are
working from a cached version or from a printout)...

Robert

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From j.schoffelen at PSY.GLA.AC.UK  Fri Oct  3 22:11:49 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Fri, 3 Oct 2008 21:11:49 +0100
Subject: cross-spectrum to cross-correlogram
In-Reply-To: <200809290754.m8T7sv6F002791@ns1.intern.nin.knaw.nl>
Message-ID: <FRI.3.OCT.2008.211149.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jasper,

I did not yet completely think it through, but I see two problems
here. Obviously, you would like to verify whether multiplication in
the frequency domain is equivalent to convolution in the time
domain ;o),
actually that conjugate multiplication is equivalent to cross-
covariancing (shouldn't you use xcov, instead of xcorr?)

1 you apply a hanning taper in your frequency analysis; to make a
fair comparison you probably should specify cfg.taper='rectwin',
because your time domain data is not tapered in the xcorr-analysis
2 mathematically the convolution vs. multiplication holds when you
also take into account the 'negative frequencies' in your ifft.
However, freqanalysis does not output these in the first place
3 (sorry there's a third thing): probably you should specify the
additional option 'unbiased' when calling xcorr (or xcov), because
fft assumes circular data so the ifft'ed csd does not taper off at
the edges (which in the xcov/xcorr is due to a decrease in the number
of overlapping samples).

Hopefully these thoughts help.

Yours,

Jan-Mathijs



On Sep 29, 2008, at 8:54 AM, Jasper Poort wrote:

> CS=freq.fourierspctrm(:,1,:).*conj(freq.fourierspctrm(:,2,:));
> y = real((squeeze(mean(CS))));
> figure;plot(y)
>
> % inverse fft of cross-spectrum
> y = real(ifft(squeeze(mean(CS))));
> figure;plot(y)
>
> % compare to cross-correlation function
> [c,lags] = xcorr(mean(squeeze(wav(:,:,1)),2),mean(squeeze(wav(:,:,
> 2)),2));
> figure;plot(lags,c)


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From shehsu at INDIANA.EDU  Mon Oct  6 09:43:15 2008
From: shehsu at INDIANA.EDU (Hsu, Shen-Mou)
Date: Mon, 6 Oct 2008 03:43:15 -0400
Subject: cfg.layout and clusterplot
Message-ID: <MON.6.OCT.2008.034315.0400.FIELDTRIP@NIC.SURFNET.NL>

Dear users,

I was wondering if someone could help me sort out the following problem. I tried to plot significant clusters using clusterplot after permutation tests.  When I ran the script as below, it returned the message like this:

reverting to 151 channel CTF default
??? Error using ==> topoplotER at 330
labels in data and labels in layout do not match

Error in ==> clusterplot at 240
          topoplotER(cfg, stat);

However, I checked both cfg.layout.labels and cfg.layout.pnt. Everything seems fine.

Many thanks in advance.



My script:

%load data
load GA_N_HV_base; load GA_N_LV_base;
%load statistics
load stat_N_HVvsLV_400;
%load layout
load Sub19_ERP_HVN;

GA_N_HVvsLV = GA_N_HV_base;
GA_N_HVvsLV.avg = GA_N_HV_base.avg - GA_N_LV_base.avg;

% clusterplot
cfg = [];
cfg.alpha = 0.05;
cfg.layout = ERPdata.elec
clusterplot(cfg,stat_N_HVvsLV)

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From shehsu at INDIANA.EDU  Mon Oct  6 10:02:56 2008
From: shehsu at INDIANA.EDU (Hsu, Shen-Mou)
Date: Mon, 6 Oct 2008 04:02:56 -0400
Subject: plot the raw effects
Message-ID: <MON.6.OCT.2008.040256.0400.FIELDTRIP@NIC.SURFNET.NL>

Dear users,

I was wondering if someone could help me sort out the another problem. I tried to plot the raw effect (the difference between two conditions using the script like this

%load data
load GA_N_HV_base; load GA_N_LV_base;

GA_N_HVvsLV = GA_N_HV_base;
GA_N_HVvsLV.avg = GA_N_HV_base.avg - GA_N_LV_base.avg;

cfg = [];
cfg.xlim = [0 0.5];
cfg.channel = 'P3';
clf;
singleplotER(cfg,GA_N_HVvsLV);

However, I noticed that the graph is exactly the same as the graph from GA_N_HV_base. In other words, the singleplotER did not plot the raw effect, GA_N_HVvsLV.avg.

I am indebted to your kindness in this matter.

Shen-Mou Hsu

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From j.lange at FCDONDERS.RU.NL  Mon Oct  6 10:21:45 2008
From: j.lange at FCDONDERS.RU.NL (Jo Lange)
Date: Mon, 6 Oct 2008 10:21:45 +0200
Subject: postdoctoral position
Message-ID: <MON.6.OCT.2008.102145.0200.FIELDTRIP@NIC.SURFNET.NL>

A three-year postdoctoral position is available in the lab of Prof. Schnitzler in 
the Institute of Clinical Neuroscience and Medical Psychology at Heinrich-
Heine-University Düsseldorf, Germany. The position is available from February 
2009, funded by the European Commision (ERAT-NET NEURON). 

The successful candidate will conduct MEG experiments to study the effects 
of Deep Brain Stimulation on cortico-subcortical pathways in Parkinson’s 
disease. The project is part of an international collaboration with partners in 
Germany, Scotland, and Italy. The lab of Prof. Schnitzler offers outstanding 
experience with Deep Brain Stimulation and a whole-head MEG system.

Applicants should have a doctoral degree (PhD) in Neuroscience, Physics, 
Psychology, or related disciplines, experience with MEG recordings and an 
outstanding academic record, including publications. Expertise in Matlab and 
time-frequency analysis (FieldTrip) is desirable.

Salary follows the German Public Service Regulations. To apply, please submit 
your applications with full CV, list of publications, and three references. 
Submission deadline is the 15th of November. For more information about the 
position, contact Prof. A. Schnitzler (alfons.schnitzler at uni-duesseldorf.de) or 
Dr. J. Lange (joachim.lange at med.uni-duesseldorf.de). 

Contact Information
Prof. Dr. Alfons Schnitzler
Institute of Clinical Neuroscience and Medical Psychology
Heinrich-Heine University Düsseldorf
Universitätstr. 1
40225 Düsseldorf
Germany  
Phone: +49-211-81-13014 
Fax: +49-211-81-13015 
E-mail: alfons.schnitzler at uni-duesseldorf.de 

----------------------------------
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From A.Stancak at LIVERPOOL.AC.UK  Mon Oct  6 12:31:12 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Mon, 6 Oct 2008 11:31:12 +0100
Subject: 4D data reading
Message-ID: <MON.6.OCT.2008.113112.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear all,

  we have some problems reading 4D Neuroimaging MEG data (148 sensors). For now, we export original 4D data into BESA format, and then read those into FieldTrip. This is not optimal, as e.g. gradient coils information is not transferred into FieldTrip. We would be grateful for a plugin or a hint enabling us to read the 4D data directly into FieldTrip.

  Best wishes
  Andrej Stancak


Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12


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From j.schoffelen at PSY.GLA.AC.UK  Mon Oct  6 12:44:54 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Mon, 6 Oct 2008 11:44:54 +0100
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CAF@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <MON.6.OCT.2008.114454.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Andrej,

As far as I know, 4D data can be read in directly into fieldtrip. At
least it works with our 248-channel system.
There is no need to convert the data into whatever format, meaning
you should be able to read from the raw
datafiles directly. Please let me know if this does not work for you.

Yours,

Jan-Mathijs



On Oct 6, 2008, at 11:31 AM, Stancak, Andrej wrote:

> Dear all,
>
>   we have some problems reading 4D Neuroimaging MEG data (148
> sensors). For now, we export original 4D data into BESA format, and
> then read those into FieldTrip. This is not optimal, as e.g.
> gradient coils information is not transferred into FieldTrip. We
> would be grateful for a plugin or a hint enabling us to read the 4D
> data directly into FieldTrip.
>
>   Best wishes
>   Andrej Stancak
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>


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From venug001 at BAMA.UA.EDU  Mon Oct  6 14:22:17 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 6 Oct 2008 07:22:17 -0500
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CAF@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <MON.6.OCT.2008.072217.0500.FIELDTRIP@NIC.SURFNET.NL>

Hello everyone, I have been wrestling with these problems for a while
too.
Here is what I found: Fieldtrip/EEGLAB will read neuroscan files (.avg,
and .eeg), and will read raw data (e,..)from 4D.
I believe that EEGLAB/Fieldtrip may not have a template for the 148-
Channel system co-ordinates. Christian and Don Rojas created one for me
in early April this year.
A FIF export from the 4D system may also solve this problem. Stephen
Moratti helped me with this a while a ago. It puts out three
files .xyz, .4D and the original e,.. file. But, if the .xyz file which
has coordinates for 148 channels does not match with the template, then
the data will not load. I think for one may have to load a create a 148
channel template for this purpose. This is my experience with EEGLAB,
and I think that they underlying engine is the same for both EEGLAB and
Fieldtrip
Then again, I may be completely wrong about everything except the
templates that were created for me.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear all,
>
>   we have some problems reading 4D Neuroimaging MEG data (148
> sensors). For now, we export original 4D data into BESA format, and
> then read those into FieldTrip. This is not optimal, as e.g. gradient
> coils information is not transferred into FieldTrip. We would be
> grateful for a plugin or a hint enabling us to read the 4D data
> directly into FieldTrip.
>
>   Best wishes
>   Andrej Stancak
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From a.capilla at PSY.GLA.AC.UK  Mon Oct  6 15:02:44 2008
From: a.capilla at PSY.GLA.AC.UK (Almudena Capilla)
Date: Mon, 6 Oct 2008 14:02:44 +0100
Subject: 4D data reading
In-Reply-To: <1223295737.48ea02f9caab1@bamamail.ua.edu>
Message-ID: <MON.6.OCT.2008.140244.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Gopa,

I have got a template for the 4D - 148 channels system. I could give it to
the Fieldtrip developers if this is helpful for other users of this system.

Best,
Almu

-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Gopakumar Venugopalan
Sent: 06 October 2008 13:22
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading

Hello everyone, I have been wrestling with these problems for a while
too.
Here is what I found: Fieldtrip/EEGLAB will read neuroscan files (.avg,
and .eeg), and will read raw data (e,..)from 4D.
I believe that EEGLAB/Fieldtrip may not have a template for the 148-
Channel system co-ordinates. Christian and Don Rojas created one for me
in early April this year.
A FIF export from the 4D system may also solve this problem. Stephen
Moratti helped me with this a while a ago. It puts out three
files .xyz, .4D and the original e,.. file. But, if the .xyz file which
has coordinates for 148 channels does not match with the template, then
the data will not load. I think for one may have to load a create a 148
channel template for this purpose. This is my experience with EEGLAB,
and I think that they underlying engine is the same for both EEGLAB and
Fieldtrip
Then again, I may be completely wrong about everything except the
templates that were created for me.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear all,
>
>   we have some problems reading 4D Neuroimaging MEG data (148
> sensors). For now, we export original 4D data into BESA format, and
> then read those into FieldTrip. This is not optimal, as e.g. gradient
> coils information is not transferred into FieldTrip. We would be
> grateful for a plugin or a hint enabling us to read the 4D data
> directly into FieldTrip.
>
>   Best wishes
>   Andrej Stancak
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the
FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
and EEG analysis. See also
http://listserv.surfnet.nl/archives/fieldtrip.html and
http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From venug001 at BAMA.UA.EDU  Mon Oct  6 15:12:33 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 6 Oct 2008 08:12:33 -0500
Subject: 4D data reading
In-Reply-To: <001001c927b3$e4e14e90$5757d182@DEPT6788A09EF4>
Message-ID: <MON.6.OCT.2008.081233.0500.FIELDTRIP@NIC.SURFNET.NL>

Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
the other users. There was also a discussion about whether the systems
were using third order gradiometers and/or magnetometers as the
reference. There are mail postings in that thread.
Everyone: I apologize for the typos in my hastily composed response
earlier.
regards
gopa


Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:

> Dear Gopa,
>
> I have got a template for the 4D - 148 channels system. I could give
> it to
> the Fieldtrip developers if this is helpful for other users of this
> system.
>
> Best,
> Almu
>
> -----Original Message-----
> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf
> Of Gopakumar Venugopalan
> Sent: 06 October 2008 13:22
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Hello everyone, I have been wrestling with these problems for a while
>
> too.
> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> (.avg,
> and .eeg), and will read raw data (e,..)from 4D.
> I believe that EEGLAB/Fieldtrip may not have a template for the 148-
> Channel system co-ordinates. Christian and Don Rojas created one for
> me
> in early April this year.
> A FIF export from the 4D system may also solve this problem. Stephen
>
> Moratti helped me with this a while a ago. It puts out three
> files .xyz, .4D and the original e,.. file. But, if the .xyz file
> which
> has coordinates for 148 channels does not match with the template,
> then
> the data will not load. I think for one may have to load a create a
> 148
> channel template for this purpose. This is my experience with EEGLAB,
>
> and I think that they underlying engine is the same for both EEGLAB
> and
> Fieldtrip
> Then again, I may be completely wrong about everything except the
> templates that were created for me.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
> > Dear all,
> >
> >   we have some problems reading 4D Neuroimaging MEG data (148
> > sensors). For now, we export original 4D data into BESA format,
> and
> > then read those into FieldTrip. This is not optimal, as e.g.
> gradient
> > coils information is not transferred into FieldTrip. We would be
> > grateful for a plugin or a hint enabling us to read the 4D data
> > directly into FieldTrip.
> >
> >   Best wishes
> >   Andrej Stancak
> >
> >
> > Prof. Andrej Stancak, PhD.
> > The University of Liverpool
> > School of Psychology
> > The Eleanor Rathbone Building
> > Bedford Street South, Room 209
> > Liverpool
> > L69 7ZA
> >
> > E:mail: a.stancak at liverpool.ac.uk  (primary)
> >            stancak at centrum.cz (secondary)
> > Phone: 0151 7946951
> > Office hours: Monday 10-12, Wednesday 10-12
> >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for
> MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From A.Stancak at LIVERPOOL.AC.UK  Mon Oct  6 16:11:20 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Mon, 6 Oct 2008 15:11:20 +0100
Subject: 4D data reading
Message-ID: <MON.6.OCT.2008.151120.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Gopa and Almu,

  do I understand the procedure correctly: we should export data from 4D in FIF format (currently we export in native e,... (binary), and the text files for the header and the surface points), and then use a modified xyz file containing the layout of 148 sensors. I would be grateful for one sample xyz file to see whether we can read data this way. Naturally, the best would be to incorporate it into the reading procedures of FieldTrip.

Best wishes
Andrej


Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
Sent: Mon 06/10/2008 14:12
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian 
Weinbruch and Arno (EEGLAB) may be the ones who can make it work for 
the other users. There was also a discussion about whether the systems 
were using third order gradiometers and/or magnetometers as the 
reference. There are mail postings in that thread.
Everyone: I apologize for the typos in my hastily composed response 
earlier.
regards
gopa


Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:

> Dear Gopa,
> 
> I have got a template for the 4D - 148 channels system. I could give
> it to
> the Fieldtrip developers if this is helpful for other users of this
> system.
> 
> Best,
> Almu
> 
> -----Original Message-----
> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf
> Of Gopakumar Venugopalan
> Sent: 06 October 2008 13:22
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
> 
> Hello everyone, I have been wrestling with these problems for a while
> 
> too.
> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> (.avg, 
> and .eeg), and will read raw data (e,..)from 4D.
> I believe that EEGLAB/Fieldtrip may not have a template for the 148-
> Channel system co-ordinates. Christian and Don Rojas created one for
> me 
> in early April this year.
> A FIF export from the 4D system may also solve this problem. Stephen
> 
> Moratti helped me with this a while a ago. It puts out three 
> files .xyz, .4D and the original e,.. file. But, if the .xyz file
> which 
> has coordinates for 148 channels does not match with the template,
> then 
> the data will not load. I think for one may have to load a create a
> 148 
> channel template for this purpose. This is my experience with EEGLAB,
> 
> and I think that they underlying engine is the same for both EEGLAB
> and 
> Fieldtrip
> Then again, I may be completely wrong about everything except the 
> templates that were created for me.
> regards
> gopa
> 
> 
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> 
> > Dear all,
> > 
> >   we have some problems reading 4D Neuroimaging MEG data (148
> > sensors). For now, we export original 4D data into BESA format,
> and
> > then read those into FieldTrip. This is not optimal, as e.g.
> gradient
> > coils information is not transferred into FieldTrip. We would be
> > grateful for a plugin or a hint enabling us to read the 4D data
> > directly into FieldTrip.
> > 
> >   Best wishes
> >   Andrej Stancak
> > 
> > 
> > Prof. Andrej Stancak, PhD. 
> > The University of Liverpool
> > School of Psychology
> > The Eleanor Rathbone Building
> > Bedford Street South, Room 209
> > Liverpool
> > L69 7ZA
> > 
> > E:mail: a.stancak at liverpool.ac.uk  (primary)
> >            stancak at centrum.cz (secondary)
> > Phone: 0151 7946951
> > Office hours: Monday 10-12, Wednesday 10-12
> > 
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for
> MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
-------------- next part --------------
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From venug001 at BAMA.UA.EDU  Mon Oct  6 16:31:28 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 6 Oct 2008 09:31:28 -0500
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CB0@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <MON.6.OCT.2008.093128.0500.FIELDTRIP@NIC.SURFNET.NL>

Sure will send you those files. Please remember in my files there are
only 146 channel locations as we turned off two channels.I also have a
matlab file from Don Rojas for the 148 channel layout and a file which
he created for the 146 channel layout. Please give some time today, as
I run those programs on a different machine.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopa and Almu,
>
>   do I understand the procedure correctly: we should export data from
> 4D in FIF format (currently we export in native e,... (binary), and
> the text files for the header and the surface points), and then use a
> modified xyz file containing the layout of 148 sensors. I would be
> grateful for one sample xyz file to see whether we can read data this
> way. Naturally, the best would be to incorporate it into the reading
> procedures of FieldTrip.
>
> Best wishes
> Andrej
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 14:12
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>
> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>
> the other users. There was also a discussion about whether the
> systems
> were using third order gradiometers and/or magnetometers as the
> reference. There are mail postings in that thread.
> Everyone: I apologize for the typos in my hastily composed response
> earlier.
> regards
> gopa
>
>
> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>
> > Dear Gopa,
> >
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of
> this
> > system.
> >
> > Best,
> > Almu
> >
> > -----Original Message-----
> > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> On
> > Behalf
> > Of Gopakumar Venugopalan
> > Sent: 06 October 2008 13:22
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> >
> > Hello everyone, I have been wrestling with these problems for a
> while
> >
> > too.
> > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > (.avg,
> > and .eeg), and will read raw data (e,..)from 4D.
> > I believe that EEGLAB/Fieldtrip may not have a template for the
> 148-
> > Channel system co-ordinates. Christian and Don Rojas created one
> for
> > me
> > in early April this year.
> > A FIF export from the 4D system may also solve this problem.
> Stephen
> >
> > Moratti helped me with this a while a ago. It puts out three
> > files .xyz, .4D and the original e,.. file. But, if the .xyz file
> > which
> > has coordinates for 148 channels does not match with the template,
> > then
> > the data will not load. I think for one may have to load a create
> a
> > 148
> > channel template for this purpose. This is my experience with
> EEGLAB,
> >
> > and I think that they underlying engine is the same for both
> EEGLAB
> > and
> > Fieldtrip
> > Then again, I may be completely wrong about everything except the
> > templates that were created for me.
> > regards
> > gopa
> >
> >
> > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> >
> > > Dear all,
> > >
> > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > sensors). For now, we export original 4D data into BESA format,
> > and
> > > then read those into FieldTrip. This is not optimal, as e.g.
> > gradient
> > > coils information is not transferred into FieldTrip. We would be
> > > grateful for a plugin or a hint enabling us to read the 4D data
> > > directly into FieldTrip.
> > >
> > >   Best wishes
> > >   Andrej Stancak
> > >
> > >
> > > Prof. Andrej Stancak, PhD.
> > > The University of Liverpool
> > > School of Psychology
> > > The Eleanor Rathbone Building
> > > Bedford Street South, Room 209
> > > Liverpool
> > > L69 7ZA
> > >
> > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > >            stancak at centrum.cz (secondary)
> > > Phone: 0151 7946951
> > > Office hours: Monday 10-12, Wednesday 10-12
> > >
> > >
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the
> > FieldTrip  toolbox, to share experiences and to discuss new ideas
> for
> > MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From j.schoffelen at PSY.GLA.AC.UK  Mon Oct  6 16:54:57 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Mon, 6 Oct 2008 15:54:57 +0100
Subject: 4D data reading
In-Reply-To: <1223303488.48ea21405717d@bamamail.ua.edu>
Message-ID: <MON.6.OCT.2008.155457.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Andrej, dear Gopa,

Sorry to bother you again, but I tried to make a point in my last
mail that it is not necessary to intermediately convert your raw
epoched or continuous 4D-data into another format, prior to be able
to read it into Fieldtrip. Of course you are free to do so, but the
most natural way to me would seem to work on the raw datafiles
directly. Fieldtrip should support this and it has reading routines
for the raw data-file (beginning with e, or c,), the config-file, and
the file containing the digitized head-surface positions.
You should be able to obtain the header information directly by
calling: hdr = read_header('e,thenameofyourrawdatafile') (give or
take an accidental 'keyboard'-statement in the low-level function
read_4d_hdr, this will be fixed in tonight's release version: if it
occurs now, just type dbcont on the command line when it prompts:
K>>) As far as I know hdr contains a structure grad, which specifies
the sensor-positions. At least it works on our Glaswegian 248-sensor
system.

Yours,

Jan-Mathijs


On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:

> Sure will send you those files. Please remember in my files there are
> only 146 channel locations as we turned off two channels.I also have a
> matlab file from Don Rojas for the 148 channel layout and a file which
> he created for the 146 channel layout. Please give some time today, as
> I run those programs on a different machine.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
>> Dear Gopa and Almu,
>>
>>   do I understand the procedure correctly: we should export data from
>> 4D in FIF format (currently we export in native e,... (binary), and
>> the text files for the header and the surface points), and then use a
>> modified xyz file containing the layout of 148 sensors. I would be
>> grateful for one sample xyz file to see whether we can read data this
>> way. Naturally, the best would be to incorporate it into the reading
>> procedures of FieldTrip.
>>
>> Best wishes
>> Andrej
>>
>>
>> Prof. Andrej Stancak, PhD.
>> The University of Liverpool
>> School of Psychology
>> The Eleanor Rathbone Building
>> Bedford Street South, Room 209
>> Liverpool
>> L69 7ZA
>>
>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>            stancak at centrum.cz (secondary)
>> Phone: 0151 7946951
>> Office hours: Monday 10-12, Wednesday 10-12
>>
>>
>>
>> -----Original Message-----
>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>> Sent: Mon 06/10/2008 14:12
>> To: FIELDTRIP at NIC.SURFNET.NL
>> Subject: Re: [FIELDTRIP] 4D data reading
>>
>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>
>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>
>> the other users. There was also a discussion about whether the
>> systems
>> were using third order gradiometers and/or magnetometers as the
>> reference. There are mail postings in that thread.
>> Everyone: I apologize for the typos in my hastily composed response
>> earlier.
>> regards
>> gopa
>>
>>
>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>
>>> Dear Gopa,
>>>
>>> I have got a template for the 4D - 148 channels system. I could
>> give
>>> it to
>>> the Fieldtrip developers if this is helpful for other users of
>> this
>>> system.
>>>
>>> Best,
>>> Almu
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>> On
>>> Behalf
>>> Of Gopakumar Venugopalan
>>> Sent: 06 October 2008 13:22
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Hello everyone, I have been wrestling with these problems for a
>> while
>>>
>>> too.
>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>> (.avg,
>>> and .eeg), and will read raw data (e,..)from 4D.
>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>> 148-
>>> Channel system co-ordinates. Christian and Don Rojas created one
>> for
>>> me
>>> in early April this year.
>>> A FIF export from the 4D system may also solve this problem.
>> Stephen
>>>
>>> Moratti helped me with this a while a ago. It puts out three
>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>> which
>>> has coordinates for 148 channels does not match with the template,
>>> then
>>> the data will not load. I think for one may have to load a create
>> a
>>> 148
>>> channel template for this purpose. This is my experience with
>> EEGLAB,
>>>
>>> and I think that they underlying engine is the same for both
>> EEGLAB
>>> and
>>> Fieldtrip
>>> Then again, I may be completely wrong about everything except the
>>> templates that were created for me.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>
>>>> Dear all,
>>>>
>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>> sensors). For now, we export original 4D data into BESA format,
>>> and
>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>> gradient
>>>> coils information is not transferred into FieldTrip. We would be
>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>> directly into FieldTrip.
>>>>
>>>>   Best wishes
>>>>   Andrej Stancak
>>>>
>>>>
>>>> Prof. Andrej Stancak, PhD.
>>>> The University of Liverpool
>>>> School of Psychology
>>>> The Eleanor Rathbone Building
>>>> Bedford Street South, Room 209
>>>> Liverpool
>>>> L69 7ZA
>>>>
>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>            stancak at centrum.cz (secondary)
>>>> Phone: 0151 7946951
>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between
>> users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the
>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for
>>> MEG
>>> and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From venug001 at BAMA.UA.EDU  Mon Oct  6 17:03:35 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 6 Oct 2008 10:03:35 -0500
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CB0@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <MON.6.OCT.2008.100335.0500.FIELDTRIP@NIC.SURFNET.NL>

Andrej, I see an error in my mail below. The three files
.xyz, .m4d and the acutal pdf is produced using the command:

pdf2set -u

You post the selection in the propreitary MSI environment, then type in
the command given above. It will put out the three files mentioned for
each data set.
I shall include only the .xyz and .m4d files from grand averaged files,
as they do not contain any identifiable information.
I believe that the .m4d file is also called the header file and
the .xyz is called the location or coordinate file.
Ken Velarde was immensely helpful with this, as were Christian
Weinbruch, and Don Rojas. Don Rojas's colleague Dr. Eugene Kronberg
also has  created an interface that can read 4D data, and he was going
to create such a template as well--as per our last email exchange.
I also have a xls2matlab function that I used to create my own
template, as the sensor location file is usually a product of
individual MEG systems. If I may have mislead anyone it is
unintentional as I am constantly learning.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopa and Almu,
>
>   do I understand the procedure correctly: we should export data from
> 4D in FIF format (currently we export in native e,... (binary), and
> the text files for the header and the surface points), and then use a
> modified xyz file containing the layout of 148 sensors. I would be
> grateful for one sample xyz file to see whether we can read data this
> way. Naturally, the best would be to incorporate it into the reading
> procedures of FieldTrip.
>
> Best wishes
> Andrej
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 14:12
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>
> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>
> the other users. There was also a discussion about whether the
> systems
> were using third order gradiometers and/or magnetometers as the
> reference. There are mail postings in that thread.
> Everyone: I apologize for the typos in my hastily composed response
> earlier.
> regards
> gopa
>
>
> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>
> > Dear Gopa,
> >
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of
> this
> > system.
> >
> > Best,
> > Almu
> >
> > -----Original Message-----
> > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> On
> > Behalf
> > Of Gopakumar Venugopalan
> > Sent: 06 October 2008 13:22
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> >
> > Hello everyone, I have been wrestling with these problems for a
> while
> >
> > too.
> > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > (.avg,
> > and .eeg), and will read raw data (e,..)from 4D.
> > I believe that EEGLAB/Fieldtrip may not have a template for the
> 148-
> > Channel system co-ordinates. Christian and Don Rojas created one
> for
> > me
> > in early April this year.
> > A FIF export from the 4D system may also solve this problem.
> Stephen
> >
> > Moratti helped me with this a while a ago. It puts out three
> > files .xyz, .4D and the original e,.. file. But, if the .xyz file
> > which
> > has coordinates for 148 channels does not match with the template,
> > then
> > the data will not load. I think for one may have to load a create
> a
> > 148
> > channel template for this purpose. This is my experience with
> EEGLAB,
> >
> > and I think that they underlying engine is the same for both
> EEGLAB
> > and
> > Fieldtrip
> > Then again, I may be completely wrong about everything except the
> > templates that were created for me.
> > regards
> > gopa
> >
> >
> > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> >
> > > Dear all,
> > >
> > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > sensors). For now, we export original 4D data into BESA format,
> > and
> > > then read those into FieldTrip. This is not optimal, as e.g.
> > gradient
> > > coils information is not transferred into FieldTrip. We would be
> > > grateful for a plugin or a hint enabling us to read the 4D data
> > > directly into FieldTrip.
> > >
> > >   Best wishes
> > >   Andrej Stancak
> > >
> > >
> > > Prof. Andrej Stancak, PhD.
> > > The University of Liverpool
> > > School of Psychology
> > > The Eleanor Rathbone Building
> > > Bedford Street South, Room 209
> > > Liverpool
> > > L69 7ZA
> > >
> > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > >            stancak at centrum.cz (secondary)
> > > Phone: 0151 7946951
> > > Office hours: Monday 10-12, Wednesday 10-12
> > >
> > >
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the
> > FieldTrip  toolbox, to share experiences and to discuss new ideas
> for
> > MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From A.Stancak at LIVERPOOL.AC.UK  Mon Oct  6 17:45:08 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Mon, 6 Oct 2008 16:45:08 +0100
Subject: 4D data reading
Message-ID: <MON.6.OCT.2008.164508.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Gopa,

 thanks you so much for the files and infomation, I will follow your path, and try what you suggest tomorrow. Jan-Mathijs thinks it should be also possible to read directly from the raw data + config file, and I will try this way too. I will report to the community once I am done as it may be useful for 148-4D researchers.

 Best wishes
 Andrej

Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
Sent: Mon 06/10/2008 16:03
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Andrej, I see an error in my mail below. The three files
.xyz, .m4d and the acutal pdf is produced using the command:

pdf2set -u

You post the selection in the propreitary MSI environment, then type in 
the command given above. It will put out the three files mentioned for 
each data set.
I shall include only the .xyz and .m4d files from grand averaged files, 
as they do not contain any identifiable information.
I believe that the .m4d file is also called the header file and 
the .xyz is called the location or coordinate file.
Ken Velarde was immensely helpful with this, as were Christian 
Weinbruch, and Don Rojas. Don Rojas's colleague Dr. Eugene Kronberg 
also has  created an interface that can read 4D data, and he was going 
to create such a template as well--as per our last email exchange.
I also have a xls2matlab function that I used to create my own 
template, as the sensor location file is usually a product of 
individual MEG systems. If I may have mislead anyone it is 
unintentional as I am constantly learning.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopa and Almu,
> 
>   do I understand the procedure correctly: we should export data from
> 4D in FIF format (currently we export in native e,... (binary), and
> the text files for the header and the surface points), and then use a
> modified xyz file containing the layout of 148 sensors. I would be
> grateful for one sample xyz file to see whether we can read data this
> way. Naturally, the best would be to incorporate it into the reading
> procedures of FieldTrip.
> 
> Best wishes
> Andrej
> 
> 
> Prof. Andrej Stancak, PhD. 
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
> 
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
> 
> 
> 
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 14:12
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>  
> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
> 
> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
> 
> the other users. There was also a discussion about whether the
> systems 
> were using third order gradiometers and/or magnetometers as the 
> reference. There are mail postings in that thread.
> Everyone: I apologize for the typos in my hastily composed response 
> earlier.
> regards
> gopa
> 
> 
> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
> 
> > Dear Gopa,
> > 
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of
> this
> > system.
> > 
> > Best,
> > Almu
> > 
> > -----Original Message-----
> > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> On
> > Behalf
> > Of Gopakumar Venugopalan
> > Sent: 06 October 2008 13:22
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> > 
> > Hello everyone, I have been wrestling with these problems for a
> while
> > 
> > too.
> > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > (.avg, 
> > and .eeg), and will read raw data (e,..)from 4D.
> > I believe that EEGLAB/Fieldtrip may not have a template for the
> 148-
> > Channel system co-ordinates. Christian and Don Rojas created one
> for
> > me 
> > in early April this year.
> > A FIF export from the 4D system may also solve this problem.
> Stephen
> > 
> > Moratti helped me with this a while a ago. It puts out three 
> > files .xyz, .4D and the original e,.. file. But, if the .xyz file
> > which 
> > has coordinates for 148 channels does not match with the template,
> > then 
> > the data will not load. I think for one may have to load a create
> a
> > 148 
> > channel template for this purpose. This is my experience with
> EEGLAB,
> > 
> > and I think that they underlying engine is the same for both
> EEGLAB
> > and 
> > Fieldtrip
> > Then again, I may be completely wrong about everything except the 
> > templates that were created for me.
> > regards
> > gopa
> > 
> > 
> > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> > 
> > > Dear all,
> > > 
> > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > sensors). For now, we export original 4D data into BESA format,
> > and
> > > then read those into FieldTrip. This is not optimal, as e.g.
> > gradient
> > > coils information is not transferred into FieldTrip. We would be
> > > grateful for a plugin or a hint enabling us to read the 4D data
> > > directly into FieldTrip.
> > > 
> > >   Best wishes
> > >   Andrej Stancak
> > > 
> > > 
> > > Prof. Andrej Stancak, PhD. 
> > > The University of Liverpool
> > > School of Psychology
> > > The Eleanor Rathbone Building
> > > Bedford Street South, Room 209
> > > Liverpool
> > > L69 7ZA
> > > 
> > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > >            stancak at centrum.cz (secondary)
> > > Phone: 0151 7946951
> > > Office hours: Monday 10-12, Wednesday 10-12
> > > 
> > > 
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > > 
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the
> > FieldTrip  toolbox, to share experiences and to discuss new ideas
> for
> > MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
-------------- next part --------------
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From A.Stancak at LIVERPOOL.AC.UK  Mon Oct  6 17:50:37 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Mon, 6 Oct 2008 16:50:37 +0100
Subject: 4D data reading
Message-ID: <MON.6.OCT.2008.165037.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs,

  thanks for further information. I need to copy the config file from the MSI server as that is not saved automatically with our
recordings, and then give another try. 

Best wishes
Andrej


Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
Sent: Mon 06/10/2008 15:54
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Dear Andrej, dear Gopa,

Sorry to bother you again, but I tried to make a point in my last  
mail that it is not necessary to intermediately convert your raw  
epoched or continuous 4D-data into another format, prior to be able  
to read it into Fieldtrip. Of course you are free to do so, but the  
most natural way to me would seem to work on the raw datafiles  
directly. Fieldtrip should support this and it has reading routines  
for the raw data-file (beginning with e, or c,), the config-file, and  
the file containing the digitized head-surface positions.
You should be able to obtain the header information directly by  
calling: hdr = read_header('e,thenameofyourrawdatafile') (give or  
take an accidental 'keyboard'-statement in the low-level function  
read_4d_hdr, this will be fixed in tonight's release version: if it  
occurs now, just type dbcont on the command line when it prompts:  
K>>) As far as I know hdr contains a structure grad, which specifies  
the sensor-positions. At least it works on our Glaswegian 248-sensor  
system.

Yours,

Jan-Mathijs


On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:

> Sure will send you those files. Please remember in my files there are
> only 146 channel locations as we turned off two channels.I also have a
> matlab file from Don Rojas for the 148 channel layout and a file which
> he created for the 146 channel layout. Please give some time today, as
> I run those programs on a different machine.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
>> Dear Gopa and Almu,
>>
>>   do I understand the procedure correctly: we should export data from
>> 4D in FIF format (currently we export in native e,... (binary), and
>> the text files for the header and the surface points), and then use a
>> modified xyz file containing the layout of 148 sensors. I would be
>> grateful for one sample xyz file to see whether we can read data this
>> way. Naturally, the best would be to incorporate it into the reading
>> procedures of FieldTrip.
>>
>> Best wishes
>> Andrej
>>
>>
>> Prof. Andrej Stancak, PhD.
>> The University of Liverpool
>> School of Psychology
>> The Eleanor Rathbone Building
>> Bedford Street South, Room 209
>> Liverpool
>> L69 7ZA
>>
>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>            stancak at centrum.cz (secondary)
>> Phone: 0151 7946951
>> Office hours: Monday 10-12, Wednesday 10-12
>>
>>
>>
>> -----Original Message-----
>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>> Sent: Mon 06/10/2008 14:12
>> To: FIELDTRIP at NIC.SURFNET.NL
>> Subject: Re: [FIELDTRIP] 4D data reading
>>
>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>
>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>
>> the other users. There was also a discussion about whether the
>> systems
>> were using third order gradiometers and/or magnetometers as the
>> reference. There are mail postings in that thread.
>> Everyone: I apologize for the typos in my hastily composed response
>> earlier.
>> regards
>> gopa
>>
>>
>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>
>>> Dear Gopa,
>>>
>>> I have got a template for the 4D - 148 channels system. I could
>> give
>>> it to
>>> the Fieldtrip developers if this is helpful for other users of
>> this
>>> system.
>>>
>>> Best,
>>> Almu
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>> On
>>> Behalf
>>> Of Gopakumar Venugopalan
>>> Sent: 06 October 2008 13:22
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Hello everyone, I have been wrestling with these problems for a
>> while
>>>
>>> too.
>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>> (.avg,
>>> and .eeg), and will read raw data (e,..)from 4D.
>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>> 148-
>>> Channel system co-ordinates. Christian and Don Rojas created one
>> for
>>> me
>>> in early April this year.
>>> A FIF export from the 4D system may also solve this problem.
>> Stephen
>>>
>>> Moratti helped me with this a while a ago. It puts out three
>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>> which
>>> has coordinates for 148 channels does not match with the template,
>>> then
>>> the data will not load. I think for one may have to load a create
>> a
>>> 148
>>> channel template for this purpose. This is my experience with
>> EEGLAB,
>>>
>>> and I think that they underlying engine is the same for both
>> EEGLAB
>>> and
>>> Fieldtrip
>>> Then again, I may be completely wrong about everything except the
>>> templates that were created for me.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>
>>>> Dear all,
>>>>
>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>> sensors). For now, we export original 4D data into BESA format,
>>> and
>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>> gradient
>>>> coils information is not transferred into FieldTrip. We would be
>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>> directly into FieldTrip.
>>>>
>>>>   Best wishes
>>>>   Andrej Stancak
>>>>
>>>>
>>>> Prof. Andrej Stancak, PhD.
>>>> The University of Liverpool
>>>> School of Psychology
>>>> The Eleanor Rathbone Building
>>>> Bedford Street South, Room 209
>>>> Liverpool
>>>> L69 7ZA
>>>>
>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>            stancak at centrum.cz (secondary)
>>>> Phone: 0151 7946951
>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between
>> users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the
>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for
>>> MEG
>>> and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users  
> of the FieldTrip  toolbox, to share experiences and to discuss new  
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ 
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From r.oostenveld at FCDONDERS.RU.NL  Tue Oct  7 09:19:29 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Tue, 7 Oct 2008 09:19:29 +0200
Subject: 4D data reading
In-Reply-To: <001001c927b3$e4e14e90$5757d182@DEPT6788A09EF4>
Message-ID: <TUE.7.OCT.2008.091929.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear all,

I have received the layout from Almu and have added the 4D148.lay
layout to the fieldtirp/template directory (where the other layouts
are now also to be found). See attached for how it looks.

thanks,
Robert


On 6 Oct 2008, at 15:02, Almudena Capilla wrote:

> Dear Gopa,
>
> I have got a template for the 4D - 148 channels system. I could give
> it to
> the Fieldtrip developers if this is helpful for other users of this
> system.
>
> Best,
> Almu



----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

From venug001 at BAMA.UA.EDU  Tue Oct  7 13:11:41 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Tue, 7 Oct 2008 06:11:41 -0500
Subject: 4D data reading
In-Reply-To: <5E2A6C3F-3335-4B61-A24E-D608947C471D@fcdonders.ru.nl>
Message-ID: <TUE.7.OCT.2008.061141.0500.FIELDTRIP@NIC.SURFNET.NL>

Dear Almu, Robert, fantastic. Is there anyway this can be incorporated
with EEGLAB? I know that is a separate topic, but as Robert will tell,
EEGLAB uses many Fieldtrip routines. Thanking all of you.
regards
gopa


Quoting Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>:

> Dear all,
>
> I have received the layout from Almu and have added the 4D148.lay
> layout to the fieldtirp/template directory (where the other layouts
>
> are now also to be found). See attached for how it looks.
>
> thanks,
> Robert
>
>
> On 6 Oct 2008, at 15:02, Almudena Capilla wrote:
>
> > Dear Gopa,
> >
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of this
>
> > system.
> >
> > Best,
> > Almu
>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From venug001 at BAMA.UA.EDU  Tue Oct  7 14:26:19 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Tue, 7 Oct 2008 07:26:19 -0500
Subject: 4D data reading
In-Reply-To: <5E2A6C3F-3335-4B61-A24E-D608947C471D@fcdonders.ru.nl>
Message-ID: <TUE.7.OCT.2008.072619.0500.FIELDTRIP@NIC.SURFNET.NL>

Robert, (I know I used to address you more formally than that!), is
there a reason why some channels are a different color than others?
Is there a way that a t-test say NC versus NIC will show up for
significances in Fieldtrip/EEGLAB for all of the 148 channels. I can do
that my dissertation will really look nice. I shall be able to show the
regions where the N400 was significant and contrast it to the regions
where the P600 was significant. Thanks in advance.
regards
gopa

Quoting Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>:

> Dear all,
>
> I have received the layout from Almu and have added the 4D148.lay
> layout to the fieldtirp/template directory (where the other layouts
>
> are now also to be found). See attached for how it looks.
>
> thanks,
> Robert
>
>
> On 6 Oct 2008, at 15:02, Almudena Capilla wrote:
>
> > Dear Gopa,
> >
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of this
>
> > system.
> >
> > Best,
> > Almu
>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From r.oostenveld at FCDONDERS.RU.NL  Tue Oct  7 15:18:47 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Tue, 7 Oct 2008 15:18:47 +0200
Subject: 4D data reading
In-Reply-To: <1223377901.48eb43ed8a08b@bamamail.ua.edu>
Message-ID: <TUE.7.OCT.2008.151847.0200.FIELDTRIP@NIC.SURFNET.NL>

On 7 Oct 2008, at 13:11, Gopakumar Venugopalan wrote:

> Dear Almu, Robert, fantastic. Is there anyway this can be incorporated
> with EEGLAB? I know that is a separate topic, but as Robert will tell,
> EEGLAB uses many Fieldtrip routines. Thanking all of you.
> regards
> gopa

Although EEGLAB also includes a function that goes with the name
"topoplot", just like FIELDTRIP, the two toolboxes do not share any
functionality for plotting. So the answer is no, the 4D148 layout
cannot be used in EEGLAB.

Recent EEGLAB versions (at least the "current" version) do allow to
use the same low level reading functions as used in FieldTrip. That is
done by selecting in eeglab: "file -> import -> from other formats
using fileio". You probably would want to replace the fileio version
included in eeglab with the latest one included in fieldtrip (or
available from http://www2.ru.nl/fcdonders/fieldtrip/doku.php?id=fieldtrip:development:fileio)
.

best regards,
Robert

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From r.oostenveld at FCDONDERS.RU.NL  Tue Oct  7 15:24:45 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Tue, 7 Oct 2008 15:24:45 +0200
Subject: cfg.layout and clusterplot
In-Reply-To: <7F00B6A0D4D0674E80A6C1D6DA873B5701CC652B55@iu-mssg-mbx05.ads.iu.edu>
Message-ID: <TUE.7.OCT.2008.152445.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi

On 6 Oct 2008, at 9:43, Hsu, Shen-Mou wrote:
> I was wondering if someone could help me sort out the following
> problem. I tried to plot significant clusters using clusterplot
> after permutation tests.  When I ran the script as below, it
> returned the message like this:
>
> reverting to 151 channel CTF default

are you working with 151 channel CTF data. If not, then this explains
it.

> ??? Error using ==> topoplotER at 330
> labels in data and labels in layout do not match
>
> Error in ==> clusterplot at 240
>          topoplotER(cfg, stat);
>
> However, I checked both cfg.layout.labels and cfg.layout.pnt.
> Everything seems fine.

You might want to check with the matlab debugger that the COMNT and
SCALE are not messing it up. These two fake channels are included in
the layout files to position the comment and scale. Recently quite
some changes were made to plotting, so you might also want to download
the latest version to test whether the problem persists.

best regards,
Robert

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From A.Stancak at LIVERPOOL.AC.UK  Tue Oct  7 17:44:22 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Tue, 7 Oct 2008 16:44:22 +0100
Subject: 4D data reading
Message-ID: <TUE.7.OCT.2008.164422.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Gopakumar,

  I followed your advice (pdf2set -u), and was almost successful in reading the 4d-148 data into FieldTrip. 
I can read header all right with exception of one line that turns out to be decisive during reading data (read_data):

D=read_data ('d:\data\meg\windup\T1\2\c,rfdc','dataformat','4d');
??? Reference to non-existent field 'ChannelUnitsPerBit'.

Error in ==> read_data at 477
    upb        = hdr.orig.ChannelUnitsPerBit;


Clearly, we miss the field ChannelUnitsPerBit in hdr.orig structure. As read_event.m also calls read_data.m, this problem precludes reading events as well.

To test the rest of the code, I simply put upb = grad (grad is 1 line above in read_data) and then it works all very well (as grad is equal to 1 in all channel fields). So my hope is that if we can sort out the missing field in hdr.orig., we will be able to read all data very well. 
 
I would be grateful for a hint here as have no idea how can we miss that field.

Best wishes
Andrej




Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
Sent: Mon 06/10/2008 16:03
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Andrej, I see an error in my mail below. The three files
.xyz, .m4d and the acutal pdf is produced using the command:

pdf2set -u

You post the selection in the propreitary MSI environment, then type in 
the command given above. It will put out the three files mentioned for 
each data set.
I shall include only the .xyz and .m4d files from grand averaged files, 
as they do not contain any identifiable information.
I believe that the .m4d file is also called the header file and 
the .xyz is called the location or coordinate file.
Ken Velarde was immensely helpful with this, as were Christian 
Weinbruch, and Don Rojas. Don Rojas's colleague Dr. Eugene Kronberg 
also has  created an interface that can read 4D data, and he was going 
to create such a template as well--as per our last email exchange.
I also have a xls2matlab function that I used to create my own 
template, as the sensor location file is usually a product of 
individual MEG systems. If I may have mislead anyone it is 
unintentional as I am constantly learning.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopa and Almu,
> 
>   do I understand the procedure correctly: we should export data from
> 4D in FIF format (currently we export in native e,... (binary), and
> the text files for the header and the surface points), and then use a
> modified xyz file containing the layout of 148 sensors. I would be
> grateful for one sample xyz file to see whether we can read data this
> way. Naturally, the best would be to incorporate it into the reading
> procedures of FieldTrip.
> 
> Best wishes
> Andrej
> 
> 
> Prof. Andrej Stancak, PhD. 
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
> 
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
> 
> 
> 
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 14:12
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>  
> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
> 
> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
> 
> the other users. There was also a discussion about whether the
> systems 
> were using third order gradiometers and/or magnetometers as the 
> reference. There are mail postings in that thread.
> Everyone: I apologize for the typos in my hastily composed response 
> earlier.
> regards
> gopa
> 
> 
> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
> 
> > Dear Gopa,
> > 
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of
> this
> > system.
> > 
> > Best,
> > Almu
> > 
> > -----Original Message-----
> > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> On
> > Behalf
> > Of Gopakumar Venugopalan
> > Sent: 06 October 2008 13:22
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> > 
> > Hello everyone, I have been wrestling with these problems for a
> while
> > 
> > too.
> > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > (.avg, 
> > and .eeg), and will read raw data (e,..)from 4D.
> > I believe that EEGLAB/Fieldtrip may not have a template for the
> 148-
> > Channel system co-ordinates. Christian and Don Rojas created one
> for
> > me 
> > in early April this year.
> > A FIF export from the 4D system may also solve this problem.
> Stephen
> > 
> > Moratti helped me with this a while a ago. It puts out three 
> > files .xyz, .4D and the original e,.. file. But, if the .xyz file
> > which 
> > has coordinates for 148 channels does not match with the template,
> > then 
> > the data will not load. I think for one may have to load a create
> a
> > 148 
> > channel template for this purpose. This is my experience with
> EEGLAB,
> > 
> > and I think that they underlying engine is the same for both
> EEGLAB
> > and 
> > Fieldtrip
> > Then again, I may be completely wrong about everything except the 
> > templates that were created for me.
> > regards
> > gopa
> > 
> > 
> > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> > 
> > > Dear all,
> > > 
> > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > sensors). For now, we export original 4D data into BESA format,
> > and
> > > then read those into FieldTrip. This is not optimal, as e.g.
> > gradient
> > > coils information is not transferred into FieldTrip. We would be
> > > grateful for a plugin or a hint enabling us to read the 4D data
> > > directly into FieldTrip.
> > > 
> > >   Best wishes
> > >   Andrej Stancak
> > > 
> > > 
> > > Prof. Andrej Stancak, PhD. 
> > > The University of Liverpool
> > > School of Psychology
> > > The Eleanor Rathbone Building
> > > Bedford Street South, Room 209
> > > Liverpool
> > > L69 7ZA
> > > 
> > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > >            stancak at centrum.cz (secondary)
> > > Phone: 0151 7946951
> > > Office hours: Monday 10-12, Wednesday 10-12
> > > 
> > > 
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > > 
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the
> > FieldTrip  toolbox, to share experiences and to discuss new ideas
> for
> > MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From venug001 at BAMA.UA.EDU  Tue Oct  7 18:22:23 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Tue, 7 Oct 2008 11:22:23 -0500
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CBF@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <TUE.7.OCT.2008.112223.0500.FIELDTRIP@NIC.SURFNET.NL>

Andrew, I am glad. Thanks to Ken and  and Stephen's assistant. I have
not tweaked around with Cupb settings myself. I would defer that to
folks like Robert, Stephen or Christian. I don't know if Ken is on this
listserv, but I know that he likes to keep up with anything that is 4D
related. I can help with any thing else if I can.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopakumar,
>
>   I followed your advice (pdf2set -u), and was almost successful in
> reading the 4d-148 data into FieldTrip.
> I can read header all right with exception of one line that turns out
> to be decisive during reading data (read_data):
>
> D=read_data ('d:\data\meg\windup\T1\2\c,rfdc','dataformat','4d');
> ??? Reference to non-existent field 'ChannelUnitsPerBit'.
>
> Error in ==> read_data at 477
>     upb        = hdr.orig.ChannelUnitsPerBit;
>
>
> Clearly, we miss the field ChannelUnitsPerBit in hdr.orig structure.
> As read_event.m also calls read_data.m, this problem precludes
> reading events as well.
>
> To test the rest of the code, I simply put upb = grad (grad is 1 line
> above in read_data) and then it works all very well (as grad is equal
> to 1 in all channel fields). So my hope is that if we can sort out
> the missing field in hdr.orig., we will be able to read all data very
> well.
>
> I would be grateful for a hint here as have no idea how can we miss
> that field.
>
> Best wishes
> Andrej
>
>
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 16:03
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Andrej, I see an error in my mail below. The three files
> .xyz, .m4d and the acutal pdf is produced using the command:
>
> pdf2set -u
>
> You post the selection in the propreitary MSI environment, then type
> in
> the command given above. It will put out the three files mentioned
> for
> each data set.
> I shall include only the .xyz and .m4d files from grand averaged
> files,
> as they do not contain any identifiable information.
> I believe that the .m4d file is also called the header file and
> the .xyz is called the location or coordinate file.
> Ken Velarde was immensely helpful with this, as were Christian
> Weinbruch, and Don Rojas. Don Rojas's colleague Dr. Eugene Kronberg
> also has  created an interface that can read 4D data, and he was
> going
> to create such a template as well--as per our last email exchange.
> I also have a xls2matlab function that I used to create my own
> template, as the sensor location file is usually a product of
> individual MEG systems. If I may have mislead anyone it is
> unintentional as I am constantly learning.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
> > Dear Gopa and Almu,
> >
> >   do I understand the procedure correctly: we should export data
> from
> > 4D in FIF format (currently we export in native e,... (binary),
> and
> > the text files for the header and the surface points), and then use
> a
> > modified xyz file containing the layout of 148 sensors. I would be
> > grateful for one sample xyz file to see whether we can read data
> this
> > way. Naturally, the best would be to incorporate it into the
> reading
> > procedures of FieldTrip.
> >
> > Best wishes
> > Andrej
> >
> >
> > Prof. Andrej Stancak, PhD.
> > The University of Liverpool
> > School of Psychology
> > The Eleanor Rathbone Building
> > Bedford Street South, Room 209
> > Liverpool
> > L69 7ZA
> >
> > E:mail: a.stancak at liverpool.ac.uk  (primary)
> >            stancak at centrum.cz (secondary)
> > Phone: 0151 7946951
> > Office hours: Monday 10-12, Wednesday 10-12
> >
> >
> >
> > -----Original Message-----
> > From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> > Sent: Mon 06/10/2008 14:12
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> >
> > Dear Almu (that is a nice name!) thank you  Rob Oostenveld,
> Christian
> >
> > Weinbruch and Arno (EEGLAB) may be the ones who can make it work
> for
> >
> > the other users. There was also a discussion about whether the
> > systems
> > were using third order gradiometers and/or magnetometers as the
> > reference. There are mail postings in that thread.
> > Everyone: I apologize for the typos in my hastily composed response
>
> > earlier.
> > regards
> > gopa
> >
> >
> > Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
> >
> > > Dear Gopa,
> > >
> > > I have got a template for the 4D - 148 channels system. I could
> > give
> > > it to
> > > the Fieldtrip developers if this is helpful for other users of
> > this
> > > system.
> > >
> > > Best,
> > > Almu
> > >
> > > -----Original Message-----
> > > From: FieldTrip discussion list
> [mailto:FIELDTRIP at NIC.SURFNET.NL]
> > On
> > > Behalf
> > > Of Gopakumar Venugopalan
> > > Sent: 06 October 2008 13:22
> > > To: FIELDTRIP at NIC.SURFNET.NL
> > > Subject: Re: [FIELDTRIP] 4D data reading
> > >
> > > Hello everyone, I have been wrestling with these problems for a
> > while
> > >
> > > too.
> > > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > > (.avg,
> > > and .eeg), and will read raw data (e,..)from 4D.
> > > I believe that EEGLAB/Fieldtrip may not have a template for the
> > 148-
> > > Channel system co-ordinates. Christian and Don Rojas created one
> > for
> > > me
> > > in early April this year.
> > > A FIF export from the 4D system may also solve this problem.
> > Stephen
> > >
> > > Moratti helped me with this a while a ago. It puts out three
> > > files .xyz, .4D and the original e,.. file. But, if the .xyz
> file
> > > which
> > > has coordinates for 148 channels does not match with the
> template,
> > > then
> > > the data will not load. I think for one may have to load a
> create
> > a
> > > 148
> > > channel template for this purpose. This is my experience with
> > EEGLAB,
> > >
> > > and I think that they underlying engine is the same for both
> > EEGLAB
> > > and
> > > Fieldtrip
> > > Then again, I may be completely wrong about everything except the
>
> > > templates that were created for me.
> > > regards
> > > gopa
> > >
> > >
> > > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> > >
> > > > Dear all,
> > > >
> > > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > > sensors). For now, we export original 4D data into BESA
> format,
> > > and
> > > > then read those into FieldTrip. This is not optimal, as e.g.
> > > gradient
> > > > coils information is not transferred into FieldTrip. We would
> be
> > > > grateful for a plugin or a hint enabling us to read the 4D
> data
> > > > directly into FieldTrip.
> > > >
> > > >   Best wishes
> > > >   Andrej Stancak
> > > >
> > > >
> > > > Prof. Andrej Stancak, PhD.
> > > > The University of Liverpool
> > > > School of Psychology
> > > > The Eleanor Rathbone Building
> > > > Bedford Street South, Room 209
> > > > Liverpool
> > > > L69 7ZA
> > > >
> > > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > > >            stancak at centrum.cz (secondary)
> > > > Phone: 0151 7946951
> > > > Office hours: Monday 10-12, Wednesday 10-12
> > > >
> > > >
> > > > ----------------------------------
> > > > The aim of this list is to facilitate the discussion between
> > users
> > > of
> > > > the FieldTrip  toolbox, to share experiences and to discuss
> new
> > > ideas
> > > > for MEG and EEG analysis. See also
> > > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > > http://www.ru.nl/fcdonders/fieldtrip.
> > > >
> > >
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the
> > > FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for
> > > MEG
> > > and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > >
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From A.Stancak at LIVERPOOL.AC.UK  Tue Oct  7 18:40:04 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Tue, 7 Oct 2008 17:40:04 +0100
Subject: 4D data reading
Message-ID: <TUE.7.OCT.2008.174004.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs,

  I have followed your path (in parallel to the one suggested by Gopakumar) and it worked. It took me a while to dig out the configuration file in the MSI server and to realise it needs to be renamed and put into the data directory, but it works now. 

  As you write, the procedures change the prompt to K:> and continue after typing dbcont. I do not mind this if it is for once, but what about running batch files? Or is the idea to read data, the header, and the events and then save all for further processing in some different format (e.g. Matlab?). I work with the FieldTrip_20051006 version that I downloaded today, and I do not know whether it has been fixed or whether this feature (K:> dbcont) will stay.

Thank you for your advice. Thanks to you and Gopakumar and few other colleagues we are now close to smooth reading our MEG data into FieldTrip.

 Best wishes
 Andrej

Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
Sent: Mon 06/10/2008 15:54
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Dear Andrej, dear Gopa,

Sorry to bother you again, but I tried to make a point in my last  
mail that it is not necessary to intermediately convert your raw  
epoched or continuous 4D-data into another format, prior to be able  
to read it into Fieldtrip. Of course you are free to do so, but the  
most natural way to me would seem to work on the raw datafiles  
directly. Fieldtrip should support this and it has reading routines  
for the raw data-file (beginning with e, or c,), the config-file, and  
the file containing the digitized head-surface positions.
You should be able to obtain the header information directly by  
calling: hdr = read_header('e,thenameofyourrawdatafile') (give or  
take an accidental 'keyboard'-statement in the low-level function  
read_4d_hdr, this will be fixed in tonight's release version: if it  
occurs now, just type dbcont on the command line when it prompts:  
K>>) As far as I know hdr contains a structure grad, which specifies  
the sensor-positions. At least it works on our Glaswegian 248-sensor  
system.

Yours,

Jan-Mathijs


On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:

> Sure will send you those files. Please remember in my files there are
> only 146 channel locations as we turned off two channels.I also have a
> matlab file from Don Rojas for the 148 channel layout and a file which
> he created for the 146 channel layout. Please give some time today, as
> I run those programs on a different machine.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
>> Dear Gopa and Almu,
>>
>>   do I understand the procedure correctly: we should export data from
>> 4D in FIF format (currently we export in native e,... (binary), and
>> the text files for the header and the surface points), and then use a
>> modified xyz file containing the layout of 148 sensors. I would be
>> grateful for one sample xyz file to see whether we can read data this
>> way. Naturally, the best would be to incorporate it into the reading
>> procedures of FieldTrip.
>>
>> Best wishes
>> Andrej
>>
>>
>> Prof. Andrej Stancak, PhD.
>> The University of Liverpool
>> School of Psychology
>> The Eleanor Rathbone Building
>> Bedford Street South, Room 209
>> Liverpool
>> L69 7ZA
>>
>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>            stancak at centrum.cz (secondary)
>> Phone: 0151 7946951
>> Office hours: Monday 10-12, Wednesday 10-12
>>
>>
>>
>> -----Original Message-----
>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>> Sent: Mon 06/10/2008 14:12
>> To: FIELDTRIP at NIC.SURFNET.NL
>> Subject: Re: [FIELDTRIP] 4D data reading
>>
>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>
>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>
>> the other users. There was also a discussion about whether the
>> systems
>> were using third order gradiometers and/or magnetometers as the
>> reference. There are mail postings in that thread.
>> Everyone: I apologize for the typos in my hastily composed response
>> earlier.
>> regards
>> gopa
>>
>>
>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>
>>> Dear Gopa,
>>>
>>> I have got a template for the 4D - 148 channels system. I could
>> give
>>> it to
>>> the Fieldtrip developers if this is helpful for other users of
>> this
>>> system.
>>>
>>> Best,
>>> Almu
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>> On
>>> Behalf
>>> Of Gopakumar Venugopalan
>>> Sent: 06 October 2008 13:22
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Hello everyone, I have been wrestling with these problems for a
>> while
>>>
>>> too.
>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>> (.avg,
>>> and .eeg), and will read raw data (e,..)from 4D.
>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>> 148-
>>> Channel system co-ordinates. Christian and Don Rojas created one
>> for
>>> me
>>> in early April this year.
>>> A FIF export from the 4D system may also solve this problem.
>> Stephen
>>>
>>> Moratti helped me with this a while a ago. It puts out three
>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>> which
>>> has coordinates for 148 channels does not match with the template,
>>> then
>>> the data will not load. I think for one may have to load a create
>> a
>>> 148
>>> channel template for this purpose. This is my experience with
>> EEGLAB,
>>>
>>> and I think that they underlying engine is the same for both
>> EEGLAB
>>> and
>>> Fieldtrip
>>> Then again, I may be completely wrong about everything except the
>>> templates that were created for me.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>
>>>> Dear all,
>>>>
>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>> sensors). For now, we export original 4D data into BESA format,
>>> and
>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>> gradient
>>>> coils information is not transferred into FieldTrip. We would be
>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>> directly into FieldTrip.
>>>>
>>>>   Best wishes
>>>>   Andrej Stancak
>>>>
>>>>
>>>> Prof. Andrej Stancak, PhD.
>>>> The University of Liverpool
>>>> School of Psychology
>>>> The Eleanor Rathbone Building
>>>> Bedford Street South, Room 209
>>>> Liverpool
>>>> L69 7ZA
>>>>
>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>            stancak at centrum.cz (secondary)
>>>> Phone: 0151 7946951
>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between
>> users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the
>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for
>>> MEG
>>> and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users  
> of the FieldTrip  toolbox, to share experiences and to discuss new  
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ 
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From j.schoffelen at PSY.GLA.AC.UK  Tue Oct  7 19:58:32 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Tue, 7 Oct 2008 18:58:32 +0100
Subject: 4D data reading
Message-ID: <TUE.7.OCT.2008.185832.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Andrej,

I am glad it works now. The keyboard statement in the code (leading to  
K>>) was just to debug some code. I forgot to clear it when I was  
done. I fixed it yesterday, and it should be correct in the latest  
version of fieldtrip (20081007). The idea is certainly not to read the  
events/header/data only once, store it, and refer to it for later use.  
However, depending on what you want, it could be useful (I often save  
my trial definitions after artifact rejection because this is a time  
consuming step). Hopefully you can run batch with the keyboard  
statement removed.
As far as I understood from the formatting of the data coming from our  
248-channel system, each recording is automatically saved with a  
config-file, which is a copy of the system config-file, and which is  
adjusted with run-specific parameters (most importantly weight tables  
for the denoising, and filter setting (I am not entirely sure about  
the filter settings). Anyway, as it is programmed at the moment, the  
code assumes the run-specific config file to be present in the  
run-directory, and it assumes the file to be named 'config'. This of  
course can be made a bit more flexible (for example one could provide  
an explicit path/filename to the system's config file).
Do I understand correctly, that the data you record does not generally  
contain a config-file in the data-directories themselves?

Yours,

Jan-Mathijs


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Jan-Mathijs,
>
>   I have followed your path (in parallel to the one suggested by   
> Gopakumar) and it worked. It took me a while to dig out the   
> configuration file in the MSI server and to realise it needs to be   
> renamed and put into the data directory, but it works now.
>
>   As you write, the procedures change the prompt to K:> and continue  
>  after typing dbcont. I do not mind this if it is for once, but what  
>  about running batch files? Or is the idea to read data, the header,  
>  and the events and then save all for further processing in some   
> different format (e.g. Matlab?). I work with the FieldTrip_20051006   
> version that I downloaded today, and I do not know whether it has   
> been fixed or whether this feature (K:> dbcont) will stay.
>
> Thank you for your advice. Thanks to you and Gopakumar and few other  
>  colleagues we are now close to smooth reading our MEG data into   
> FieldTrip.
>
>  Best wishes
>  Andrej
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
> Sent: Mon 06/10/2008 15:54
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Dear Andrej, dear Gopa,
>
> Sorry to bother you again, but I tried to make a point in my last
> mail that it is not necessary to intermediately convert your raw
> epoched or continuous 4D-data into another format, prior to be able
> to read it into Fieldtrip. Of course you are free to do so, but the
> most natural way to me would seem to work on the raw datafiles
> directly. Fieldtrip should support this and it has reading routines
> for the raw data-file (beginning with e, or c,), the config-file, and
> the file containing the digitized head-surface positions.
> You should be able to obtain the header information directly by
> calling: hdr = read_header('e,thenameofyourrawdatafile') (give or
> take an accidental 'keyboard'-statement in the low-level function
> read_4d_hdr, this will be fixed in tonight's release version: if it
> occurs now, just type dbcont on the command line when it prompts:
> K>>) As far as I know hdr contains a structure grad, which specifies
> the sensor-positions. At least it works on our Glaswegian 248-sensor
> system.
>
> Yours,
>
> Jan-Mathijs
>
>
> On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:
>
>> Sure will send you those files. Please remember in my files there are
>> only 146 channel locations as we turned off two channels.I also have a
>> matlab file from Don Rojas for the 148 channel layout and a file which
>> he created for the 146 channel layout. Please give some time today, as
>> I run those programs on a different machine.
>> regards
>> gopa
>>
>>
>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>
>>> Dear Gopa and Almu,
>>>
>>>   do I understand the procedure correctly: we should export data from
>>> 4D in FIF format (currently we export in native e,... (binary), and
>>> the text files for the header and the surface points), and then use a
>>> modified xyz file containing the layout of 148 sensors. I would be
>>> grateful for one sample xyz file to see whether we can read data this
>>> way. Naturally, the best would be to incorporate it into the reading
>>> procedures of FieldTrip.
>>>
>>> Best wishes
>>> Andrej
>>>
>>>
>>> Prof. Andrej Stancak, PhD.
>>> The University of Liverpool
>>> School of Psychology
>>> The Eleanor Rathbone Building
>>> Bedford Street South, Room 209
>>> Liverpool
>>> L69 7ZA
>>>
>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>            stancak at centrum.cz (secondary)
>>> Phone: 0151 7946951
>>> Office hours: Monday 10-12, Wednesday 10-12
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>>> Sent: Mon 06/10/2008 14:12
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>>
>>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>>
>>> the other users. There was also a discussion about whether the
>>> systems
>>> were using third order gradiometers and/or magnetometers as the
>>> reference. There are mail postings in that thread.
>>> Everyone: I apologize for the typos in my hastily composed response
>>> earlier.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>>
>>>> Dear Gopa,
>>>>
>>>> I have got a template for the 4D - 148 channels system. I could
>>> give
>>>> it to
>>>> the Fieldtrip developers if this is helpful for other users of
>>> this
>>>> system.
>>>>
>>>> Best,
>>>> Almu
>>>>
>>>> -----Original Message-----
>>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>>> On
>>>> Behalf
>>>> Of Gopakumar Venugopalan
>>>> Sent: 06 October 2008 13:22
>>>> To: FIELDTRIP at NIC.SURFNET.NL
>>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>>
>>>> Hello everyone, I have been wrestling with these problems for a
>>> while
>>>>
>>>> too.
>>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>>> (.avg,
>>>> and .eeg), and will read raw data (e,..)from 4D.
>>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>>> 148-
>>>> Channel system co-ordinates. Christian and Don Rojas created one
>>> for
>>>> me
>>>> in early April this year.
>>>> A FIF export from the 4D system may also solve this problem.
>>> Stephen
>>>>
>>>> Moratti helped me with this a while a ago. It puts out three
>>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>>> which
>>>> has coordinates for 148 channels does not match with the template,
>>>> then
>>>> the data will not load. I think for one may have to load a create
>>> a
>>>> 148
>>>> channel template for this purpose. This is my experience with
>>> EEGLAB,
>>>>
>>>> and I think that they underlying engine is the same for both
>>> EEGLAB
>>>> and
>>>> Fieldtrip
>>>> Then again, I may be completely wrong about everything except the
>>>> templates that were created for me.
>>>> regards
>>>> gopa
>>>>
>>>>
>>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>>
>>>>> Dear all,
>>>>>
>>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>>> sensors). For now, we export original 4D data into BESA format,
>>>> and
>>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>>> gradient
>>>>> coils information is not transferred into FieldTrip. We would be
>>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>>> directly into FieldTrip.
>>>>>
>>>>>   Best wishes
>>>>>   Andrej Stancak
>>>>>
>>>>>
>>>>> Prof. Andrej Stancak, PhD.
>>>>> The University of Liverpool
>>>>> School of Psychology
>>>>> The Eleanor Rathbone Building
>>>>> Bedford Street South, Room 209
>>>>> Liverpool
>>>>> L69 7ZA
>>>>>
>>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>>            stancak at centrum.cz (secondary)
>>>>> Phone: 0151 7946951
>>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>>
>>>>>
>>>>> ----------------------------------
>>>>> The aim of this list is to facilitate the discussion between
>>> users
>>>> of
>>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>>> ideas
>>>>> for MEG and EEG analysis. See also
>>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between users
>>> of
>>>> the
>>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for
>>>> MEG
>>>> and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of
>>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of
>>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
>> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users   
> of the FieldTrip  toolbox, to share experiences and to discuss new   
> ideas for MEG and EEG analysis. See also   
> http://listserv.surfnet.nl/archives/fieldtrip.html and   
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users   
> of the FieldTrip  toolbox, to share experiences and to discuss new   
> ideas for MEG and EEG analysis. See also   
> http://listserv.surfnet.nl/archives/fieldtrip.html and   
> http://www.ru.nl/fcdonders/fieldtrip.
>



------------------------------------------------------------------
The University of Glasgow, Department of Psychology WebMail system
------------------------------------------------------------------

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From A.Stancak at LIVERPOOL.AC.UK  Wed Oct  8 15:07:40 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Wed, 8 Oct 2008 14:07:40 +0100
Subject: 4D data reading
Message-ID: <WED.8.OCT.2008.140740.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs,

  thanks for your e-mail and further information. It turned out that the archive data I used for testing the data reading did not have a config file, and neither it is displayed in the MSI window in the list of posted/non-posted files so I was not sure where to find it. Today I have exported data using the MSI disk/tape utilities, and the config file was there as it should be.  

I have now tested reading the 4D files with a correct config file on board and it worked well. I still have to do "dbcont" but this is a small cosmetic issue compared to the way we handled data before. Again many thanks for your advice and information.

 With best wishes
 Andrej

   


  

Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
Sent: Tue 07/10/2008 18:58
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Dear Andrej,

I am glad it works now. The keyboard statement in the code (leading to  
K>>) was just to debug some code. I forgot to clear it when I was  
done. I fixed it yesterday, and it should be correct in the latest  
version of fieldtrip (20081007). The idea is certainly not to read the  
events/header/data only once, store it, and refer to it for later use.  
However, depending on what you want, it could be useful (I often save  
my trial definitions after artifact rejection because this is a time  
consuming step). Hopefully you can run batch with the keyboard  
statement removed.
As far as I understood from the formatting of the data coming from our  
248-channel system, each recording is automatically saved with a  
config-file, which is a copy of the system config-file, and which is  
adjusted with run-specific parameters (most importantly weight tables  
for the denoising, and filter setting (I am not entirely sure about  
the filter settings). Anyway, as it is programmed at the moment, the  
code assumes the run-specific config file to be present in the  
run-directory, and it assumes the file to be named 'config'. This of  
course can be made a bit more flexible (for example one could provide  
an explicit path/filename to the system's config file).
Do I understand correctly, that the data you record does not generally  
contain a config-file in the data-directories themselves?

Yours,

Jan-Mathijs


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Jan-Mathijs,
>
>   I have followed your path (in parallel to the one suggested by   
> Gopakumar) and it worked. It took me a while to dig out the   
> configuration file in the MSI server and to realise it needs to be   
> renamed and put into the data directory, but it works now.
>
>   As you write, the procedures change the prompt to K:> and continue  
>  after typing dbcont. I do not mind this if it is for once, but what  
>  about running batch files? Or is the idea to read data, the header,  
>  and the events and then save all for further processing in some   
> different format (e.g. Matlab?). I work with the FieldTrip_20051006   
> version that I downloaded today, and I do not know whether it has   
> been fixed or whether this feature (K:> dbcont) will stay.
>
> Thank you for your advice. Thanks to you and Gopakumar and few other  
>  colleagues we are now close to smooth reading our MEG data into   
> FieldTrip.
>
>  Best wishes
>  Andrej
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
> Sent: Mon 06/10/2008 15:54
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Dear Andrej, dear Gopa,
>
> Sorry to bother you again, but I tried to make a point in my last
> mail that it is not necessary to intermediately convert your raw
> epoched or continuous 4D-data into another format, prior to be able
> to read it into Fieldtrip. Of course you are free to do so, but the
> most natural way to me would seem to work on the raw datafiles
> directly. Fieldtrip should support this and it has reading routines
> for the raw data-file (beginning with e, or c,), the config-file, and
> the file containing the digitized head-surface positions.
> You should be able to obtain the header information directly by
> calling: hdr = read_header('e,thenameofyourrawdatafile') (give or
> take an accidental 'keyboard'-statement in the low-level function
> read_4d_hdr, this will be fixed in tonight's release version: if it
> occurs now, just type dbcont on the command line when it prompts:
> K>>) As far as I know hdr contains a structure grad, which specifies
> the sensor-positions. At least it works on our Glaswegian 248-sensor
> system.
>
> Yours,
>
> Jan-Mathijs
>
>
> On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:
>
>> Sure will send you those files. Please remember in my files there are
>> only 146 channel locations as we turned off two channels.I also have a
>> matlab file from Don Rojas for the 148 channel layout and a file which
>> he created for the 146 channel layout. Please give some time today, as
>> I run those programs on a different machine.
>> regards
>> gopa
>>
>>
>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>
>>> Dear Gopa and Almu,
>>>
>>>   do I understand the procedure correctly: we should export data from
>>> 4D in FIF format (currently we export in native e,... (binary), and
>>> the text files for the header and the surface points), and then use a
>>> modified xyz file containing the layout of 148 sensors. I would be
>>> grateful for one sample xyz file to see whether we can read data this
>>> way. Naturally, the best would be to incorporate it into the reading
>>> procedures of FieldTrip.
>>>
>>> Best wishes
>>> Andrej
>>>
>>>
>>> Prof. Andrej Stancak, PhD.
>>> The University of Liverpool
>>> School of Psychology
>>> The Eleanor Rathbone Building
>>> Bedford Street South, Room 209
>>> Liverpool
>>> L69 7ZA
>>>
>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>            stancak at centrum.cz (secondary)
>>> Phone: 0151 7946951
>>> Office hours: Monday 10-12, Wednesday 10-12
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>>> Sent: Mon 06/10/2008 14:12
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>>
>>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>>
>>> the other users. There was also a discussion about whether the
>>> systems
>>> were using third order gradiometers and/or magnetometers as the
>>> reference. There are mail postings in that thread.
>>> Everyone: I apologize for the typos in my hastily composed response
>>> earlier.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>>
>>>> Dear Gopa,
>>>>
>>>> I have got a template for the 4D - 148 channels system. I could
>>> give
>>>> it to
>>>> the Fieldtrip developers if this is helpful for other users of
>>> this
>>>> system.
>>>>
>>>> Best,
>>>> Almu
>>>>
>>>> -----Original Message-----
>>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>>> On
>>>> Behalf
>>>> Of Gopakumar Venugopalan
>>>> Sent: 06 October 2008 13:22
>>>> To: FIELDTRIP at NIC.SURFNET.NL
>>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>>
>>>> Hello everyone, I have been wrestling with these problems for a
>>> while
>>>>
>>>> too.
>>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>>> (.avg,
>>>> and .eeg), and will read raw data (e,..)from 4D.
>>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>>> 148-
>>>> Channel system co-ordinates. Christian and Don Rojas created one
>>> for
>>>> me
>>>> in early April this year.
>>>> A FIF export from the 4D system may also solve this problem.
>>> Stephen
>>>>
>>>> Moratti helped me with this a while a ago. It puts out three
>>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>>> which
>>>> has coordinates for 148 channels does not match with the template,
>>>> then
>>>> the data will not load. I think for one may have to load a create
>>> a
>>>> 148
>>>> channel template for this purpose. This is my experience with
>>> EEGLAB,
>>>>
>>>> and I think that they underlying engine is the same for both
>>> EEGLAB
>>>> and
>>>> Fieldtrip
>>>> Then again, I may be completely wrong about everything except the
>>>> templates that were created for me.
>>>> regards
>>>> gopa
>>>>
>>>>
>>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>>
>>>>> Dear all,
>>>>>
>>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>>> sensors). For now, we export original 4D data into BESA format,
>>>> and
>>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>>> gradient
>>>>> coils information is not transferred into FieldTrip. We would be
>>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>>> directly into FieldTrip.
>>>>>
>>>>>   Best wishes
>>>>>   Andrej Stancak
>>>>>
>>>>>
>>>>> Prof. Andrej Stancak, PhD.
>>>>> The University of Liverpool
>>>>> School of Psychology
>>>>> The Eleanor Rathbone Building
>>>>> Bedford Street South, Room 209
>>>>> Liverpool
>>>>> L69 7ZA
>>>>>
>>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>>            stancak at centrum.cz (secondary)
>>>>> Phone: 0151 7946951
>>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>>
>>>>>
>>>>> ----------------------------------
>>>>> The aim of this list is to facilitate the discussion between
>>> users
>>>> of
>>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>>> ideas
>>>>> for MEG and EEG analysis. See also
>>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between users
>>> of
>>>> the
>>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for
>>>> MEG
>>>> and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of
>>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of
>>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
>> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users   
> of the FieldTrip  toolbox, to share experiences and to discuss new   
> ideas for MEG and EEG analysis. See also   
> http://listserv.surfnet.nl/archives/fieldtrip.html and   
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users   
> of the FieldTrip  toolbox, to share experiences and to discuss new   
> ideas for MEG and EEG analysis. See also   
> http://listserv.surfnet.nl/archives/fieldtrip.html and   
> http://www.ru.nl/fcdonders/fieldtrip.
>



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

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.



----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From julian.keil at GMAIL.COM  Wed Oct  8 17:22:14 2008
From: julian.keil at GMAIL.COM (Julian Keil)
Date: Wed, 8 Oct 2008 17:22:14 +0200
Subject: 4D data reading -> 148 channel system
Message-ID: <WED.8.OCT.2008.172214.0200.FIELDTRIP@NIC.SURFNET.NL>

Hello everyone,

i just tried to read 4D raw data as was suggested in the recent
discussion.
Unfortunately, I encountered 2 Problems:

First, Matlab still enters the debug-mode, although I'm using the
latest version of Fieldtrip
Second, though I can read the raw datal, the labels for the MEG
channels are missing. The data.hdr.label contains the 165 recorded
channels but the labels are not the Names but - as I think - the
locations.
(e.g. A3+03).
Could it be, that the definition for the 148-channel 4d-system is
missing?
Does anyone have a hint hw to solve this?

Thanks a lot

Julian Keil


Dipl. Psych. Julian Keil

OBOB-Lab
University of Konstanz
Department of Psychology
P.O. Box D23
78457 Konstanz
Germany

Tel: ++49 - (0)7531 - 88 45 84
Email: julian.keil at uni-konstanz.de
Homepage: http://www.uni-konstanz.de/obob





----------------------------------
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From j.schoffelen at PSY.GLA.AC.UK  Wed Oct  8 17:53:58 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Wed, 8 Oct 2008 16:53:58 +0100
Subject: 4D data reading -> 148 channel system
In-Reply-To: <BD4DCA44-4C7F-4076-9BFA-2531597267A7@GMAIL.COM>
Message-ID: <WED.8.OCT.2008.165358.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Julian,

As of the debugging thingy: sorry about that, I thought I adjusted it
but apparently something went wrong. You can easily fix this yourself
by going to the appropriate function. It's read_4d_hdr and you just
have to remove the keyboard-statement somewhere in the code. I don't
know where the function is located in the release version of
fieldtrip, but it should be somewhere like fieldtrip/private, or
fieldtrip/fileio/private. I hope that as of tomorrow the trailing
keyboard statement is removed from the release version.
Regarding your second point: I tried it out with a 148-channel
dataset I have lying around, and you're absolutely right.
Interestingly, for the 248-system it works just fine. Give me some
time to look into this. I hope to get it working robustly for both
systems. Could you for the time being check whether the field
data.hdr.orig.Channel looks meaningful for your data? A solution for
now would be to replace data.hdr.label (and data.label) with
hdr.orig.Channel.


Yours,

Jan-Mathijs



On Oct 8, 2008, at 4:22 PM, Julian Keil wrote:

> Hello everyone,
>
> i just tried to read 4D raw data as was suggested in the recent
> discussion.
> Unfortunately, I encountered 2 Problems:
>
> First, Matlab still enters the debug-mode, although I'm using the
> latest version of Fieldtrip
> Second, though I can read the raw datal, the labels for the MEG
> channels are missing. The data.hdr.label contains the 165 recorded
> channels but the labels are not the Names but - as I think - the
> locations.
> (e.g. A3+03).
> Could it be, that the definition for the 148-channel 4d-system is
> missing?
> Does anyone have a hint hw to solve this?
>
> Thanks a lot
>
> Julian Keil
>
>
> Dipl. Psych. Julian Keil
>
> OBOB-Lab
> University of Konstanz
> Department of Psychology
> P.O. Box D23
> 78457 Konstanz
> Germany
>
> Tel: ++49 - (0)7531 - 88 45 84
> Email: julian.keil at uni-konstanz.de
> Homepage: http://www.uni-konstanz.de/obob
>
>
>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From julian.keil at GMAIL.COM  Thu Oct  9 12:01:38 2008
From: julian.keil at GMAIL.COM (Julian Keil)
Date: Thu, 9 Oct 2008 12:01:38 +0200
Subject: 4D data reading -> 148 channel system
In-Reply-To: <AAD7D620-D190-4A0E-8649-4F2706ECC5DB@psy.gla.ac.uk>
Message-ID: <THU.9.OCT.2008.120138.0200.FIELDTRIP@NIC.SURFNET.NL>

Hello Jan-Mathijs,

thanks for the fast fix of problem 1.
As for problem 2: the data.hdr.orig.channel indeed looks meaningful
and replacing the files as you mentioned works fine.

Thanks a lot.

Julian

Am 08.10.2008 um 17:53 schrieb jan-mathijs schoffelen:

> Dear Julian,
>
> As of the debugging thingy: sorry about that, I thought I adjusted
> it but apparently something went wrong. You can easily fix this
> yourself by going to the appropriate function. It's read_4d_hdr and
> you just have to remove the keyboard-statement somewhere in the
> code. I don't know where the function is located in the release
> version of fieldtrip, but it should be somewhere like fieldtrip/
> private, or fieldtrip/fileio/private. I hope that as of tomorrow the
> trailing keyboard statement is removed from the release version.
> Regarding your second point: I tried it out with a 148-channel
> dataset I have lying around, and you're absolutely right.
> Interestingly, for the 248-system it works just fine. Give me some
> time to look into this. I hope to get it working robustly for both
> systems. Could you for the time being check whether the field
> data.hdr.orig.Channel looks meaningful for your data? A solution for
> now would be to replace data.hdr.label (and data.label) with
> hdr.orig.Channel.
>
>
> Yours,
>
> Jan-Mathijs
>
>
>
> On Oct 8, 2008, at 4:22 PM, Julian Keil wrote:
>
>> Hello everyone,
>>
>> i just tried to read 4D raw data as was suggested in the recent
>> discussion.
>> Unfortunately, I encountered 2 Problems:
>>
>> First, Matlab still enters the debug-mode, although I'm using the
>> latest version of Fieldtrip
>> Second, though I can read the raw datal, the labels for the MEG
>> channels are missing. The data.hdr.label contains the 165 recorded
>> channels but the labels are not the Names but - as I think - the
>> locations.
>> (e.g. A3+03).
>> Could it be, that the definition for the 148-channel 4d-system is
>> missing?
>> Does anyone have a hint hw to solve this?
>>
>> Thanks a lot
>>
>> Julian Keil
>>
>>
>> Dipl. Psych. Julian Keil
>>
>> OBOB-Lab
>> University of Konstanz
>> Department of Psychology
>> P.O. Box D23
>> 78457 Konstanz
>> Germany
>>
>> Tel: ++49 - (0)7531 - 88 45 84
>> Email: julian.keil at uni-konstanz.de
>> Homepage: http://www.uni-konstanz.de/obob
>>
>>
>>
>>
>> ----------------------------------
>>
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis.
>>
>> http://listserv.surfnet.nl/archives/fieldtrip.html
>>
>> http://www.ru.nl/fcdonders/fieldtrip/
>>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From j.schoffelen at PSY.GLA.AC.UK  Thu Oct  9 12:28:34 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Thu, 9 Oct 2008 11:28:34 +0100
Subject: 4D data reading -> 148 channel system
In-Reply-To: <3423F7AA-91CB-4B9A-81AD-2411538B516C@gmail.com>
Message-ID: <THU.9.OCT.2008.112834.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Julian,

You can easily make this change yourself in the appropriate place of
read_4d_hdr for the time being.
I made the change as well (it seems to look ok for both the 148 and
248 channel systems) and put it in the fieldtrip release.

Yours,

Jan-Mathijs

On Oct 9, 2008, at 11:01 AM, Julian Keil wrote:

> Hello Jan-Mathijs,
>
> thanks for the fast fix of problem 1.
> As for problem 2: the data.hdr.orig.channel indeed looks meaningful
> and replacing the files as you mentioned works fine.
>
> Thanks a lot.
>
> Julian
>
> Am 08.10.2008 um 17:53 schrieb jan-mathijs schoffelen:
>
>> Dear Julian,
>>
>> As of the debugging thingy: sorry about that, I thought I adjusted
>> it but apparently something went wrong. You can easily fix this
>> yourself by going to the appropriate function. It's read_4d_hdr
>> and you just have to remove the keyboard-statement somewhere in
>> the code. I don't know where the function is located in the
>> release version of fieldtrip, but it should be somewhere like
>> fieldtrip/private, or fieldtrip/fileio/private. I hope that as of
>> tomorrow the trailing keyboard statement is removed from the
>> release version.
>> Regarding your second point: I tried it out with a 148-channel
>> dataset I have lying around, and you're absolutely right.
>> Interestingly, for the 248-system it works just fine. Give me some
>> time to look into this. I hope to get it working robustly for both
>> systems. Could you for the time being check whether the field
>> data.hdr.orig.Channel looks meaningful for your data? A solution
>> for now would be to replace data.hdr.label (and data.label) with
>> hdr.orig.Channel.
>>
>>
>> Yours,
>>
>> Jan-Mathijs
>>
>>
>>
>> On Oct 8, 2008, at 4:22 PM, Julian Keil wrote:
>>
>>> Hello everyone,
>>>
>>> i just tried to read 4D raw data as was suggested in the recent
>>> discussion.
>>> Unfortunately, I encountered 2 Problems:
>>>
>>> First, Matlab still enters the debug-mode, although I'm using the
>>> latest version of Fieldtrip
>>> Second, though I can read the raw datal, the labels for the MEG
>>> channels are missing. The data.hdr.label contains the 165
>>> recorded channels but the labels are not the Names but - as I
>>> think - the locations.
>>> (e.g. A3+03).
>>> Could it be, that the definition for the 148-channel 4d-system is
>>> missing?
>>> Does anyone have a hint hw to solve this?
>>>
>>> Thanks a lot
>>>
>>> Julian Keil
>>>
>>>
>>> Dipl. Psych. Julian Keil
>>>
>>> OBOB-Lab
>>> University of Konstanz
>>> Department of Psychology
>>> P.O. Box D23
>>> 78457 Konstanz
>>> Germany
>>>
>>> Tel: ++49 - (0)7531 - 88 45 84
>>> Email: julian.keil at uni-konstanz.de
>>> Homepage: http://www.uni-konstanz.de/obob
>>>
>>>
>>>
>>>
>>> ----------------------------------
>>>
>>> The aim of this list is to facilitate the discussion between
>>> users of the FieldTrip toolbox, to share experiences and to
>>> discuss new ideas for MEG and EEG analysis.
>>>
>>> http://listserv.surfnet.nl/archives/fieldtrip.html
>>>
>>> http://www.ru.nl/fcdonders/fieldtrip/
>>>
>>
>> ----------------------------------
>>
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis.
>>
>> http://listserv.surfnet.nl/archives/fieldtrip.html
>>
>> http://www.ru.nl/fcdonders/fieldtrip/
>>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From michelic72 at GMAIL.COM  Fri Oct 10 09:27:28 2008
From: michelic72 at GMAIL.COM (Cristiano Micheli)
Date: Fri, 10 Oct 2008 09:27:28 +0200
Subject: sourceplot - 'surface'
Message-ID: <FRI.10.OCT.2008.092728.0200.FIELDTRIP@NIC.SURFNET.NL>

I am trying to visualize coherence on a 3D surface, after DICS processing,
with a template given in Fieldtrip :

    cfg              = [];
    cfg.parameter    = 'coh'; 
    cfg.downsample = 1;
    cfg.sourceunits  = 'cm';
    cfg.mriunits       = 'mm';
    interp                = sourceinterpolate(cfg, source, mri); 

    cfg                   = [];
    cfg.coordinates = 'ctf';
    cfg.template     = '/home/common/matlab/spm2/templates/T1.mnc'; 
    sourceN  = volumenormalise(cfg, interp);

    sourceN = rmfield(sourceN,'inside'); 
    cfg = [];
    cfg.method = 'surface';
    cfg.funparameter = 'coh';
    cfg.funcolorlim = [0.0 0.5e-3];
    cfg.funcolormap = 'jet';
    cfg.opacitylim = [0.0 0.1]; 
    cfg.opacitymap = 'rampup';  
    cfg.projmethod = 'nearest'; 
    cfg.surffile = 'surface_l4_both.mat';
    cfg.surfdownsample = 10; 
    figure, sourceplot(cfg,sourceN); view ([90 0])

I get stuck at the normalisation when I get this error:

??? Error using ==> spm_create_vol>create_vol at 32
"dim" field is the wrong size (1  4).

Error in ==> spm_create_vol at 16
        v = create_vol(V(i));

Error in ==> fieldtrip-20080729/private/volumewrite_spm at 61
Va         = spm_create_vol(Va);

Error in ==> volumenormalise at 178
VF = volumewrite_spm([cfg.intermediatename,'_anatomy.img'], interp.anatomy,
interp.transform);


I thank you in advance for any suggestion
Cristiano

M.Sc. Ing. Cristiano Micheli
Institute of Medical Psychology and Behavioral Neurobiology MEG-Center
Otfried-Müller-Strasse 47 72076 Tübingen
Phone: +49-7071-29-87689
Fax:   +49-7071-29-5706
Privat: +49-176-26326149
Email: cristiano.micheli at med.uni-tuebingen.de 

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From jlucan at NKI.RFMH.ORG  Tue Oct 14 20:15:33 2008
From: jlucan at NKI.RFMH.ORG (Joshua Lucan)
Date: Tue, 14 Oct 2008 20:15:33 +0200
Subject: within subjects partitioning
Message-ID: <TUE.14.OCT.2008.201533.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi,
  I'm using timelockstatistics to perform a within subjects cluster based non-
parametric test.  I have two conditions and ten subjects.  The data from each 
subject consists of a spatial array of 160 electrodes at one time point.
  My question is how are the data randomly partitioned. Are all samples across 
subjects and conditions put into one group and 20 random drawings (10 
subjects, 2 conditions) of 160 electrodes performed?  Or is data within each 
subject preserved so that there are 10 groups of 320 electrodes from each of 
which two partitions are made?
  Thanks so much,
  Josh

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From e.maris at DONDERS.RU.NL  Tue Oct 14 21:21:08 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Tue, 14 Oct 2008 21:21:08 +0200
Subject: within subjects partitioning
In-Reply-To: <LISTSERV%200810142015333110.139F@NIC.SURFNET.NL>
Message-ID: <TUE.14.OCT.2008.212108.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Josh,


>   I'm using timelockstatistics to perform a within subjects cluster based
non-
> parametric test.  I have two conditions and ten subjects.  The data from
each
> subject consists of a spatial array of 160 electrodes at one time point.
>   My question is how are the data randomly partitioned. Are all samples
across
> subjects and conditions put into one group and 20 random drawings (10
> subjects, 2 conditions) of 160 electrodes performed?  Or is data within
each
> subject preserved so that there are 10 groups of 320 electrodes from each
of
> which two partitions are made?


In a within-subjects design with two conditions, the permutation is
performed as follows: the two spatio-spectral-temporal (possibly with empty
spectral and temporal dimensions) data matrices (one for every condition)
per subject are randomly permuted WITHIN every subject. This is also
described in Maris & Oostenveld (JNM, 2007).


Good luck,

Eric Maris




>   Thanks so much,
>   Josh
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip
> toolbox, to share experiences and to discuss new ideas for MEG and EEG
analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From jlucan at NKI.RFMH.ORG  Tue Oct 14 21:33:09 2008
From: jlucan at NKI.RFMH.ORG (Joshua Lucan)
Date: Tue, 14 Oct 2008 21:33:09 +0200
Subject: within subjects partitioning
Message-ID: <TUE.14.OCT.2008.213309.0200.FIELDTRIP@NIC.SURFNET.NL>

Excellent! Thank you!

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From v.litvak at ION.UCL.AC.UK  Thu Oct 16 09:05:08 2008
From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak)
Date: Thu, 16 Oct 2008 08:05:08 +0100
Subject: Postdoctoral position in neuroimaging
Message-ID: <THU.16.OCT.2008.080508.0100.FIELDTRIP@NIC.SURFNET.NL>

Please contact Prof. Huber directly about this ad.


Title of the advert
Postdoctoral position in neuroimaging

Description
A one year postdoctoral position is available for a first year
post-doc at the University Children's Hospital Zurich, Switzerland.

The group of Prof. Reto Huber is seeking a postdoctoral fellow to
develop and apply advanced MRI techniques, including diffusion tensor
imaging (DTI), in combination with high-density
electroencephalographic recordings in children and adolescents.

The topic of research will be the study of the relationship between
anatomical and electrophysiological markers of brain maturation. Both
MRI and EEG data of healthy children between 8 and 18 years of age are
available.

Education
We are looking for a qualified candidate with research experience in
computational and statistical methods for MRI imaging (e.g. SPM,
MatLab, DTI and gray matter density analysis). Strong image
processing, data analysis and computing skills are essential.
Applicants should have a PhD, preferably in neuroscience. The position
is fully funded for 1 year and is offered to a first year post-doc.

Start
Available now.

Link
http://www.kispi.uzh.ch/sleep


Please send your CV with scientific record, letter of motivation and 2
referees (including e-mail addresses) as a single PDF file by e-mail
to: reto.huber at kispi.uzh.ch

----------------------------------
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From h.leuthold at PSY.GLA.AC.UK  Thu Oct 16 18:44:40 2008
From: h.leuthold at PSY.GLA.AC.UK (Hartmut Leuthold)
Date: Thu, 16 Oct 2008 17:44:40 +0100
Subject: 1-year postdoctoral position
Message-ID: <THU.16.OCT.2008.174440.0100.FIELDTRIP@NIC.SURFNET.NL>

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From florisdelange at GMAIL.COM  Fri Oct 17 16:44:39 2008
From: florisdelange at GMAIL.COM (Floris de Lange)
Date: Fri, 17 Oct 2008 16:44:39 +0200
Subject: cluster statistic on one sample
Message-ID: <FRI.17.OCT.2008.164439.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrippers,

I have a question about statistical analysis on the sensor level.
I would like to make use of the cluster size thresholding of the
clusterrand routine in Fieldtrip. Unfortunately, in the current
wrapper, it seems there is no option for a one-sample T-test? There is
an activation-baseline test, and a (in)dependent samples test between
two conditions, but what I want to do is simply test whether a 14
(subjects) x 275 (channels) matrix is different from zero, taking into
account the spatial relations between adjacent sensors. (The data
points are regression weights from a multiple-regression analysis, so
there's no easy way to split it into two parts.)
I assume this should be easy to tweak, but I couldn't come up with any
smart ideas how to do it.
Anyone any ideas?

Thanks in advance!

Floris

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From ali.mazaheri at FCDONDERS.RU.NL  Fri Oct 17 16:57:09 2008
From: ali.mazaheri at FCDONDERS.RU.NL (Ali Mazaheri)
Date: Fri, 17 Oct 2008 16:57:09 +0200
Subject: cluster statistic on one sample
Message-ID: <FRI.17.OCT.2008.165709.0200.FIELDTRIP@NIC.SURFNET.NL>

Dearest Floris,

Why not just create a zero matrices with a 14 x 275 dimension
 and do a dependent samples test between
your regresion weights and the zero matrices ?



Hope this helps !


best

Ali



----- Original Message -----
From: Floris de Lange <florisdelange at GMAIL.COM>
Date: Friday, October 17, 2008 4:44 pm
Subject: [FIELDTRIP] cluster statistic on one sample

> Dear Fieldtrippers,
>
> I have a question about statistical analysis on the sensor level.
> I would like to make use of the cluster size thresholding of the
> clusterrand routine in Fieldtrip. Unfortunately, in the current
> wrapper, it seems there is no option for a one-sample T-test? There is
> an activation-baseline test, and a (in)dependent samples test between
> two conditions, but what I want to do is simply test whether a 14
> (subjects) x 275 (channels) matrix is different from zero, taking into
> account the spatial relations between adjacent sensors. (The data
> points are regression weights from a multiple-regression analysis, so
> there's no easy way to split it into two parts.)
> I assume this should be easy to tweak, but I couldn't come up with any
> smart ideas how to do it.
> Anyone any ideas?
>
> Thanks in advance!
>
> Floris
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From zanasilva at GMAIL.COM  Fri Oct 17 18:04:14 2008
From: zanasilva at GMAIL.COM (Susana Silva)
Date: Fri, 17 Oct 2008 18:04:14 +0200
Subject: clusterrandanalysis vs timelockstatistics
Message-ID: <FRI.17.OCT.2008.180414.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi all

I have run both clusterrandanalysis and timelockstatistics (with
cfg.correctm=cluster) over the same data.
The t values in clusrand (clusterrandanalysis) are equal to the t values in
stat (timelockstatistics).

However, in timelockstatistics, the number of clusters is much higher and
the prob is much lower than in the clusterrandanalysis procedure.

1-Should I expect it?
2-where can I get some more information on clusrandanalysis function (the
tutorial does not seem to have)?

Thank you
Susana Silva

----------------------------------
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From spike377 at KOREA.COM  Sat Oct 18 22:05:36 2008
From: spike377 at KOREA.COM (=?EUC-KR?B?udrH/LW/?=)
Date: Sun, 19 Oct 2008 05:05:36 +0900
Subject: time-frequency representation of PLV
Message-ID: <SUN.19.OCT.2008.050536.0900.FIELDTRIP@NIC.SURFNET.NL>

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From e.maris at DONDERS.RU.NL  Mon Oct 20 11:17:19 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Mon, 20 Oct 2008 11:17:19 +0200
Subject: cluster statistic on one sample
In-Reply-To: <9fb563140810170744m400d703dkf66c6e6a22145e24@mail.gmail.com>
Message-ID: <MON.20.OCT.2008.111719.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Floris,



> I have a question about statistical analysis on the sensor level.
> I would like to make use of the cluster size thresholding of the
> clusterrand routine in Fieldtrip. Unfortunately, in the current
> wrapper, it seems there is no option for a one-sample T-test? There is
> an activation-baseline test, and a (in)dependent samples test between
> two conditions, but what I want to do is simply test whether a 14
> (subjects) x 275 (channels) matrix is different from zero, taking into
> account the spatial relations between adjacent sensors. (The data
> points are regression weights from a multiple-regression analysis, so
> there's no easy way to split it into two parts.)
> I assume this should be easy to tweak, but I couldn't come up with any
> smart ideas how to do it.
> Anyone any ideas?

I'm afraid that I have to disappoint you, Floris. Your null hypothesis is a
typical parametric null hypothesis; the expected value of some
(matrix-valued) variable being equal to zero. The null hypothesis that is
tested by a nonparametric permutation test is equality across experimental
conditions of the probability distribution from which the
(condition-specific) data are drawn. Since you have single condition only, I
see no way of applying the theory behind nonparametric permutation testing
(of the type described by Maris & Oostenveld, 2007) to your data.

To solve your problem we need a brilliant theoretical insight.


Greetings,

Eric






>
> Thanks in advance!
>
> Floris
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip
> toolbox, to share experiences and to discuss new ideas for MEG and EEG
analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From v.litvak at ION.UCL.AC.UK  Mon Oct 20 12:05:30 2008
From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak)
Date: Mon, 20 Oct 2008 11:05:30 +0100
Subject: cluster statistic on one sample
In-Reply-To: <e1e7c57c0810200304v45bd0061j18c2afce55a16ce@mail.gmail.com>
Message-ID: <MON.20.OCT.2008.110530.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Floris and Eric,

Parametric tests at scalp level taking into account spatial
relationship between sensors can be done in SPM (with RFT correction).
That'll require using some low-level functions to convert
coefficients to images but in principle shouldn't be that difficult.

Best,

Vladimir
>
> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris <e.maris at donders.ru.nl> wrote:
>> Dear Floris,
>>
>>
>>
>>> I have a question about statistical analysis on the sensor level.
>>> I would like to make use of the cluster size thresholding of the
>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
>>> wrapper, it seems there is no option for a one-sample T-test? There is
>>> an activation-baseline test, and a (in)dependent samples test between
>>> two conditions, but what I want to do is simply test whether a 14
>>> (subjects) x 275 (channels) matrix is different from zero, taking into
>>> account the spatial relations between adjacent sensors. (The data
>>> points are regression weights from a multiple-regression analysis, so
>>> there's no easy way to split it into two parts.)
>>> I assume this should be easy to tweak, but I couldn't come up with any
>>> smart ideas how to do it.
>>> Anyone any ideas?
>>
>> I'm afraid that I have to disappoint you, Floris. Your null hypothesis is a
>> typical parametric null hypothesis; the expected value of some
>> (matrix-valued) variable being equal to zero. The null hypothesis that is
>> tested by a nonparametric permutation test is equality across experimental
>> conditions of the probability distribution from which the
>> (condition-specific) data are drawn. Since you have single condition only, I
>> see no way of applying the theory behind nonparametric permutation testing
>> (of the type described by Maris & Oostenveld, 2007) to your data.
>>
>> To solve your problem we need a brilliant theoretical insight.
>>
>>
>> Greetings,
>>
>> Eric
>>
>>
>>
>>
>>
>>
>>>
>>> Thanks in advance!
>>>
>>> Floris
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of the
>> FieldTrip
>>> toolbox, to share experiences and to discuss new ideas for MEG and EEG
>> analysis.
>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>>
>>
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From marco.buiatti at UNITN.IT  Mon Oct 20 14:00:30 2008
From: marco.buiatti at UNITN.IT (Marco Buiatti)
Date: Mon, 20 Oct 2008 14:00:30 +0200
Subject: data format for 'between trials' cluster randomization analysis
Message-ID: <MON.20.OCT.2008.140030.0200.>

Dear Fieldtrippers,

I have data from a single subject with two conditions, and I am trying
to perform the cluster randomization analysis on the statistical
difference between the conditions - therefore a 'between trials'
analysis.

However, my data are not in the fieldtrip format, and I have problems
in converting them in the correct format. Could anyone provide me an
example of such format?

Also, the eeglab2fieldtrip function (which I tried without success) is
not included in the last Fieldtrip release: is it because there are
some problems with that function?

Thank you in advance,

Marco Buiatti

-- 
Marco Buiatti, PhD
Postdoctoral Researcher
Functional NeuroImaging Laboratory
Center for Mind Brain Sciences
Trento University
Via delle Regole, 101
38060, Mattarello (TN) - ITALY
email: marco.buiatti at unitn.it
http://www.cimec.unitn.it
Telephone: +39-0461-88 3077
Fax: +39-0461-88 3066

***********************************************
In occasione del 70° anniversario della promulgazione delle leggi
razziali, LEGGI FIRMA E DIFFONDI IL MANIFESTO ANTIRAZZISTA!
http://www.regione.toscana.it/regione/opencms/RT/sito-RT/MenuUtility/SanRossore-Firma-Manifesto-Antirazzismo
***********************************************

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From j.schoffelen at PSY.GLA.AC.UK  Mon Oct 20 14:13:11 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Mon, 20 Oct 2008 13:13:11 +0100
Subject: cluster statistic on one sample
In-Reply-To: <e1e7c57c0810200305w7ea38eddt767591636ff2b926@mail.gmail.com>
Message-ID: <MON.20.OCT.2008.131311.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Floris, Eric, Vladimir and all other people reading this message,

What about performing a nonparametric test, based on the bootstrap
distribution of the beta weights under the null-hypothesis?
This problem sounds similar to one I came across recently (and which
I still have to write something about on fieldtrip's wiki-page (sorry
Eric)), which has to do with the testing of the significance of the F-
value for interaction in a 2x2 repeated measure anova. Also in this
case, one also wants to test a parametric null-hypothesis, as Eric
phrased it in his last e-mail. One way to test this (I don't have the
reference at hand), is to test the observed F-statistic against a
null-distribution, obtained from bootstrapping your data, which you
preconditioned as to impose the null-hypothesis (in the case of an
anova it would be to remove from each of the observations the mean of
the cell to which the observation belongs). I don't know yet how to
impose the null-hypothesis in the regression case, but would this
line of thought be a possibility?
As to a potential implementation: Robert and I are pretty close to
have the bootstrapping implemented.

Yours,

Jan-Mathijs


On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:

> Dear Floris and Eric,
>
> Parametric tests at scalp level taking into account spatial
> relationship between sensors can be done in SPM (with RFT correction).
> That'll require using some low-level functions to convert
> coefficients to images but in principle shouldn't be that difficult.
>
> Best,
>
> Vladimir
>>
>> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris
>> <e.maris at donders.ru.nl> wrote:
>>> Dear Floris,
>>>
>>>
>>>
>>>> I have a question about statistical analysis on the sensor level.
>>>> I would like to make use of the cluster size thresholding of the
>>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
>>>> wrapper, it seems there is no option for a one-sample T-test?
>>>> There is
>>>> an activation-baseline test, and a (in)dependent samples test
>>>> between
>>>> two conditions, but what I want to do is simply test whether a 14
>>>> (subjects) x 275 (channels) matrix is different from zero,
>>>> taking into
>>>> account the spatial relations between adjacent sensors. (The data
>>>> points are regression weights from a multiple-regression
>>>> analysis, so
>>>> there's no easy way to split it into two parts.)
>>>> I assume this should be easy to tweak, but I couldn't come up
>>>> with any
>>>> smart ideas how to do it.
>>>> Anyone any ideas?
>>>
>>> I'm afraid that I have to disappoint you, Floris. Your null
>>> hypothesis is a
>>> typical parametric null hypothesis; the expected value of some
>>> (matrix-valued) variable being equal to zero. The null hypothesis
>>> that is
>>> tested by a nonparametric permutation test is equality across
>>> experimental
>>> conditions of the probability distribution from which the
>>> (condition-specific) data are drawn. Since you have single
>>> condition only, I
>>> see no way of applying the theory behind nonparametric
>>> permutation testing
>>> (of the type described by Maris & Oostenveld, 2007) to your data.
>>>
>>> To solve your problem we need a brilliant theoretical insight.
>>>
>>>
>>> Greetings,
>>>
>>> Eric
>>>
>>>
>>>
>>>
>>>
>>>
>>>>
>>>> Thanks in advance!
>>>>
>>>> Floris
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between
>>>> users of the
>>> FieldTrip
>>>> toolbox, to share experiences and to discuss new ideas for MEG
>>>> and EEG
>>> analysis.
>>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between
>>> users of the FieldTrip  toolbox, to share experiences and to
>>> discuss new ideas for MEG and EEG analysis. See also http://
>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/
>>> fcdonders/fieldtrip.
>>>
>>>
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From venug001 at BAMA.UA.EDU  Mon Oct 20 14:27:31 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 20 Oct 2008 07:27:31 -0500
Subject: cluster statistic on one sample
In-Reply-To: <66D7BE2A-86F7-48BA-A94C-0561DF0A568E@psy.gla.ac.uk>
Message-ID: <MON.20.OCT.2008.072731.0500.FIELDTRIP@NIC.SURFNET.NL>

Hello everyone, I just finished testing the null across two conditions
using EEGLAB which puts out t-values at various points on the waveform,
and then by exporting values to excel converting them to RMS and
averaging them over left vs right and post vs ant. I have the SPSS
multivariate code, I have been wondering about this for months now how
to integrate something like this into all the packages. Off course
since MATLAB is very powerful I suspect that adding the required MANOVA
code into those routines will solve the problem.After that is done, the
mathematical formula for generating the F distribution, and the root of
which is the t distribution can be placed in a separate sheet for a
parametric test, even though the data is non-parametric. We can make
parametric assumptions of our data even though it is non-parametric by
nature. I hand did this using a combination of excel, spss, eeglab, and
scan 4.3 which--runs on a matlab engine and is a commercial product.
A paper by Pascual-Marqui (2002) talks about how the F values in the
dipole fit and Current Density Reconstruction is a pseudo-statistic.
That paper also provides a correction so that they can be used as
parametric values. I wonder if such a correction can be applied to the
non-parametric values here, so that they can be treated and interpreted
as parametric values.
 I can see this in my mind by can tweak the c code in MATLAB with some
guidance. Am not a programmer by any strech of imagination.
regards
gopa


Quoting jan-mathijs schoffelen <j.schoffelen at PSY.GLA.AC.UK>:

> Dear Floris, Eric, Vladimir and all other people reading this
> message,
>
> What about performing a nonparametric test, based on the bootstrap
> distribution of the beta weights under the null-hypothesis?
> This problem sounds similar to one I came across recently (and which
>
> I still have to write something about on fieldtrip's wiki-page (sorry
>
> Eric)), which has to do with the testing of the significance of the
> F-
> value for interaction in a 2x2 repeated measure anova. Also in this
>
> case, one also wants to test a parametric null-hypothesis, as Eric
> phrased it in his last e-mail. One way to test this (I don't have the
>
> reference at hand), is to test the observed F-statistic against a
> null-distribution, obtained from bootstrapping your data, which you
>
> preconditioned as to impose the null-hypothesis (in the case of an
> anova it would be to remove from each of the observations the mean of
>
> the cell to which the observation belongs). I don't know yet how to
>
> impose the null-hypothesis in the regression case, but would this
> line of thought be a possibility?
> As to a potential implementation: Robert and I are pretty close to
> have the bootstrapping implemented.
>
> Yours,
>
> Jan-Mathijs
>
>
> On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:
>
> > Dear Floris and Eric,
> >
> > Parametric tests at scalp level taking into account spatial
> > relationship between sensors can be done in SPM (with RFT
> correction).
> > That'll require using some low-level functions to convert
> > coefficients to images but in principle shouldn't be that
> difficult.
> >
> > Best,
> >
> > Vladimir
> >>
> >> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris
> >> <e.maris at donders.ru.nl> wrote:
> >>> Dear Floris,
> >>>
> >>>
> >>>
> >>>> I have a question about statistical analysis on the sensor
> level.
> >>>> I would like to make use of the cluster size thresholding of
> the
> >>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
> >>>> wrapper, it seems there is no option for a one-sample T-test?
> >>>> There is
> >>>> an activation-baseline test, and a (in)dependent samples test
> >>>> between
> >>>> two conditions, but what I want to do is simply test whether a
> 14
> >>>> (subjects) x 275 (channels) matrix is different from zero,
> >>>> taking into
> >>>> account the spatial relations between adjacent sensors. (The
> data
> >>>> points are regression weights from a multiple-regression
> >>>> analysis, so
> >>>> there's no easy way to split it into two parts.)
> >>>> I assume this should be easy to tweak, but I couldn't come up
> >>>> with any
> >>>> smart ideas how to do it.
> >>>> Anyone any ideas?
> >>>
> >>> I'm afraid that I have to disappoint you, Floris. Your null
> >>> hypothesis is a
> >>> typical parametric null hypothesis; the expected value of some
> >>> (matrix-valued) variable being equal to zero. The null hypothesis
>
> >>> that is
> >>> tested by a nonparametric permutation test is equality across
> >>> experimental
> >>> conditions of the probability distribution from which the
> >>> (condition-specific) data are drawn. Since you have single
> >>> condition only, I
> >>> see no way of applying the theory behind nonparametric
> >>> permutation testing
> >>> (of the type described by Maris & Oostenveld, 2007) to your
> data.
> >>>
> >>> To solve your problem we need a brilliant theoretical insight.
> >>>
> >>>
> >>> Greetings,
> >>>
> >>> Eric
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>
> >>>> Thanks in advance!
> >>>>
> >>>> Floris
> >>>>
> >>>> ----------------------------------
> >>>> The aim of this list is to facilitate the discussion between
> >>>> users of the
> >>> FieldTrip
> >>>> toolbox, to share experiences and to discuss new ideas for MEG
>
> >>>> and EEG
> >>> analysis.
> >>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> >>>> http://www.ru.nl/fcdonders/fieldtrip.
> >>>
> >>> ----------------------------------
> >>> The aim of this list is to facilitate the discussion between
> >>> users of the FieldTrip  toolbox, to share experiences and to
> >>> discuss new ideas for MEG and EEG analysis. See also http://
> >>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/
>
> >>> fcdonders/fieldtrip.
> >>>
> >>>
> >>
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
>
> > of the FieldTrip  toolbox, to share experiences and to discuss new
>
> > ideas for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/
> > archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From e.maris at DONDERS.RU.NL  Mon Oct 20 16:02:39 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Mon, 20 Oct 2008 16:02:39 +0200
Subject: cluster statistic on one sample
In-Reply-To: <66D7BE2A-86F7-48BA-A94C-0561DF0A568E@psy.gla.ac.uk>
Message-ID: <MON.20.OCT.2008.160239.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrip-list-readers,


> What about performing a nonparametric test, based on the bootstrap
> distribution of the beta weights under the null-hypothesis?
> This problem sounds similar to one I came across recently (and which
> I still have to write something about on fieldtrip's wiki-page (sorry
> Eric)), which has to do with the testing of the significance of the F-
> value for interaction in a 2x2 repeated measure anova. Also in this
> case, one also wants to test a parametric null-hypothesis, as Eric
> phrased it in his last e-mail. One way to test this (I don't have the
> reference at hand), is to test the observed F-statistic against a
> null-distribution, obtained from bootstrapping your data, which you
> preconditioned as to impose the null-hypothesis (in the case of an
> anova it would be to remove from each of the observations the mean of
> the cell to which the observation belongs). I don't know yet how to
> impose the null-hypothesis in the regression case, but would this
> line of thought be a possibility?
> As to a potential implementation: Robert and I are pretty close to
> have the bootstrapping implemented.

Again, I can only try to clarify some points here. I will not be able to
offer a solution for your problems.

1. Contrary to the permutation test, there is no useful statistical theory
for statistical tests based on the bootstrap distribution. By "useful", I
mean a theory that allows one to specify a scientifically interesting null
hypothesis (such as, "An expected value equal to 0") under which the false
alarm rate of a boostrap-p-value-based test can be controlled.

2. The bootstrap distribution has a nice intuitive appeal, because the
procedure to generate it (sampling with replacement) mimicks the sampling
process behind the sampling distribution (which is the ultimate "thing to
get" if you want to quantify the reliability of some quantity). But that is
not a proof of false alarm rate control!

3. I think the bootstrap distribution can be useful in situations where
parametric statistical tests do not exists, but I know of no rigourous
statistical argument to substantiate this claim.


Greetings,

Eric Maris


>
> Yours,
>
> Jan-Mathijs
>
>
> On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:
>
> > Dear Floris and Eric,
> >
> > Parametric tests at scalp level taking into account spatial
> > relationship between sensors can be done in SPM (with RFT correction).
> > That'll require using some low-level functions to convert
> > coefficients to images but in principle shouldn't be that difficult.
> >
> > Best,
> >
> > Vladimir
> >>
> >> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris
> >> <e.maris at donders.ru.nl> wrote:
> >>> Dear Floris,
> >>>
> >>>
> >>>
> >>>> I have a question about statistical analysis on the sensor level.
> >>>> I would like to make use of the cluster size thresholding of the
> >>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
> >>>> wrapper, it seems there is no option for a one-sample T-test?
> >>>> There is
> >>>> an activation-baseline test, and a (in)dependent samples test
> >>>> between
> >>>> two conditions, but what I want to do is simply test whether a 14
> >>>> (subjects) x 275 (channels) matrix is different from zero,
> >>>> taking into
> >>>> account the spatial relations between adjacent sensors. (The data
> >>>> points are regression weights from a multiple-regression
> >>>> analysis, so
> >>>> there's no easy way to split it into two parts.)
> >>>> I assume this should be easy to tweak, but I couldn't come up
> >>>> with any
> >>>> smart ideas how to do it.
> >>>> Anyone any ideas?
> >>>
> >>> I'm afraid that I have to disappoint you, Floris. Your null
> >>> hypothesis is a
> >>> typical parametric null hypothesis; the expected value of some
> >>> (matrix-valued) variable being equal to zero. The null hypothesis
> >>> that is
> >>> tested by a nonparametric permutation test is equality across
> >>> experimental
> >>> conditions of the probability distribution from which the
> >>> (condition-specific) data are drawn. Since you have single
> >>> condition only, I
> >>> see no way of applying the theory behind nonparametric
> >>> permutation testing
> >>> (of the type described by Maris & Oostenveld, 2007) to your data.
> >>>
> >>> To solve your problem we need a brilliant theoretical insight.
> >>>
> >>>
> >>> Greetings,
> >>>
> >>> Eric
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>
> >>>> Thanks in advance!
> >>>>
> >>>> Floris
> >>>>
> >>>> ----------------------------------
> >>>> The aim of this list is to facilitate the discussion between
> >>>> users of the
> >>> FieldTrip
> >>>> toolbox, to share experiences and to discuss new ideas for MEG
> >>>> and EEG
> >>> analysis.
> >>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> >>>> http://www.ru.nl/fcdonders/fieldtrip.
> >>>
> >>> ----------------------------------
> >>> The aim of this list is to facilitate the discussion between
> >>> users of the FieldTrip  toolbox, to share experiences and to
> >>> discuss new ideas for MEG and EEG analysis. See also http://
> >>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/
> >>> fcdonders/fieldtrip.
> >>>
> >>>
> >>
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> > of the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> > archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip
> toolbox, to share experiences and to discuss new ideas for MEG and EEG
analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From g.rousselet at PSY.GLA.AC.UK  Mon Oct 20 18:00:47 2008
From: g.rousselet at PSY.GLA.AC.UK (Guillaume Rousselet)
Date: Mon, 20 Oct 2008 17:00:47 +0100
Subject: cluster statistic on one sample
In-Reply-To: <20081020140232.D0CA2AA0B6@smtp.ru.nl>
Message-ID: <MON.20.OCT.2008.170047.0100.FIELDTRIP@NIC.SURFNET.NL>

Hey Eric,

I am not sure I understand your point against the bootstrap. My main
source of information about robust statistics is Wilcox, R. R. (2005).
Introduction to Robust Estimation and Hypothesis Testing (2nd Ed.
ed.): Academic Press.
In this book, Wilcox makes an extensive use of the bootstrap
technique. The validation of the technique, when it has been
performed, relies on Monte-Carlo simulations. Also, over almost 600
pages, Wilcox spends only one page on permutations, basically saying
that it is a special case of the bootstrap and that there is no
particular reason to use it.
Do you have references showing validation tests with a direct
comparison of bootstrap and permutation? My understanding is that such
comparisons do not exist for EEG/MEG data.
Also, one must keep in mind that bootstrap is particularly efficient
when applied to robust measures of central tendency, like trimmed
means and M-estimators, see my recent EEG paper for instance (http://www.journalofvision.org/8/12/3/
).
Finally, Wilcox provides a large number of recipes to test
significance of linear regression results, that could be applied to
the problem outlined earlier about the hypothesis test against zero.

Best,

GAR




On 20 Oct 2008, at 15:02, Eric Maris wrote:

> Dear Fieldtrip-list-readers,
>
>
>> What about performing a nonparametric test, based on the bootstrap
>> distribution of the beta weights under the null-hypothesis?
>> This problem sounds similar to one I came across recently (and which
>> I still have to write something about on fieldtrip's wiki-page (sorry
>> Eric)), which has to do with the testing of the significance of the
>> F-
>> value for interaction in a 2x2 repeated measure anova. Also in this
>> case, one also wants to test a parametric null-hypothesis, as Eric
>> phrased it in his last e-mail. One way to test this (I don't have the
>> reference at hand), is to test the observed F-statistic against a
>> null-distribution, obtained from bootstrapping your data, which you
>> preconditioned as to impose the null-hypothesis (in the case of an
>> anova it would be to remove from each of the observations the mean of
>> the cell to which the observation belongs). I don't know yet how to
>> impose the null-hypothesis in the regression case, but would this
>> line of thought be a possibility?
>> As to a potential implementation: Robert and I are pretty close to
>> have the bootstrapping implemented.
>
> Again, I can only try to clarify some points here. I will not be
> able to
> offer a solution for your problems.
>
> 1. Contrary to the permutation test, there is no useful statistical
> theory
> for statistical tests based on the bootstrap distribution. By
> "useful", I
> mean a theory that allows one to specify a scientifically
> interesting null
> hypothesis (such as, "An expected value equal to 0") under which the
> false
> alarm rate of a boostrap-p-value-based test can be controlled.
>
> 2. The bootstrap distribution has a nice intuitive appeal, because the
> procedure to generate it (sampling with replacement) mimicks the
> sampling
> process behind the sampling distribution (which is the ultimate
> "thing to
> get" if you want to quantify the reliability of some quantity). But
> that is
> not a proof of false alarm rate control!
>
> 3. I think the bootstrap distribution can be useful in situations
> where
> parametric statistical tests do not exists, but I know of no rigourous
> statistical argument to substantiate this claim.
>
>
> Greetings,
>
> Eric Maris
>
>
>>
>> Yours,
>>
>> Jan-Mathijs
>>
>>
>> On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:
>>
>>> Dear Floris and Eric,
>>>
>>> Parametric tests at scalp level taking into account spatial
>>> relationship between sensors can be done in SPM (with RFT
>>> correction).
>>> That'll require using some low-level functions to convert
>>> coefficients to images but in principle shouldn't be that difficult.
>>>
>>> Best,
>>>
>>> Vladimir
>>>>
>>>> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris
>>>> <e.maris at donders.ru.nl> wrote:
>>>>> Dear Floris,
>>>>>
>>>>>
>>>>>
>>>>>> I have a question about statistical analysis on the sensor level.
>>>>>> I would like to make use of the cluster size thresholding of the
>>>>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
>>>>>> wrapper, it seems there is no option for a one-sample T-test?
>>>>>> There is
>>>>>> an activation-baseline test, and a (in)dependent samples test
>>>>>> between
>>>>>> two conditions, but what I want to do is simply test whether a 14
>>>>>> (subjects) x 275 (channels) matrix is different from zero,
>>>>>> taking into
>>>>>> account the spatial relations between adjacent sensors. (The data
>>>>>> points are regression weights from a multiple-regression
>>>>>> analysis, so
>>>>>> there's no easy way to split it into two parts.)
>>>>>> I assume this should be easy to tweak, but I couldn't come up
>>>>>> with any
>>>>>> smart ideas how to do it.
>>>>>> Anyone any ideas?
>>>>>
>>>>> I'm afraid that I have to disappoint you, Floris. Your null
>>>>> hypothesis is a
>>>>> typical parametric null hypothesis; the expected value of some
>>>>> (matrix-valued) variable being equal to zero. The null hypothesis
>>>>> that is
>>>>> tested by a nonparametric permutation test is equality across
>>>>> experimental
>>>>> conditions of the probability distribution from which the
>>>>> (condition-specific) data are drawn. Since you have single
>>>>> condition only, I
>>>>> see no way of applying the theory behind nonparametric
>>>>> permutation testing
>>>>> (of the type described by Maris & Oostenveld, 2007) to your data.
>>>>>
>>>>> To solve your problem we need a brilliant theoretical insight.
>>>>>
>>>>>
>>>>> Greetings,
>>>>>
>>>>> Eric
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>> Thanks in advance!
>>>>>>
>>>>>> Floris
>>>>>>
>>>>>> ----------------------------------
>>>>>> The aim of this list is to facilitate the discussion between
>>>>>> users of the
>>>>> FieldTrip
>>>>>> toolbox, to share experiences and to discuss new ideas for MEG
>>>>>> and EEG
>>>>> analysis.
>>>>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>>
>>>>> ----------------------------------
>>>>> The aim of this list is to facilitate the discussion between
>>>>> users of the FieldTrip  toolbox, to share experiences and to
>>>>> discuss new ideas for MEG and EEG analysis. See also http://
>>>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/
>>>>> fcdonders/fieldtrip.
>>>>>
>>>>>
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>>> of the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
>>> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the
> FieldTrip
>> toolbox, to share experiences and to discuss new ideas for MEG and
>> EEG
> analysis.
>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/fcdonders/fieldtrip.






************************************************************************************
Guillaume A. Rousselet, Ph.D.

Lecturer

Centre for Cognitive Neuroimaging (CCNi)
Department of Psychology
Faculty of Information & Mathematical Sciences (FIMS)
University of Glasgow
58 Hillhead Street
Glasgow, UK
G12 8QB

The University of Glasgow, charity number SC004401

http://web.me.com/rousseg/GARs_website/

Email: g.rousselet at psy.gla.ac.uk
Fax. +44 (0)141 330 4606
Tel. +44 (0)141 330 6652
Cell +44 (0)791 779 7833


"no test based upon a theory of probability can by itself
provide any valuable evidence of the truth or falsehood
of a hypothesis.

But we may look at the purpose of tests from another
viewpoint. Without hoping to know whether each separate
hypothesis is true or false, we may search for
rules to govern our behaviour with regard to them, in
following which we insure that, in the long run of
experience, we shall not often be wrong."

	Neyman J & Pearson E, 1933
************************************************************************************







----------------------------------
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From e.maris at DONDERS.RU.NL  Mon Oct 20 21:15:30 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Mon, 20 Oct 2008 21:15:30 +0200
Subject: cluster statistic on one sample
In-Reply-To: <287D1AC6-92F5-466A-BD05-535711CA5AD0@psy.gla.ac.uk>
Message-ID: <MON.20.OCT.2008.211530.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Guillaume,





I am not sure I understand your point against the bootstrap. My main source
of information about robust statistics is Wilcox, R. R. (2005). Introduction
to Robust Estimation and Hypothesis Testing (2nd Ed. ed.): Academic Press.

In this book, Wilcox makes an extensive use of the bootstrap technique. The
validation of the technique, when it has been performed, relies on
Monte-Carlo simulations. Also, over almost 600 pages, Wilcox spends only one
page on permutations, basically saying that it is a special case of the
bootstrap and that there is no particular reason to use it.

Do you have references showing validation tests with a direct comparison of
bootstrap and permutation? My understanding is that such comparisons do not
exist for EEG/MEG data.

Also, one must keep in mind that bootstrap is particularly efficient when
applied to robust measures of central tendency, like trimmed means and
M-estimators, see my recent EEG paper for instance
(http://www.journalofvision.org/8/12/3/).

Finally, Wilcox provides a large number of recipes to test significance of
linear regression results, that could be applied to the problem outlined
earlier about the hypothesis test against zero.





Please do not misunderstand me. I would love to see rigorous mathematical
proofs substantiating the use of the bootstrap distribution for false alarm
rate control under some scientifically interesting null hypothesis. Also, I
am not married to permutation tests (fortunately!). However, I cannot ignore
the fact that a very nice proof exists (which is even very intuitive)
showing that permutation tests control the false alarm rate of any test
statistic and for any correlation pattern in data of arbitrary
dimensionality. Moreover, it does so under a null hypothesis that is
scientifically interesting (data from multiple  experimental conditions
governed by the same probability distribution).



Please forgive for being explicit, but I do not think it is scientifically
appropriate to ask me for "references showing validation tests with a direct
comparison of bootstrap and permutation". The burden of the proof is
completely on the side of the side of the advocates of the bootstrap. They
have to show that a statistical test based on a bootstrap p-value controls
the false alarm rate under a scientifically interesting null hypothesis.
With such a proof on the table, I will become a vigourous defender of the
bootstrap, but until that I will only present it as procedure with an
intuitively appealing rationale.



After showing false alarm rate control by the bootstrap (i.e., under some
null hypothesis), there is the issue of comparing it with permutation tests
with respect to statistical sensitivity (i.e., under the alternative
hypothesis). I have no idea about the relative performance of bootstrap and
permutation tests in this respect, but intuitively I do not expect a big
difference. However, what will make a big difference is the type of test
statistic that is evaluated in under either the permutation or the bootstrap
distribution.







Greetings,



Eric Maris











Best,



GAR









On 20 Oct 2008, at 15:02, Eric Maris wrote:





Dear Fieldtrip-list-readers,





What about performing a nonparametric test, based on the bootstrap

distribution of the beta weights under the null-hypothesis?

This problem sounds similar to one I came across recently (and which

I still have to write something about on fieldtrip's wiki-page (sorry

Eric)), which has to do with the testing of the significance of the F-

value for interaction in a 2x2 repeated measure anova. Also in this

case, one also wants to test a parametric null-hypothesis, as Eric

phrased it in his last e-mail. One way to test this (I don't have the

reference at hand), is to test the observed F-statistic against a

null-distribution, obtained from bootstrapping your data, which you

preconditioned as to impose the null-hypothesis (in the case of an

anova it would be to remove from each of the observations the mean of

the cell to which the observation belongs). I don't know yet how to

impose the null-hypothesis in the regression case, but would this

line of thought be a possibility?

As to a potential implementation: Robert and I are pretty close to

have the bootstrapping implemented.


Again, I can only try to clarify some points here. I will not be able to
offer a solution for your problems.

1. Contrary to the permutation test, there is no useful statistical theory
for statistical tests based on the bootstrap distribution. By "useful", I
mean a theory that allows one to specify a scientifically interesting null
hypothesis (such as, "An expected value equal to 0") under which the false
alarm rate of a boostrap-p-value-based test can be controlled.

2. The bootstrap distribution has a nice intuitive appeal, because the
procedure to generate it (sampling with replacement) mimicks the sampling
process behind the sampling distribution (which is the ultimate "thing to
get" if you want to quantify the reliability of some quantity). But that is
not a proof of false alarm rate control!

3. I think the bootstrap distribution can be useful in situations where
parametric statistical tests do not exists, but I know of no rigourous
statistical argument to substantiate this claim.


Greetings,

Eric Maris







Yours,



Jan-Mathijs





On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:



Dear Floris and Eric,



Parametric tests at scalp level taking into account spatial

relationship between sensors can be done in SPM (with RFT correction).

That'll require using some low-level functions to convert

coefficients to images but in principle shouldn't be that difficult.



Best,



Vladimir



On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris

<e.maris at donders.ru.nl> wrote:

Dear Floris,







I have a question about statistical analysis on the sensor level.

I would like to make use of the cluster size thresholding of the

clusterrand routine in Fieldtrip. Unfortunately, in the current

wrapper, it seems there is no option for a one-sample T-test?

There is

an activation-baseline test, and a (in)dependent samples test

between

two conditions, but what I want to do is simply test whether a 14

(subjects) x 275 (channels) matrix is different from zero,

taking into

account the spatial relations between adjacent sensors. (The data

points are regression weights from a multiple-regression

analysis, so

there's no easy way to split it into two parts.)

I assume this should be easy to tweak, but I couldn't come up

with any

smart ideas how to do it.

Anyone any ideas?



I'm afraid that I have to disappoint you, Floris. Your null

hypothesis is a

typical parametric null hypothesis; the expected value of some

(matrix-valued) variable being equal to zero. The null hypothesis

that is

tested by a nonparametric permutation test is equality across

experimental

conditions of the probability distribution from which the

(condition-specific) data are drawn. Since you have single

condition only, I

see no way of applying the theory behind nonparametric

permutation testing

(of the type described by Maris & Oostenveld, 2007) to your data.



To solve your problem we need a brilliant theoretical insight.





Greetings,



Eric















Thanks in advance!



Floris



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

The aim of this list is to facilitate the discussion between

users of the

FieldTrip

toolbox, to share experiences and to discuss new ideas for MEG

and EEG

analysis.

See also http://listserv.surfnet.nl/archives/fieldtrip.html and

http://www.ru.nl/fcdonders/fieldtrip.



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

The aim of this list is to facilitate the discussion between

users of the FieldTrip  toolbox, to share experiences and to

discuss new ideas for MEG and EEG analysis. See also http://

listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/

fcdonders/fieldtrip.









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

The aim of this list is to facilitate the discussion between users

of the FieldTrip  toolbox, to share experiences and to discuss new

ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/

archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.



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

The aim of this list is to facilitate the discussion between users of the

FieldTrip



toolbox, to share experiences and to discuss new ideas for MEG and EEG

analysis.



See also http://listserv.surfnet.nl/archives/fieldtrip.html and

http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the
FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
and EEG analysis. See also
http://listserv.surfnet.nl/archives/fieldtrip.html and
http://www.ru.nl/fcdonders/fieldtrip.











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

Guillaume A. Rousselet, Ph.D.



Lecturer



Centre for Cognitive Neuroimaging (CCNi)

Department of Psychology

Faculty of Information & Mathematical Sciences (FIMS)

University of Glasgow

58 Hillhead Street

Glasgow, UK

G12 8QB



The University of Glasgow, charity number SC004401



http://web.me.com/rousseg/GARs_website/



Email: g.rousselet at psy.gla.ac.uk

Fax. +44 (0)141 330 4606

Tel. +44 (0)141 330 6652

Cell +44 (0)791 779 7833





"no test based upon a theory of probability can by itself

provide any valuable evidence of the truth or falsehood

of a hypothesis.



But we may look at the purpose of tests from another

viewpoint. Without hoping to know whether each separate

hypothesis is true or false, we may search for

rules to govern our behaviour with regard to them, in

following which we insure that, in the long run of

experience, we shall not often be wrong."



             Neyman J & Pearson E, 1933

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













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

The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/fieldtrip/


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From florisdelange at GMAIL.COM  Tue Oct 21 00:33:45 2008
From: florisdelange at GMAIL.COM (Floris de Lange)
Date: Tue, 21 Oct 2008 00:33:45 +0200
Subject: cluster statistic on one sample
Message-ID: <TUE.21.OCT.2008.003345.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Eric and other fieldtrippers,

I am a bit puzzled about your comment that:
"Your null hypothesis is a typical parametric null hypothesis; the
expected value of some
(matrix-valued) variable being equal to zero.The null hypothesis that is
tested by a nonparametric permutation test is equality across experimental
conditions of the probability distribution from which the
(condition-specific) data are drawn."

If I understand what SnPM (for fMRI) does well, it uses a permutation
test on one sample, creating a probability distribution by randomly
changing the sign of the observations. I quote (taken from
http://www.sph.umich.edu/ni-stat/SnPM/)

"Under the null hypothesis we can permute the labels of the effects of
interest. One way of implementing this with contrast images is to
randomly change the sign of each subject's contrast. This
sign-flipping approach can be justified by a symmetric distribution
for each voxel's data under the null hypothesis. While symmetry may
sound like a strong assumption, it is weaker than Normality, and can
be justified by a subtraction of two sample means with the same
(arbitrary) distribution.

Hence the null hypothesis here is:
    H0: The symmetric distribution of (the voxel values of the)
subjects' contrast images have zero mean.

And some more detail on the assumptions:

(..) to analyze a group of subjects for population inference, we need
to only assume exchangeability of subjects. The conventional
assumption of independent subjects implies exchangeability, and hence
a single exchangeability block (EB) consisting of all subjects.

(On a technical note, the assumption of exchangeability can actually
be relaxed for the one-sample case considered here. A sufficient
assumption for the contrast data to have a symmetric distribution, is
for each subject's contrast data to have a symmetric but possibly
different distribution. Such differences between subjects violates
exchangeability of all the data; however, since the null distribution
of the statistic of interest is invariant with respect to
sign-flipping, the test is valid.)

I don't see why this approach wouldn't be applicable for MEG data?
As a side note, comparing my regression weights with a condition of
all zeros with a dependent sample T-test works well, and is
mathematically equivalent to a one-sample T-test as far as I can see,
at least in the parametric domain?


Best wishes,
Floris

--
--
Floris de Lange
http://www.florisdelange.com

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From e.maris at DONDERS.RU.NL  Tue Oct 21 11:03:50 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Tue, 21 Oct 2008 11:03:50 +0200
Subject: cluster statistic on one sample
In-Reply-To: <9fb563140810201533i7e045770n8b88936106ed34b4@mail.gmail.com>
Message-ID: <TUE.21.OCT.2008.110350.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Floris and others,



> If I understand what SnPM (for fMRI) does well, it uses a permutation
> test on one sample, creating a probability distribution by randomly
> changing the sign of the observations. I quote (taken from
> http://www.sph.umich.edu/ni-stat/SnPM/)
>
> "Under the null hypothesis we can permute the labels of the effects of
> interest. One way of implementing this with contrast images is to
> randomly change the sign of each subject's contrast. This
> sign-flipping approach can be justified by a symmetric distribution
> for each voxel's data under the null hypothesis. While symmetry may
> sound like a strong assumption, it is weaker than Normality, and can
> be justified by a subtraction of two sample means with the same
> (arbitrary) distribution.

This quote is about a study involving TWO experimental conditions that are
manipulated within every subject. This is also called a paired-samples
design. So, it is NOT a one-sample study. The confusion probably arises from
the fact that a paired-samples (dependent-samples) T-test is identical to a
one-sample T-test on the difference scores. For a paired-samples T-test it
makes sense to construct a reference distribution by randomly switching the
signs of the difference scores. For a one-sample T-test on the data of a
single condition (e.g., the IQ-scores of a group of students), however, it
does not make sense to think about such an operation. (This is a brief,
intuitive explanation, which could be made more precise, but only at the
expense of more text.)

In your quote, also the concepts "symmetry of the distribution" and
"exchangeability" are mentioned. To keep things clear in our minds, it is
good to know that

1. Some statisticians (e.g., Tom Nichols, the author of your quote) motivate
permutation tests from considerations involving the shape of the probability
distribution (such as symmetry). Other statisticians (like Fortunato
Pesarin, and I) motivate permutation tests from considerations about
exchangeability between experimental conditions.

2. "Exchangeability" is a very general concept that can be used in very
different contexts. Some statisticians (e.g., Tom Nichols) use the term
"exchangeability" to denote a property of the probability distribution from
which the subjects are drawn, not mentioning the fact that these subjects
were observed in two experimental conditions. Other statisticians (like I)
use "exchangeability" with explicit reference to the data observed in the
two experimental conditions. For me, exchangeability involves that the
probability distribution of paired observations is invariant under random
permutations of the members of these pairs. This assumption of
exchangeability implies that the data in the two experimental conditions
have the same marginal probability distribution.


(If you like this explanation, Floris, you could join Jan-Mathijs in his
effort to make a Wiki-tutorial about the statistical rationale of
permutation tests.)




Don't start cursing the statisticians now!


Eric Maris

>
> Hence the null hypothesis here is:
>     H0: The symmetric distribution of (the voxel values of the)
> subjects' contrast images have zero mean.
>
> And some more detail on the assumptions:
>
> (..) to analyze a group of subjects for population inference, we need
> to only assume exchangeability of subjects. The conventional
> assumption of independent subjects implies exchangeability, and hence
> a single exchangeability block (EB) consisting of all subjects.
>
> (On a technical note, the assumption of exchangeability can actually
> be relaxed for the one-sample case considered here. A sufficient
> assumption for the contrast data to have a symmetric distribution, is
> for each subject's contrast data to have a symmetric but possibly
> different distribution. Such differences between subjects violates
> exchangeability of all the data; however, since the null distribution
> of the statistic of interest is invariant with respect to
> sign-flipping, the test is valid.)
>
> I don't see why this approach wouldn't be applicable for MEG data?
> As a side note, comparing my regression weights with a condition of
> all zeros with a dependent sample T-test works well, and is
> mathematically equivalent to a one-sample T-test as far as I can see,
> at least in the parametric domain?
>
>
> Best wishes,
> Floris
>
> --
> --
> Floris de Lange
> http://www.florisdelange.com
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip
> toolbox, to share experiences and to discuss new ideas for MEG and EEG
analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From florisdelange at GMAIL.COM  Tue Oct 21 17:47:30 2008
From: florisdelange at GMAIL.COM (Floris de Lange)
Date: Tue, 21 Oct 2008 17:47:30 +0200
Subject: cluster statistic on one sample
Message-ID: <TUE.21.OCT.2008.174730.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Eric,

>This quote is about a study involving TWO experimental conditions that are
>manipulated within every subject. This is also called a paired-samples
>design. So, it is NOT a one-sample study. 

I agree. Note that in my original question I didn't ask about a one-sample
*study*, but a one-sample *T-test* (on regression weights, which reflect a
weighted difference between several conditions, so not a one-sample study).
Ali's suggestion of simply comparing the regression weights against a matrix
of zeros, using paired samples T-test is excellent I think, and amounts to
the same as sign-flipping in a one-sample T-test. 

Thanks at any rate for your clarification, and best wishes from Paris
Floris

>In your quote, also the concepts "symmetry of the distribution" and
>"exchangeability" are mentioned. To keep things clear in our minds, it is
>good to know that
>
>1. Some statisticians (e.g., Tom Nichols, the author of your quote) motivate
>permutation tests from considerations involving the shape of the probability
>distribution (such as symmetry). Other statisticians (like Fortunato
>Pesarin, and I) motivate permutation tests from considerations about
>exchangeability between experimental conditions.
>
>2. "Exchangeability" is a very general concept that can be used in very
>different contexts. Some statisticians (e.g., Tom Nichols) use the term
>"exchangeability" to denote a property of the probability distribution from
>which the subjects are drawn, not mentioning the fact that these subjects
>were observed in two experimental conditions. Other statisticians (like I)
>use "exchangeability" with explicit reference to the data observed in the
>two experimental conditions. For me, exchangeability involves that the
>probability distribution of paired observations is invariant under random
>permutations of the members of these pairs. This assumption of
>exchangeability implies that the data in the two experimental conditions
>have the same marginal probability distribution.
>
>
>(If you like this explanation, Floris, you could join Jan-Mathijs in his
>effort to make a Wiki-tutorial about the statistical rationale of
>permutation tests.)
>
>
>
>
>Don't start cursing the statisticians now!
>
>
>Eric Maris
>
>>
>> Hence the null hypothesis here is:
>>     H0: The symmetric distribution of (the voxel values of the)
>> subjects' contrast images have zero mean.
>>
>> And some more detail on the assumptions:
>>
>> (..) to analyze a group of subjects for population inference, we need
>> to only assume exchangeability of subjects. The conventional
>> assumption of independent subjects implies exchangeability, and hence
>> a single exchangeability block (EB) consisting of all subjects.
>>
>> (On a technical note, the assumption of exchangeability can actually
>> be relaxed for the one-sample case considered here. A sufficient
>> assumption for the contrast data to have a symmetric distribution, is
>> for each subject's contrast data to have a symmetric but possibly
>> different distribution. Such differences between subjects violates
>> exchangeability of all the data; however, since the null distribution
>> of the statistic of interest is invariant with respect to
>> sign-flipping, the test is valid.)
>>
>> I don't see why this approach wouldn't be applicable for MEG data?
>> As a side note, comparing my regression weights with a condition of
>> all zeros with a dependent sample T-test works well, and is
>> mathematically equivalent to a one-sample T-test as far as I can see,
>> at least in the parametric domain?
>>
>>
>> Best wishes,
>> Floris
>>
>> --
>> --
>> Floris de Lange
>> http://www.florisdelange.com
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of the
>FieldTrip
>> toolbox, to share experiences and to discuss new ideas for MEG and EEG
>analysis.
>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>
>----------------------------------
>The aim of this list is to facilitate the discussion between users of the
FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
and EEG analysis. See also
http://listserv.surfnet.nl/archives/fieldtrip.html and
http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From spike377 at KOREA.COM  Wed Oct 22 04:01:15 2008
From: spike377 at KOREA.COM (=?EUC-KR?B?aHlvdW5nZG9uZy5wYXJr?=)
Date: Wed, 22 Oct 2008 11:01:15 +0900
Subject: question about topoplot
Message-ID: <WED.22.OCT.2008.110115.0900.FIELDTRIP@NIC.SURFNET.NL>

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From e.maris at DONDERS.RU.NL  Wed Oct 22 11:22:44 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Wed, 22 Oct 2008 11:22:44 +0200
Subject: cluster statistic on one sample
In-Reply-To: <LISTSERV%200810211747300670.67ED@NIC.SURFNET.NL>
Message-ID: <WED.22.OCT.2008.112244.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Floris,



> >This quote is about a study involving TWO experimental conditions that
are
> >manipulated within every subject. This is also called a paired-samples
> >design. So, it is NOT a one-sample study.
>
> I agree. Note that in my original question I didn't ask about a one-sample
> *study*, but a one-sample *T-test* (on regression weights, which reflect a
> weighted difference between several conditions, so not a one-sample
study).
> Ali's suggestion of simply comparing the regression weights against a
matrix
> of zeros, using paired samples T-test is excellent I think, and amounts to
> the same as sign-flipping in a one-sample T-test.


I do not agree. If your regression weights are calculated over multiple
conditions (each indexed by some number), then the appropriate permutation
is permutation across these multiple conditions. The appropriate "statfun"
(this is Fieldtrip terminology) is "indepsamplesregrT" for a between-units
design (typically, between-trials) and "depsamplesregrT" for a within-units
design (typically, within-subjects).


Good luck,

Eric






>
> Thanks at any rate for your clarification, and best wishes from Paris
> Floris
>
> >In your quote, also the concepts "symmetry of the distribution" and
> >"exchangeability" are mentioned. To keep things clear in our minds, it is
> >good to know that
> >
> >1. Some statisticians (e.g., Tom Nichols, the author of your quote)
motivate
> >permutation tests from considerations involving the shape of the
probability
> >distribution (such as symmetry). Other statisticians (like Fortunato
> >Pesarin, and I) motivate permutation tests from considerations about
> >exchangeability between experimental conditions.
> >
> >2. "Exchangeability" is a very general concept that can be used in very
> >different contexts. Some statisticians (e.g., Tom Nichols) use the term
> >"exchangeability" to denote a property of the probability distribution
from
> >which the subjects are drawn, not mentioning the fact that these subjects
> >were observed in two experimental conditions. Other statisticians (like
I)
> >use "exchangeability" with explicit reference to the data observed in the
> >two experimental conditions. For me, exchangeability involves that the
> >probability distribution of paired observations is invariant under random
> >permutations of the members of these pairs. This assumption of
> >exchangeability implies that the data in the two experimental conditions
> >have the same marginal probability distribution.
> >
> >
> >(If you like this explanation, Floris, you could join Jan-Mathijs in his
> >effort to make a Wiki-tutorial about the statistical rationale of
> >permutation tests.)
> >
> >
> >
> >
> >Don't start cursing the statisticians now!
> >
> >
> >Eric Maris
> >
> >>
> >> Hence the null hypothesis here is:
> >>     H0: The symmetric distribution of (the voxel values of the)
> >> subjects' contrast images have zero mean.
> >>
> >> And some more detail on the assumptions:
> >>
> >> (..) to analyze a group of subjects for population inference, we need
> >> to only assume exchangeability of subjects. The conventional
> >> assumption of independent subjects implies exchangeability, and hence
> >> a single exchangeability block (EB) consisting of all subjects.
> >>
> >> (On a technical note, the assumption of exchangeability can actually
> >> be relaxed for the one-sample case considered here. A sufficient
> >> assumption for the contrast data to have a symmetric distribution, is
> >> for each subject's contrast data to have a symmetric but possibly
> >> different distribution. Such differences between subjects violates
> >> exchangeability of all the data; however, since the null distribution
> >> of the statistic of interest is invariant with respect to
> >> sign-flipping, the test is valid.)
> >>
> >> I don't see why this approach wouldn't be applicable for MEG data?
> >> As a side note, comparing my regression weights with a condition of
> >> all zeros with a dependent sample T-test works well, and is
> >> mathematically equivalent to a one-sample T-test as far as I can see,
> >> at least in the parametric domain?
> >>
> >>
> >> Best wishes,
> >> Floris
> >>
> >> --
> >> --
> >> Floris de Lange
> >> http://www.florisdelange.com
> >>
> >> ----------------------------------
> >> The aim of this list is to facilitate the discussion between users of
the
> >FieldTrip
> >> toolbox, to share experiences and to discuss new ideas for MEG and EEG
> >analysis.
> >> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> >> http://www.ru.nl/fcdonders/fieldtrip.
> >
> >----------------------------------
> >The aim of this list is to facilitate the discussion between users of the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From olga at GRAPHICMIND.INFO  Wed Oct 22 13:10:01 2008
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Wed, 22 Oct 2008 12:10:01 +0100
Subject: Fwd: RE: clusterrandomization for 2 epochs separately
Message-ID: <WED.22.OCT.2008.121001.0100.>

> Dear Eric, 
> I would like to consult with you about some our ERP data and
> application of the clusterrandomization to it. 
> 
> I am writing now the article about ERP signs of visual change
> detection. 
> 
> We have ERP to the "deviant" and "standard" stimuli sampling rate
> 512 Hz, 64 channels (Biosemi), 12 subjects. 
> 
> If we use the paired-wise t-test to compare the ERPs' amplitudes in
> response to standard and deviant stimuli separately for each
> electrode and time point (and plot it see the picture at the end of
> the letter) we can see 2 (4) time regions of differences. But
> application of clusterrandomization analysis to these data (latency
> 0-500 ms) reveal only late cluster as significant, the early cluster
> is marginally significant (p=0.1). But I really believe in this early
> effect (120-160 ms), it is very important for our paper. When I run
> the clusterrandomization analysis on the narrowed epoch (0-300 ms) I
> got the early cluster significant. But the problem than that I loose
> the late effect, which is also worth mentioning in the paper. 
> 
> Therefore, I would like you opinion about the possibility to use the
> clusterrandomization analysis separately on the 2 epochs of interest,
> let say first 250 ms post-stimulus (0-250 ms) and next (250-500 ms). 
> 
> In this case there would be two significant clusters...  
> Best Regards, 
> 
> Olga Sysoeva 
> P.S. 
> 
> I also used different parameters for clusterrandomization (ndis,
> nchannels) but this does not change the results much.  
> P.P.S. 
> 
> Additional material 
> The paired-wise t-test was used to compare the ERPs' amplitudes in
> response to standard and deviant stimuli separately for each
> electrode and time point. 
> 
> The standard and deviant ERPs comparison reveals 2(4) intervals of
> significant differences:  
> 
> Fig.1. At this weird J picture we see the boxes of significant
> differences between standard and deviant ERPs for each time point (x
> axis) and electrode (y axis). 
> Olga Sysoeva, PhD
> Institute of Higher Nervous 
> Activity and Neurophysiology
> Russian Academy of Sciences
> 5a Butlerova str.
> Moscow 117485
> RUSSIA
> tel.: (7-095)-3347011, 
> fax:(7-095)-338-85-00.    
> 
> Links:
> ------
> [2] http://www.ru.nl/master/cns/
> 
> 

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From enteka at HOTMAIL.COM  Wed Oct 22 15:24:15 2008
From: enteka at HOTMAIL.COM (Nicolas Robitaille)
Date: Wed, 22 Oct 2008 13:24:15 +0000
Subject: Fwd: RE: clusterrandomization for 2 epochs separately
In-Reply-To: <49214.1224673801@graphicmind.info>
Message-ID: <WED.22.OCT.2008.132415.0000.FIELDTRIP@NIC.SURFNET.NL>


Dear Olga,

I have a quick answer for you, and would be please to heard people's comment on it. If you had a priori reason to belive something would happen for these electrodes and time-window, you don't need cluster analysis at all. All the solutions to the multiple-comparison problem are to be used in exploratory situation, when you don't know what to expect. If you had specific hypothesis, don't be shy: test them directy with a T-Test on the average voltage for a pre-determined time-window. 

Think about it, if you did expect these effects to be there, you could had create a montage with only one or two electrodes, and the multiple-comparison problem would not apply at all.

Hope this help,

Nic

************************************
Nicolas Robitaille, candidat Ph.D
Département de Psychologie
Université de Montréal
C.P. 6128, succursale Centre-ville
Montréal, Québec H3C 3J7
Tel.: 514-343-6111 x2631
Fax: 514-343-5787
************************************


> Date: Wed, 22 Oct 2008 12:10:01 +0100
> From: olga at GRAPHICMIND.INFO
> Subject: [FIELDTRIP] Fwd: RE: clusterrandomization for 2 epochs separately
> To: FIELDTRIP at NIC.SURFNET.NL
> 
> > Dear Eric, 
> > I would like to consult with you about some our ERP data and
> > application of the clusterrandomization to it. 
> > 
> > I am writing now the article about ERP signs of visual change
> > detection. 
> > 
> > We have ERP to the "deviant" and "standard" stimuli sampling rate
> > 512 Hz, 64 channels (Biosemi), 12 subjects. 
> > 
> > If we use the paired-wise t-test to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point (and plot it see the picture at the end of
> > the letter) we can see 2 (4) time regions of differences. But
> > application of clusterrandomization analysis to these data (latency
> > 0-500 ms) reveal only late cluster as significant, the early cluster
> > is marginally significant (p=0.1). But I really believe in this early
> > effect (120-160 ms), it is very important for our paper. When I run
> > the clusterrandomization analysis on the narrowed epoch (0-300 ms) I
> > got the early cluster significant. But the problem than that I loose
> > the late effect, which is also worth mentioning in the paper. 
> > 
> > Therefore, I would like you opinion about the possibility to use the
> > clusterrandomization analysis separately on the 2 epochs of interest,
> > let say first 250 ms post-stimulus (0-250 ms) and next (250-500 ms). 
> > 
> > In this case there would be two significant clusters...  
> > Best Regards, 
> > 
> > Olga Sysoeva 
> > P.S. 
> > 
> > I also used different parameters for clusterrandomization (ndis,
> > nchannels) but this does not change the results much.  
> > P.P.S. 
> > 
> > Additional material 
> > The paired-wise t-test was used to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point. 
> > 
> > The standard and deviant ERPs comparison reveals 2(4) intervals of
> > significant differences:  
> > 
> > Fig.1. At this weird J picture we see the boxes of significant
> > differences between standard and deviant ERPs for each time point (x
> > axis) and electrode (y axis). 
> > Olga Sysoeva, PhD
> > Institute of Higher Nervous 
> > Activity and Neurophysiology
> > Russian Academy of Sciences
> > 5a Butlerova str.
> > Moscow 117485
> > RUSSIA
> > tel.: (7-095)-3347011, 
> > fax:(7-095)-338-85-00.    
> > 
> > Links:
> > ------
> > [2] http://www.ru.nl/master/cns/
> > 
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

_________________________________________________________________


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From e.maris at DONDERS.RU.NL  Wed Oct 22 15:43:01 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Wed, 22 Oct 2008 15:43:01 +0200
Subject: Fwd: RE: clusterrandomization for 2 epochs separately
In-Reply-To: <BAY136-W214848AC17B1ADB18F421EDF290@phx.gbl>
Message-ID: <WED.22.OCT.2008.154301.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Nic,

 

 

I have a quick answer for you, and would be please to heard people's comment
on it. If you had a priori reason to belive something would happen for these
electrodes and time-window, you don't need cluster analysis at all. All the
solutions to the multiple-comparison problem are to be used in exploratory
situation, when you don't know what to expect. If you had specific
hypothesis, don't be shy: test them directy with a T-Test on the average
voltage for a pre-determined time-window. 

Think about it, if you did expect these effects to be there, you could had
create a montage with only one or two electrodes, and the
multiple-comparison problem would not apply at all.



Your understanding makes me happy! I couldn’t have formulated it any better.

 

Eric Maris

 

 

 

 

 

 


Hope this help,

Nic

************************************
Nicolas Robitaille, candidat Ph.D
Département de Psychologie
Université de Montréal
C.P. 6128, succursale Centre-ville
Montréal, Québec H3C 3J7
Tel.: 514-343-6111 x2631
Fax: 514-343-5787
************************************


> Date: Wed, 22 Oct 2008 12:10:01 +0100
> From: olga at GRAPHICMIND.INFO
> Subject: [FIELDTRIP] Fwd: RE: clusterrandomization for 2 epochs separately
> To: FIELDTRIP at NIC.SURFNET.NL
> 
> > Dear Eric, 
> > I would like to consult with you about some our ERP data and
> > application of the clusterrandomization to it. 
> > 
> > I am writing now the article about ERP signs of visual change
> > detection. 
> > 
> > We have ERP to the "deviant" and "standard" stimuli sampling rate
> > 512 Hz, 64 channels (Biosemi), 12 subjects. 
> > 
> > If we use the paired-wise t-test to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point (and plot it see the picture at the end of
> > the letter) we can see 2 (4) time regions of differences. But
> > application of clusterrandomization analysis to these data (latency
> > 0-500 ms) reveal only late cluster as significant, the early cluster
> > is marginally significant (p=0.1). But I really believe in this early
> > effect (120-160 ms), it is very important for our paper. When I run
> > the clusterrandomization analysis on the narrowed epoch (0-300 ms) I
> > got the early cluster significant. But the problem than that I loose
> > the late effect, which is also worth mentioning in the paper. 
> > 
> > Therefore, I would like you opinion about the possibility to use the
> > clusterrandomization analysis separately on the 2 epochs of interest,
> > let say first 250 ms post-stimulus (0-250 ms) and next (250-500 ms). 
> > 
> > In this case there would be two significant clusters... 
> > Best Regards, 
> > 
> > Olga Sysoeva 
> > P.S. 
> > 
> > I also used different parameters for clusterrandomization (ndis,
> > nchannels) but this does not change the results much. 
> > P.P.S. 
> > 
> > Additional material 
> > The paired-wise t-test was used to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point. 
> > 
> > The standard and deviant ERPs comparison reveals 2(4) intervals of
> > significant differences: 
> > 
> > Fig.1. At this weird J picture we see the boxes of significant
> > differences between standard and deviant ERPs for each time point (x
> > axis) and electrode (y axis). 
> > Olga Sysoeva, PhD
> > Institute of Higher Nervous 
> > Activity and Neurophysiology
> > Russian Academy of Sciences
> > 5a Butlerova str.
> > Moscow 117485
> > RUSSIA
> > tel.: (7-095)-3347011, 
> > fax:(7-095)-338-85-00. 
> > 
> > Links:
> > ------
> > [2] http://www.ru.nl/master/cns/
> > 
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/fcdonders/fieldtrip.

  _____  

Obtenez votre dose d'information sur votre cellulaire. Avec MSN Mobile,
obtenez des mises à jour régulières sur l'actualité, les sports et les
finances Essayez-le aujourd'hui
<http://info.mobile.ca.msn.com/fr-ca/default.aspx>  !

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

The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/fieldtrip/


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From olga at GRAPHICMIND.INFO  Wed Oct 22 17:12:27 2008
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Wed, 22 Oct 2008 19:12:27 +0400
Subject: Fwd: RE: clusterrandomization for 2 epochs separately
In-Reply-To: <20081022134258.CECC8A9FDE@smtp.ru.nl>
Message-ID: <WED.22.OCT.2008.191227.0400.FIELDTRIP@NIC.SURFNET.NL>

Thank you all for your answer. I perfectly understand what you wrote.

Unfortunately early effect I believe in is what only our group is found
therefore we could not use the former study and take the electrode and
latency from them.

I also know the way how I can represent our data using the conventional
t-test analysis.

I just want to use here the clusterrandomization analysis for more logical
and tense description of the results.

My question is does the usage of clusterrandomization on the 2 epochs
separately make sense here. If you think that the conventional t-test is
more suitable here, I’ll stand on it.

 

Best Regards,

Olga.

 

  _____  

From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Eric Maris
Sent: Wednesday, October 22, 2008 5:43 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] Fwd: RE: clusterrandomization for 2 epochs
separately

 

Dear Nic,

 

 

I have a quick answer for you, and would be please to heard people's comment
on it. If you had a priori reason to belive something would happen for these
electrodes and time-window, you don't need cluster analysis at all. All the
solutions to the multiple-comparison problem are to be used in exploratory
situation, when you don't know what to expect. If you had specific
hypothesis, don't be shy: test them directy with a T-Test on the average
voltage for a pre-determined time-window. 

Think about it, if you did expect these effects to be there, you could had
create a montage with only one or two electrodes, and the
multiple-comparison problem would not apply at all.

Your understanding makes me happy! I couldn’t have formulated it any better.

 

Eric Maris

 

 

 

 

 

 


Hope this help,

Nic

************************************
Nicolas Robitaille, candidat Ph.D
Département de Psychologie
Université de Montréal
C.P. 6128, succursale Centre-ville
Montréal, Québec H3C 3J7
Tel.: 514-343-6111 x2631
Fax: 514-343-5787
************************************


> Date: Wed, 22 Oct 2008 12:10:01 +0100
> From: olga at GRAPHICMIND.INFO
> Subject: [FIELDTRIP] Fwd: RE: clusterrandomization for 2 epochs separately
> To: FIELDTRIP at NIC.SURFNET.NL
> 
> > Dear Eric, 
> > I would like to consult with you about some our ERP data and
> > application of the clusterrandomization to it. 
> > 
> > I am writing now the article about ERP signs of visual change
> > detection. 
> > 
> > We have ERP to the "deviant" and "standard" stimuli sampling rate
> > 512 Hz, 64 channels (Biosemi), 12 subjects. 
> > 
> > If we use the paired-wise t-test to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point (and plot it see the picture at the end of
> > the letter) we can see 2 (4) time regions of differences. But
> > application of clusterrandomization analysis to these data (latency
> > 0-500 ms) reveal only late cluster as significant, the early cluster
> > is marginally significant (p=0.1). But I really believe in this early
> > effect (120-160 ms), it is very important for our paper. When I run
> > the clusterrandomization analysis on the narrowed epoch (0-300 ms) I
> > got the early cluster significant. But the problem than that I loose
> > the late effect, which is also worth mentioning in the paper. 
> > 
> > Therefore, I would like you opinion about the possibility to use the
> > clusterrandomization analysis separately on the 2 epochs of interest,
> > let say first 250 ms post-stimulus (0-250 ms) and next (250-500 ms). 
> > 
> > In this case there would be two significant clusters... 
> > Best Regards, 
> > 
> > Olga Sysoeva 
> > P.S. 
> > 
> > I also used different parameters for clusterrandomization (ndis,
> > nchannels) but this does not change the results much. 
> > P.P.S. 
> > 
> > Additional material 
> > The paired-wise t-test was used to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point. 
> > 
> > The standard and deviant ERPs comparison reveals 2(4) intervals of
> > significant differences: 
> > 
> > Fig.1. At this weird J picture we see the boxes of significant
> > differences between standard and deviant ERPs for each time point (x
> > axis) and electrode (y axis). 
> > Olga Sysoeva, PhD
> > Institute of Higher Nervous 
> > Activity and Neurophysiology
> > Russian Academy of Sciences
> > 5a Butlerova str.
> > Moscow 117485
> > RUSSIA
> > tel.: (7-095)-3347011, 
> > fax:(7-095)-338-85-00. 
> > 
> > Links:
> > ------
> > [2] http://www.ru.nl/master/cns/
> > 
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/fcdonders/fieldtrip.

  _____  

Obtenez votre dose d'information sur votre cellulaire. Avec MSN Mobile,
obtenez des mises à jour régulières sur l'actualité, les sports et les
finances Essayez-le <http://info.mobile.ca.msn.com/fr-ca/default.aspx>
aujourd'hui !



__________ NOD32 3536 (20081019) Information __________

This message was checked by NOD32 antivirus system.
http://www.eset.com

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

The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/fieldtrip/

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

The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/fieldtrip/


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From g.rousselet at PSY.GLA.AC.UK  Fri Oct 24 18:40:44 2008
From: g.rousselet at PSY.GLA.AC.UK (Guillaume Rousselet)
Date: Fri, 24 Oct 2008 17:40:44 +0100
Subject: Launch of CCNi and SI project
Message-ID: <FRI.24.OCT.2008.174044.0100.FIELDTRIP@NIC.SURFNET.NL>

The Department of Psychology at University of Glasgow is pleased to  
announce a Joint Event to launch the Centre for Cognitive Neuroimaging  
(CCNi) and  to officially launch our project: Social Interaction: a  
Cognitive Neurosciences Approach.
Date: Friday 28th November 2008; Venue: Kelvin Gallery, Gilbert Scott  
Building, University Avenue & the Department of Psychology / CCNi,  
University of Glasgow, UK.

The Event, starting at 10am, will include presentations by Professor  
Philippe Schyns (CCNi Director), Professor Nikos Logothetis (MPI  
Tübingen, Germany), Professor Riitta Hari (Low Temperature Laboratory,  
Helsinki, Finland), Professor Alvaro Pascual-Leone (Harvard Medical  
School, Boston, USA), Professor Paula Niedenthal (Université Blaise  
Pascal, Clermont-Ferrand, France), Professor Rainer Goebel (Univeridty  
of Maastricht, The Netherlands).

A drinks reception and a Tour of CCNi with poster presentation will be  
held from 5pm onwards in the Department of Psychology. Contact:  
Heather Robertson, CCNi Administrator, Department of Psychology (Room  
519) University of Glasgow, 58 Hillhead Street, Glasgow G12 8QB. tel:  
+44 (0)141 330 6173. Email: h.robertson at psy.gla.ac.uk. Web: www.ccni.gla.ac.uk 
,www.socialinteraction.gla.ac.uk




************************************************************************************
Guillaume A. Rousselet, Ph.D.

Lecturer

Centre for Cognitive Neuroimaging (CCNi)
Department of Psychology
Faculty of Information & Mathematical Sciences (FIMS)
University of Glasgow
58 Hillhead Street
Glasgow, UK
G12 8QB

The University of Glasgow, charity number SC004401

http://web.me.com/rousseg/GARs_website/

Email: g.rousselet at psy.gla.ac.uk
Fax. +44 (0)141 330 4606
Tel. +44 (0)141 330 6652
Cell +44 (0)791 779 7833


“Computers in the future may weigh no more than 1.5 tons.”
	
	Popular Mechanics, 1949
************************************************************************************




----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From r.oostenveld at FCDONDERS.RU.NL  Mon Oct 27 10:03:39 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Mon, 27 Oct 2008 10:03:39 +0100
Subject: time-frequency representation of PLV
In-Reply-To: <1224360344780798.0.outsmtp04@outsmtp04>
Message-ID: <MON.27.OCT.2008.100339.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi Hyoungdong

On 18 Oct 2008, at 22:05, 박형동 wrote:
> Is it possible to draw a time-frequency representation of PLV using  
> singleplotTFR ?
>
> It looks like that i can only draw TFR of power spectra with  
> singleplotTFR, even though multiplotTFR and topoplotTFR supports PLV.

You can specify xparam/yparam and zparam in the singleplotTFR  
configuration. Assuming that you have something like

freq = freqanalysis(...)

cfg.cohmethod = 'plv'
fd = freqdescriptives(cfg, freq)

then your fd structure contains
   fd.time
   fd.freq
   fd.plvspctrm
which are to be specified as x, y and z params for singleplotTFR.

best regards,
Robert

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From spil at OKWF.FUW.EDU.PL  Mon Oct 27 15:12:12 2008
From: spil at OKWF.FUW.EDU.PL (=?ISO-8859-2?Q?Szymon_Pi=B3at?=)
Date: Mon, 27 Oct 2008 15:12:12 +0100
Subject: Dipolefitting output coordinates
Message-ID: <MON.27.OCT.2008.151212.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi everyone!

For several days I have been trying to figure out the "dipolefitting"
script output.

I guess its output is in xyz coordinates. But is this in MNI space or
Talairach space?

BTW: How to visualise the dipole I found? I use "dipplot" from EEGLAB
but I am looking for other simple way to visualise a dipole.

Thank you in advance for your help.
Best regards,
Szymon Pilat
--
spil at okwf.fuw.edu.pl
Department of Biomedical Physics
University of Warsaw

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From a.maye at UKE.DE  Mon Oct 27 16:04:56 2008
From: a.maye at UKE.DE (Alexander Maye)
Date: Mon, 27 Oct 2008 16:04:56 +0100
Subject: Preproc - thresholding negative z-scores too?
Message-ID: <MON.27.OCT.2008.160456.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear List!

In my dataset I have a nice EOG signal, in which the respective artifact detection routines 
nonetheless do not detect artifacts,since its polarity is negative. Consequently the 
z-scores also deviate towards negative, and are always below (the positive) threshold 
value. So, shouldn't artifact_zvalue threshold the *absolute* z-value instead of the raw 
z-score? I know this has been asked last year, but couldn't find an answer. Any 
opinions/preferred solutions? Ah, and yes, I played with hilbert and rectify, but hilbert does 
not change the polarity (what does it anyway?), and rectify rectifies the data, not the 
z-scores.

Best,

                       ALEX.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From v.litvak at ION.UCL.AC.UK  Mon Oct 27 19:26:50 2008
From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak)
Date: Mon, 27 Oct 2008 18:26:50 +0000
Subject: Dipolefitting output coordinates
In-Reply-To: <8834c95d0810270712j6941eb08xf29d3ca5881fcb98@mail.gmail.com>
Message-ID: <MON.27.OCT.2008.182650.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Szymon,

Fieldtrip can work in any coordinate system so the coordinates of the
output are determined by coordinates of the input (i.e. the sensors
and the volume model that you provided). MNI space and Talairach space
are exactly the same. The only thing different is the template brain
i.e. anatomical interpretation of the coordinates.  But the
coordinates Fieldtrip outputs can be neither unless your sensor
locations are given in MNI coordinates.

You can use headmodelplot to plot your volume and sensors and then
plot3 to add the dipole locations to that plot.

Best,

Vladimir


On Mon, Oct 27, 2008 at 2:12 PM, Szymon Piłat <spil at okwf.fuw.edu.pl> wrote:
> Hi everyone!
>
> For several days I have been trying to figure out the "dipolefitting"
> script output.
>
> I guess its output is in xyz coordinates. But is this in MNI space or
> Talairach space?
>
> BTW: How to visualise the dipole I found? I use "dipplot" from EEGLAB
> but I am looking for other simple way to visualise a dipole.
>
> Thank you in advance for your help.
> Best regards,
> Szymon Pilat
> --
> spil at okwf.fuw.edu.pl
> Department of Biomedical Physics
> University of Warsaw
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
>

From j.schoffelen at PSY.GLA.AC.UK  Tue Oct 28 10:47:06 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Tue, 28 Oct 2008 09:47:06 +0000
Subject: Preproc - thresholding negative z-scores too?
In-Reply-To: <LISTSERV%200810271604560250.00C5@NIC.SURFNET.NL>
Message-ID: <TUE.28.OCT.2008.094706.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Alex,

As far as I remember, the default settings for artifact_eog (the
'higher' level function which calls artifact_zvalue later on) contain
the (absolute of the) hilbert transform.
The hilbert-transform of a bandpass filtered signal is an estimate of
the instantaneous amplitude. Since it is an absolute value, it is
always positive and should reverse
the polarity of the EOG, as would rectification.
I do not really understand your statement that the polarity is not
changed by either rectification of hilbert transformation. Could it
be that you specified your options in
cfg.artfctdef.eog, and then called artifact_zvalue? or
cfg.artfctdef.zvalue and called artifact_eog?

I guess specifying cfg.artfctdef.XXX. rectify/hilbert = 'yes', and
subsequently calling artifact_XXX (eog or zvalue) should do the
trick. Of course, specifying cfg.artfctdef.XXX.feedback = 'yes',
gives you an idea how the data look.

Good luck

Jan-Mathijs


On Oct 27, 2008, at 3:04 PM, Alexander Maye wrote:

> Dear List!
>
> In my dataset I have a nice EOG signal, in which the respective
> artifact detection routines
> nonetheless do not detect artifacts,since its polarity is negative.
> Consequently the
> z-scores also deviate towards negative, and are always below (the
> positive) threshold
> value. So, shouldn't artifact_zvalue threshold the *absolute* z-
> value instead of the raw
> z-score? I know this has been asked last year, but couldn't find an
> answer. Any
> opinions/preferred solutions? Ah, and yes, I played with hilbert
> and rectify, but hilbert does
> not change the polarity (what does it anyway?), and rectify
> rectifies the data, not the
> z-scores.
>
> Best,
>
>                        ALEX.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From a.maye at UKE.DE  Tue Oct 28 14:14:08 2008
From: a.maye at UKE.DE (Alexander Maye)
Date: Tue, 28 Oct 2008 14:14:08 +0100
Subject: Preproc - thresholding negative z-scores too?
Message-ID: <TUE.28.OCT.2008.141408.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs and All!

Thank you for the quick response. Hilbert indeed flips my eye blinks towards positive 
z-values - at the cost of reduced discriminability. That is to say that the amplitude of the 
z-score of the eye blink is twice as high without Hilbert (but in the "wrong" direction). Apart 
from that I still would like to know the rationale behind considering deviations of the z-value 
towards +Inf as artifacts, while those towards -Inf not. This is the same concern as in 
#Item001386 of this list exactly one year ago. Any opinions?

Best,

                         ALEX.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From bps231 at NYU.EDU  Thu Oct 30 18:19:30 2008
From: bps231 at NYU.EDU (Bernhard Staresina)
Date: Thu, 30 Oct 2008 18:19:30 +0100
Subject: stats on single subject coherence
Message-ID: <THU.30.OCT.2008.181930.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear FieldTrip experts,

I was wondering if there is a way to test the significance of coherence
values between two channels across two different conditions within a single
subject (assuming, for simplicity, equal number of trials in both
conditions). As far as I know this is not implemented in the neat
randomization/cluster stats methods for now, but any advice would be greatly
appreciated.

Thanks,
Bernhard



----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From g.rousselet at PSY.GLA.AC.UK  Thu Oct 30 18:36:09 2008
From: g.rousselet at PSY.GLA.AC.UK (Guillaume Rousselet)
Date: Thu, 30 Oct 2008 17:36:09 +0000
Subject: stats on single subject coherence
In-Reply-To: <LISTSERV%200810301819306620.3CDB@NIC.SURFNET.NL>
Message-ID: <THU.30.OCT.2008.173609.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Bernhard,

what you want to do is the same as comparing 2 independent groups of
subjects. Thanks to the modular architecture of Filedtrip you can plug-
in a T-statistic for independent samples when you do the permutation +
clustering. The general procedure is described in Eric Maris' 2007 J.
Neurosci. Meth. paper.

Best,

GAR



On 30 Oct 2008, at 17:19, Bernhard Staresina wrote:

> Dear FieldTrip experts,
>
> I was wondering if there is a way to test the significance of
> coherence
> values between two channels across two different conditions within a
> single
> subject (assuming, for simplicity, equal number of trials in both
> conditions). As far as I know this is not implemented in the neat
> randomization/cluster stats methods for now, but any advice would be
> greatly
> appreciated.
>
> Thanks,
> Bernhard
>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/fcdonders/fieldtrip.



************************************************************************************
Guillaume A. Rousselet, Ph.D.

Lecturer

Centre for Cognitive Neuroimaging (CCNi)
Department of Psychology
Faculty of Information & Mathematical Sciences (FIMS)
University of Glasgow
58 Hillhead Street
Glasgow, UK
G12 8QB

The University of Glasgow, charity number SC004401

http://web.me.com/rousseg/GARs_website/

Email: g.rousselet at psy.gla.ac.uk
Fax. +44 (0)141 330 4606
Tel. +44 (0)141 330 6652
Cell +44 (0)791 779 7833


"There is, in short, a huge tacit conspiracy between the U.S.
government, its
agencies and its multinational corporations, on the one hand, and local
business and military cliques in the Third World, on the other, to
assume
complete control of these countries and "develop" them on a joint
venture
basis. The military leaders of the Third World were carefully nurtured
by the
U.S. security establishment to serve as the "enforcers" of this joint
venture
partnership, and they have been duly supplied with machine guns and the
latest data on methods of interrogation of subversives."

	Edward S. Herman - The Real terror network - 1982
************************************************************************************






----------------------------------
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From j.schoffelen at PSY.GLA.AC.UK  Fri Oct 31 10:30:09 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Fri, 31 Oct 2008 09:30:09 +0000
Subject: Preproc - thresholding negative z-scores too?
In-Reply-To: <LISTSERV%200810281414088160.05C0@NIC.SURFNET.NL>
Message-ID: <FRI.31.OCT.2008.093009.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Alex,

The answer to you question would be in this case: it's a historical
thing. The Z-value thresholding was conceived to be done on filtered-
and-subsequently-rectified/hilberted data. No need to look for low
Zvalues in that case. In itself, there's no reason not to build in an
option to look for negative Z-values as well. I would gladly help to
build it into the release version for you. I would think of an
option: cfg.artfctdef.zvalue.tail, which will be 1 by default (that
is: only looking at high positive deviations), but could be -1 (for
the large negative ones), or 0 (for both sided). Could you propose an
adjusted version of artifact_zvalue to me, and I'll check it and
build it in.
As for the reduced discriminability: I still don't understand why
this is the case. I assume you have more than 1 EOG channel?
Probably, one of these guys is picking up most of the artifacts, but
if you use both channels in a single run of artifact_eog, the same
threshold is applied to both channels, which indeed would affect the
sensitivity. An alternative would be to call artifact_eog twice, with
the different EOG in cfg.artfctdef.eog.channel, so that you can use
channel-specific thresholds.

Yours,

Jan-Mathijs

On Oct 28, 2008, at 1:14 PM, Alexander Maye wrote:

> Dear Jan-Mathijs and All!
>
> Thank you for the quick response. Hilbert indeed flips my eye
> blinks towards positive
> z-values - at the cost of reduced discriminability. That is to say
> that the amplitude of the
> z-score of the eye blink is twice as high without Hilbert (but in
> the "wrong" direction). Apart
> from that I still would like to know the rationale behind
> considering deviations of the z-value
> towards +Inf as artifacts, while those towards -Inf not. This is
> the same concern as in
> #Item001386 of this list exactly one year ago. Any opinions?
>
> Best,
>
>                          ALEX.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From miguelconstante at GMAIL.COM  Fri Oct 31 18:23:09 2008
From: miguelconstante at GMAIL.COM (Miguel Constante)
Date: Fri, 31 Oct 2008 18:23:09 +0100
Subject: low frequency cut-off and filtfilt
Message-ID: <FRI.31.OCT.2008.182309.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi
I have been trying to high-pass filter my EEG data, 
cfg.hpfilter = 'yes';
cfg.hpfreq = 0.03;
data = preprocessing(cfg);

using cut offs under 1Hz (e.g. 0.03Hz) and systematically get this type of 
error:

Warning: Matrix is close to singular or badly scaled.
         Results may be inaccurate. RCOND = 2.221255e-017.

Can someone advise on how to overcome this?
Thanks
Miguel

----------------------------------
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From r.oostenveld at FCDONDERS.RU.NL  Wed Oct  1 10:50:03 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Wed, 1 Oct 2008 10:50:03 +0200
Subject: changed default reading functions for CTF
In-Reply-To: <1222808946.17803.63.camel@kurage.nimh.nih.gov>
Message-ID: <WED.1.OCT.2008.105003.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Tom,

On 30 Sep 2008, at 23:09, Tom Holroyd wrote:
> Two questions. 1) We record data with 3rd gradient turned on by
> default.
> That is, the MEG channels have already had the background noise
> subtracted. So our datasets contain only balanced data. No further
> processing is required. Does your code take care of this case?

Hmmm, good question... I cannot immediately answer confirmative. The
data that is read will be balanced, that won't be the problem. What I
don't immediately oversee is whether the leadfield computation will
match the balanced data. In the old case it was sure not to match the
data. In the new case the reading routine should take care of that.

I don't have any 3rd order data lying around right now, so would you
please check the following
   data = preprocessing(cfg)  % with your standard config
and then look into the field
   data.grad
There should be a
   data.grad.balance
structure and
   data.grad.balance.current
string. In your case current should be G3BR.

Subsequently please check the weighing of the gradiometer coils to
channels using
   imagesc(data.grad.tra)
You should more or less see two identity matrices concatenated with
some small non-zero numbers in the rightmost part of thaht figure.
This matrix is used in the forward computation: first the field at
every individual coil is computed (keeping the coil orientation in
mind), and then the "coils" are combined to form "channels". The two
identity matrices represent the bottom and top coil, and the small
numbers in the rightmost part represent the small corrections to the
forward model required to mimic the balancing (in which also a small
part of the dipole field is subtracted from the data).

Please let us know whether those two fields are as I expect them to
be. Perhaps you could also send me (not through this email list!) a
3rd gradient dataset (preverably averaged, i.e. small MB size) for
your system, so that I can use that for testing.  You can use ftp.fcdonders.nl/pub/incoming
  or something like yousendit.com.

> 2) Why is
> the code closed source?

We discussed the release of the code in the joined context of SPM8 and
Fieldtrip with the CTF support. See below for their statement

>> ---------- Forwarded message ----------
>> From: MEG Customer Support <support at megservice.com>
>> Date: Thu, Apr 24, 2008 at 1:00 AM
>> Subject: RE: MATLAB Import/Export Routines
>> To: David Bradbury <d.bradbury at fil.ion.ucl.ac.uk>, MEG Customer
>> Support <support at megservice.com>
>> Cc: litvak.vladimir at gmail.com
>>
>>
>> Dear David (& Vladimir),
>>
>> We're most glad to hear that the issue with the stim codes may have
>> been
>> resolved.  As you say please keep us informed if it is not.
>>
>> Thank you very much for your request regarding the VSM MatLab codes.
>> Because we consider them to be covered under the systems' general
>> non-disclosure agreements you are free to use these algorithms
>> internally (i.e. by all MEG users at UCL and F.C. Donders Centre)
>> without restriction however we would like to request that you only
>> distribute these functions external to your labs in a pre-compiled
>> form.
>> Thank you for your consideration in this matter.
>>
>> With best regards,
>>
>> Brent


So I have the m-files but am not allowed to distribute them, hence the
p-files in the fieldtrip/external/ctf directory (and in spm8/external/
ctf). I guess that you as CTF user should be able to get your own copy
of the m-files from CTF support.

best regards,
Robert





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From r.oostenveld at FCDONDERS.RU.NL  Wed Oct  1 12:42:40 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Wed, 1 Oct 2008 12:42:40 +0200
Subject: problem reading old CTF data
In-Reply-To: <f7392e897f60b.48e27315@ru.nl>
Message-ID: <WED.1.OCT.2008.124240.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Barbara (CC fieldtrip list)

The problem that you have with your CTF dataset is due to a bug in the
dataset itself. Since other people might encounter the same problem,
I'll forward the information to the FT mailing list as well.

The dataset that you are trying to read has a bug in the
headcoordinates (*.hc) file. The 5th line in the file is
   stadard left ear coil position relative to dewar (cm):
but should be
   standard left ear coil position relative to dewar (cm):
Note the missing "n" in the buggy headcoordinates file.

In the previous reading routines (read_ctf_hc, see line 182) that bug
was known and the code explicitely tested for that bug. In the new
reading routines (i.e. the ones supplied to us by CTF to handle
synthetic gradients) that bug in the HC file causes a problem.

The only solution for now that I can think of is to edit the HC file
(in a text editor) and to fix the typo by adding the "n" to "stadard".

best regards,
Robert


On 30 Sep 2008, at 18:42, Barbara Haendel wrote:

> I'm not sure what happened but I can't read in my old files anymore
> (something which already had worked about two weeks go). I also
> can't make much sense out of the error message (see below). The
> problem seems to be that FT can't read the trial definition because
> cfg.trialdef.eventtype = '?'; does not give any event information
> anymore. Could it be that something has changed lately since it was
> already working before?
> It would be great if you could help me,
> Thanks,
> Barbara
>
> cfg=[];
>    cfg.dataset='AxLiPERCEPT390405.ds';
>    cfg.continuous = 'no';
>    cfg.trialdef.eventtype = 'trial';
>    cfg = definetrial(cfg);
> evaluating trialfunction 'trialfun_general'
>
> readCTFds: You are reading CTF data for use with a software-
> application tool
> 	that is not manufactured by VSM MedTech Ltd. and has not received
> marketing
> 	clearance for clinical applications.  If CTF MEG data are processed
> by this tool,
> 	they should not be later employed for clinical and/or diagnostic
> purposes.
>
> readCPersist: Stop strings (EndOfParameters) do not balance start
> strings (WS1_).
>              (No. of start strings)-(No. of stop strings)=1.
> ??? Index exceeds matrix dimensions.
>
> Error in ==> /home/common/matlab/fieldtrip/external/ctf/
> readCTFds.p>readHc at 599
>
> Error in ==> /home/common/matlab/fieldtrip/external/ctf/
> readCTFds.p>readCTFds at 203

----------------------------------
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From michael.wibral at WEB.DE  Thu Oct  2 16:02:18 2008
From: michael.wibral at WEB.DE (Michael Wibral)
Date: Thu, 2 Oct 2008 16:02:18 +0200
Subject: Missing dim filed after source analysis.
Message-ID: <THU.2.OCT.2008.160218.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Listuser,

I am having a little problem with the beamformer (dics) tutorial. If I run first sourceanalysis on 'data' like this:

SourceDataSingleTrial=sourceanalysis(cfg, data)

applying precomputed filters to single trials (as in the tutorial) and then feed SourceDataSingleTrial to sourcestatistics like this:

SourceStats=sourceanalysis(cfg,SourceDataSingleTrial )

Then sourcestatistics complains about a missing filed 'dim'. I can fix this problem by creating the field SourceStats.dim by hand, giving the voxel conuts in each dimension [voxX voxY voxZ] and the code runs. However, the function might also need the number of trials or the like ???

Any idea what could be the reason for sourceanalysis not producing the dim field?

Michael

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From r.oostenveld at FCDONDERS.RU.NL  Thu Oct  2 17:39:32 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 2 Oct 2008 17:39:32 +0200
Subject: Missing dim filed after source analysis.
In-Reply-To: <794538785@web.de>
Message-ID: <THU.2.OCT.2008.173932.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Michael,

On 2 Oct 2008, at 16:02, Michael Wibral wrote:
> I am having a little problem with the beamformer (dics) tutorial. If
> I run first sourceanalysis on 'data' like this:
>
> SourceDataSingleTrial=sourceanalysis(cfg, data)
>
> applying precomputed filters to single trials (as in the tutorial)
> and then feed SourceDataSingleTrial to sourcestatistics like this:
>
> SourceStats=sourceanalysis(cfg,SourceDataSingleTrial )
>
> Then sourcestatistics complains about a missing filed 'dim'.

Are you working wih the latest copy of fieldtirp? If not, please see
whether that fixes the problem.

> I can fix this problem by creating the field SourceStats.dim by hand,

I presume you mean that you add dim to SourceDataSingleTrial and not
to SourceStats?

> giving the voxel conuts in each dimension [voxX voxY voxZ] and the
> code runs. However, the function might also need the number of
> trials or the like ???

The number of trials is determined in the code as
length(SourceDataSingleTrial.trial) and equals size(cfg.design,2).

> Any idea what could be the reason for sourceanalysis not producing
> the dim field?

We recently started cleaning up the representation of source data. In
the FT code there was a possible confusion about sources being
represented as a "random set of points", where each point is specified
by its position, or represented as a nicely arranged 3D volume. In the
latter case you can also specify the position of each voxel, but the
latter case is more conveniently represented using a homogenous
transformation matrix in combination with voxel indices.

This cleanup was realized in the "checkdata" function, which ensures
that the input to each FT function is as what the function expects.
The checkdata function manages backward compatibility of data
structures (i.e. still allowing to work with data that was sitting in
a mat file for a long time, and not requiring to compute the data
every time) and it tries to convert data between different
representations (i.e. volume->source_positions and the other way
around if the positions are arranged in a 3D grid).

I'll try to reproduce the problem and get back to you. For the moment
you can just add the dim field, that won't break anything.

best regards,
Robert

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From wibral at BIC.UNI-FRANKFURT.DE  Thu Oct  2 17:41:58 2008
From: wibral at BIC.UNI-FRANKFURT.DE (Michael Wibral)
Date: Thu, 2 Oct 2008 17:41:58 +0200
Subject: fix pow=pow' still necessary
Message-ID: <THU.2.OCT.2008.174158.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Listusers,

a question related to my last one. In the beamformer tutorial, the pow matrix gets transposed for each trial when going form sourceanalysis to sourcestatistics. Is that still necessary at the moment (i.e. FT20081001)?

Best Regards,
Michael

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From r.oostenveld at FCDONDERS.RU.NL  Thu Oct  2 18:07:33 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 2 Oct 2008 18:07:33 +0200
Subject: fix pow=pow' still necessary
In-Reply-To: <794649790@web.de>
Message-ID: <THU.2.OCT.2008.180733.0200.FIELDTRIP@NIC.SURFNET.NL>

On 2 Oct 2008, at 17:41, Michael Wibral wrote:

> Dear Listusers,
>
> a question related to my last one. In the beamformer tutorial, the
> pow matrix gets transposed for each trial when going form
> sourceanalysis to sourcestatistics. Is that still necessary at the
> moment (i.e. FT20081001)?

Hmm, I though that I had removed the transposing of the pow just a few
days ago on the wiki, because that is indeed not needed any more in
recent versions. Could you check the wiki once more (maybe you are
working from a cached version or from a printout)...

Robert

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From j.schoffelen at PSY.GLA.AC.UK  Fri Oct  3 22:11:49 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Fri, 3 Oct 2008 21:11:49 +0100
Subject: cross-spectrum to cross-correlogram
In-Reply-To: <200809290754.m8T7sv6F002791@ns1.intern.nin.knaw.nl>
Message-ID: <FRI.3.OCT.2008.211149.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jasper,

I did not yet completely think it through, but I see two problems
here. Obviously, you would like to verify whether multiplication in
the frequency domain is equivalent to convolution in the time
domain ;o),
actually that conjugate multiplication is equivalent to cross-
covariancing (shouldn't you use xcov, instead of xcorr?)

1 you apply a hanning taper in your frequency analysis; to make a
fair comparison you probably should specify cfg.taper='rectwin',
because your time domain data is not tapered in the xcorr-analysis
2 mathematically the convolution vs. multiplication holds when you
also take into account the 'negative frequencies' in your ifft.
However, freqanalysis does not output these in the first place
3 (sorry there's a third thing): probably you should specify the
additional option 'unbiased' when calling xcorr (or xcov), because
fft assumes circular data so the ifft'ed csd does not taper off at
the edges (which in the xcov/xcorr is due to a decrease in the number
of overlapping samples).

Hopefully these thoughts help.

Yours,

Jan-Mathijs



On Sep 29, 2008, at 8:54 AM, Jasper Poort wrote:

> CS=freq.fourierspctrm(:,1,:).*conj(freq.fourierspctrm(:,2,:));
> y = real((squeeze(mean(CS))));
> figure;plot(y)
>
> % inverse fft of cross-spectrum
> y = real(ifft(squeeze(mean(CS))));
> figure;plot(y)
>
> % compare to cross-correlation function
> [c,lags] = xcorr(mean(squeeze(wav(:,:,1)),2),mean(squeeze(wav(:,:,
> 2)),2));
> figure;plot(lags,c)


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From shehsu at INDIANA.EDU  Mon Oct  6 09:43:15 2008
From: shehsu at INDIANA.EDU (Hsu, Shen-Mou)
Date: Mon, 6 Oct 2008 03:43:15 -0400
Subject: cfg.layout and clusterplot
Message-ID: <MON.6.OCT.2008.034315.0400.FIELDTRIP@NIC.SURFNET.NL>

Dear users,

I was wondering if someone could help me sort out the following problem. I tried to plot significant clusters using clusterplot after permutation tests.  When I ran the script as below, it returned the message like this:

reverting to 151 channel CTF default
??? Error using ==> topoplotER at 330
labels in data and labels in layout do not match

Error in ==> clusterplot at 240
          topoplotER(cfg, stat);

However, I checked both cfg.layout.labels and cfg.layout.pnt. Everything seems fine.

Many thanks in advance.



My script:

%load data
load GA_N_HV_base; load GA_N_LV_base;
%load statistics
load stat_N_HVvsLV_400;
%load layout
load Sub19_ERP_HVN;

GA_N_HVvsLV = GA_N_HV_base;
GA_N_HVvsLV.avg = GA_N_HV_base.avg - GA_N_LV_base.avg;

% clusterplot
cfg = [];
cfg.alpha = 0.05;
cfg.layout = ERPdata.elec
clusterplot(cfg,stat_N_HVvsLV)

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From shehsu at INDIANA.EDU  Mon Oct  6 10:02:56 2008
From: shehsu at INDIANA.EDU (Hsu, Shen-Mou)
Date: Mon, 6 Oct 2008 04:02:56 -0400
Subject: plot the raw effects
Message-ID: <MON.6.OCT.2008.040256.0400.FIELDTRIP@NIC.SURFNET.NL>

Dear users,

I was wondering if someone could help me sort out the another problem. I tried to plot the raw effect (the difference between two conditions using the script like this

%load data
load GA_N_HV_base; load GA_N_LV_base;

GA_N_HVvsLV = GA_N_HV_base;
GA_N_HVvsLV.avg = GA_N_HV_base.avg - GA_N_LV_base.avg;

cfg = [];
cfg.xlim = [0 0.5];
cfg.channel = 'P3';
clf;
singleplotER(cfg,GA_N_HVvsLV);

However, I noticed that the graph is exactly the same as the graph from GA_N_HV_base. In other words, the singleplotER did not plot the raw effect, GA_N_HVvsLV.avg.

I am indebted to your kindness in this matter.

Shen-Mou Hsu

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From j.lange at FCDONDERS.RU.NL  Mon Oct  6 10:21:45 2008
From: j.lange at FCDONDERS.RU.NL (Jo Lange)
Date: Mon, 6 Oct 2008 10:21:45 +0200
Subject: postdoctoral position
Message-ID: <MON.6.OCT.2008.102145.0200.FIELDTRIP@NIC.SURFNET.NL>

A three-year postdoctoral position is available in the lab of Prof. Schnitzler in 
the Institute of Clinical Neuroscience and Medical Psychology at Heinrich-
Heine-University Düsseldorf, Germany. The position is available from February 
2009, funded by the European Commision (ERAT-NET NEURON). 

The successful candidate will conduct MEG experiments to study the effects 
of Deep Brain Stimulation on cortico-subcortical pathways in Parkinson’s 
disease. The project is part of an international collaboration with partners in 
Germany, Scotland, and Italy. The lab of Prof. Schnitzler offers outstanding 
experience with Deep Brain Stimulation and a whole-head MEG system.

Applicants should have a doctoral degree (PhD) in Neuroscience, Physics, 
Psychology, or related disciplines, experience with MEG recordings and an 
outstanding academic record, including publications. Expertise in Matlab and 
time-frequency analysis (FieldTrip) is desirable.

Salary follows the German Public Service Regulations. To apply, please submit 
your applications with full CV, list of publications, and three references. 
Submission deadline is the 15th of November. For more information about the 
position, contact Prof. A. Schnitzler (alfons.schnitzler at uni-duesseldorf.de) or 
Dr. J. Lange (joachim.lange at med.uni-duesseldorf.de). 

Contact Information
Prof. Dr. Alfons Schnitzler
Institute of Clinical Neuroscience and Medical Psychology
Heinrich-Heine University Düsseldorf
Universitätstr. 1
40225 Düsseldorf
Germany  
Phone: +49-211-81-13014 
Fax: +49-211-81-13015 
E-mail: alfons.schnitzler at uni-duesseldorf.de 

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From A.Stancak at LIVERPOOL.AC.UK  Mon Oct  6 12:31:12 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Mon, 6 Oct 2008 11:31:12 +0100
Subject: 4D data reading
Message-ID: <MON.6.OCT.2008.113112.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear all,

  we have some problems reading 4D Neuroimaging MEG data (148 sensors). For now, we export original 4D data into BESA format, and then read those into FieldTrip. This is not optimal, as e.g. gradient coils information is not transferred into FieldTrip. We would be grateful for a plugin or a hint enabling us to read the 4D data directly into FieldTrip.

  Best wishes
  Andrej Stancak


Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From j.schoffelen at PSY.GLA.AC.UK  Mon Oct  6 12:44:54 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Mon, 6 Oct 2008 11:44:54 +0100
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CAF@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <MON.6.OCT.2008.114454.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Andrej,

As far as I know, 4D data can be read in directly into fieldtrip. At
least it works with our 248-channel system.
There is no need to convert the data into whatever format, meaning
you should be able to read from the raw
datafiles directly. Please let me know if this does not work for you.

Yours,

Jan-Mathijs



On Oct 6, 2008, at 11:31 AM, Stancak, Andrej wrote:

> Dear all,
>
>   we have some problems reading 4D Neuroimaging MEG data (148
> sensors). For now, we export original 4D data into BESA format, and
> then read those into FieldTrip. This is not optimal, as e.g.
> gradient coils information is not transferred into FieldTrip. We
> would be grateful for a plugin or a hint enabling us to read the 4D
> data directly into FieldTrip.
>
>   Best wishes
>   Andrej Stancak
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From venug001 at BAMA.UA.EDU  Mon Oct  6 14:22:17 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 6 Oct 2008 07:22:17 -0500
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CAF@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <MON.6.OCT.2008.072217.0500.FIELDTRIP@NIC.SURFNET.NL>

Hello everyone, I have been wrestling with these problems for a while
too.
Here is what I found: Fieldtrip/EEGLAB will read neuroscan files (.avg,
and .eeg), and will read raw data (e,..)from 4D.
I believe that EEGLAB/Fieldtrip may not have a template for the 148-
Channel system co-ordinates. Christian and Don Rojas created one for me
in early April this year.
A FIF export from the 4D system may also solve this problem. Stephen
Moratti helped me with this a while a ago. It puts out three
files .xyz, .4D and the original e,.. file. But, if the .xyz file which
has coordinates for 148 channels does not match with the template, then
the data will not load. I think for one may have to load a create a 148
channel template for this purpose. This is my experience with EEGLAB,
and I think that they underlying engine is the same for both EEGLAB and
Fieldtrip
Then again, I may be completely wrong about everything except the
templates that were created for me.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear all,
>
>   we have some problems reading 4D Neuroimaging MEG data (148
> sensors). For now, we export original 4D data into BESA format, and
> then read those into FieldTrip. This is not optimal, as e.g. gradient
> coils information is not transferred into FieldTrip. We would be
> grateful for a plugin or a hint enabling us to read the 4D data
> directly into FieldTrip.
>
>   Best wishes
>   Andrej Stancak
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From a.capilla at PSY.GLA.AC.UK  Mon Oct  6 15:02:44 2008
From: a.capilla at PSY.GLA.AC.UK (Almudena Capilla)
Date: Mon, 6 Oct 2008 14:02:44 +0100
Subject: 4D data reading
In-Reply-To: <1223295737.48ea02f9caab1@bamamail.ua.edu>
Message-ID: <MON.6.OCT.2008.140244.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Gopa,

I have got a template for the 4D - 148 channels system. I could give it to
the Fieldtrip developers if this is helpful for other users of this system.

Best,
Almu

-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Gopakumar Venugopalan
Sent: 06 October 2008 13:22
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading

Hello everyone, I have been wrestling with these problems for a while
too.
Here is what I found: Fieldtrip/EEGLAB will read neuroscan files (.avg,
and .eeg), and will read raw data (e,..)from 4D.
I believe that EEGLAB/Fieldtrip may not have a template for the 148-
Channel system co-ordinates. Christian and Don Rojas created one for me
in early April this year.
A FIF export from the 4D system may also solve this problem. Stephen
Moratti helped me with this a while a ago. It puts out three
files .xyz, .4D and the original e,.. file. But, if the .xyz file which
has coordinates for 148 channels does not match with the template, then
the data will not load. I think for one may have to load a create a 148
channel template for this purpose. This is my experience with EEGLAB,
and I think that they underlying engine is the same for both EEGLAB and
Fieldtrip
Then again, I may be completely wrong about everything except the
templates that were created for me.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear all,
>
>   we have some problems reading 4D Neuroimaging MEG data (148
> sensors). For now, we export original 4D data into BESA format, and
> then read those into FieldTrip. This is not optimal, as e.g. gradient
> coils information is not transferred into FieldTrip. We would be
> grateful for a plugin or a hint enabling us to read the 4D data
> directly into FieldTrip.
>
>   Best wishes
>   Andrej Stancak
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the
FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
and EEG analysis. See also
http://listserv.surfnet.nl/archives/fieldtrip.html and
http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From venug001 at BAMA.UA.EDU  Mon Oct  6 15:12:33 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 6 Oct 2008 08:12:33 -0500
Subject: 4D data reading
In-Reply-To: <001001c927b3$e4e14e90$5757d182@DEPT6788A09EF4>
Message-ID: <MON.6.OCT.2008.081233.0500.FIELDTRIP@NIC.SURFNET.NL>

Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
the other users. There was also a discussion about whether the systems
were using third order gradiometers and/or magnetometers as the
reference. There are mail postings in that thread.
Everyone: I apologize for the typos in my hastily composed response
earlier.
regards
gopa


Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:

> Dear Gopa,
>
> I have got a template for the 4D - 148 channels system. I could give
> it to
> the Fieldtrip developers if this is helpful for other users of this
> system.
>
> Best,
> Almu
>
> -----Original Message-----
> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf
> Of Gopakumar Venugopalan
> Sent: 06 October 2008 13:22
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Hello everyone, I have been wrestling with these problems for a while
>
> too.
> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> (.avg,
> and .eeg), and will read raw data (e,..)from 4D.
> I believe that EEGLAB/Fieldtrip may not have a template for the 148-
> Channel system co-ordinates. Christian and Don Rojas created one for
> me
> in early April this year.
> A FIF export from the 4D system may also solve this problem. Stephen
>
> Moratti helped me with this a while a ago. It puts out three
> files .xyz, .4D and the original e,.. file. But, if the .xyz file
> which
> has coordinates for 148 channels does not match with the template,
> then
> the data will not load. I think for one may have to load a create a
> 148
> channel template for this purpose. This is my experience with EEGLAB,
>
> and I think that they underlying engine is the same for both EEGLAB
> and
> Fieldtrip
> Then again, I may be completely wrong about everything except the
> templates that were created for me.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
> > Dear all,
> >
> >   we have some problems reading 4D Neuroimaging MEG data (148
> > sensors). For now, we export original 4D data into BESA format,
> and
> > then read those into FieldTrip. This is not optimal, as e.g.
> gradient
> > coils information is not transferred into FieldTrip. We would be
> > grateful for a plugin or a hint enabling us to read the 4D data
> > directly into FieldTrip.
> >
> >   Best wishes
> >   Andrej Stancak
> >
> >
> > Prof. Andrej Stancak, PhD.
> > The University of Liverpool
> > School of Psychology
> > The Eleanor Rathbone Building
> > Bedford Street South, Room 209
> > Liverpool
> > L69 7ZA
> >
> > E:mail: a.stancak at liverpool.ac.uk  (primary)
> >            stancak at centrum.cz (secondary)
> > Phone: 0151 7946951
> > Office hours: Monday 10-12, Wednesday 10-12
> >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for
> MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From A.Stancak at LIVERPOOL.AC.UK  Mon Oct  6 16:11:20 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Mon, 6 Oct 2008 15:11:20 +0100
Subject: 4D data reading
Message-ID: <MON.6.OCT.2008.151120.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Gopa and Almu,

  do I understand the procedure correctly: we should export data from 4D in FIF format (currently we export in native e,... (binary), and the text files for the header and the surface points), and then use a modified xyz file containing the layout of 148 sensors. I would be grateful for one sample xyz file to see whether we can read data this way. Naturally, the best would be to incorporate it into the reading procedures of FieldTrip.

Best wishes
Andrej


Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
Sent: Mon 06/10/2008 14:12
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian 
Weinbruch and Arno (EEGLAB) may be the ones who can make it work for 
the other users. There was also a discussion about whether the systems 
were using third order gradiometers and/or magnetometers as the 
reference. There are mail postings in that thread.
Everyone: I apologize for the typos in my hastily composed response 
earlier.
regards
gopa


Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:

> Dear Gopa,
> 
> I have got a template for the 4D - 148 channels system. I could give
> it to
> the Fieldtrip developers if this is helpful for other users of this
> system.
> 
> Best,
> Almu
> 
> -----Original Message-----
> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf
> Of Gopakumar Venugopalan
> Sent: 06 October 2008 13:22
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
> 
> Hello everyone, I have been wrestling with these problems for a while
> 
> too.
> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> (.avg, 
> and .eeg), and will read raw data (e,..)from 4D.
> I believe that EEGLAB/Fieldtrip may not have a template for the 148-
> Channel system co-ordinates. Christian and Don Rojas created one for
> me 
> in early April this year.
> A FIF export from the 4D system may also solve this problem. Stephen
> 
> Moratti helped me with this a while a ago. It puts out three 
> files .xyz, .4D and the original e,.. file. But, if the .xyz file
> which 
> has coordinates for 148 channels does not match with the template,
> then 
> the data will not load. I think for one may have to load a create a
> 148 
> channel template for this purpose. This is my experience with EEGLAB,
> 
> and I think that they underlying engine is the same for both EEGLAB
> and 
> Fieldtrip
> Then again, I may be completely wrong about everything except the 
> templates that were created for me.
> regards
> gopa
> 
> 
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> 
> > Dear all,
> > 
> >   we have some problems reading 4D Neuroimaging MEG data (148
> > sensors). For now, we export original 4D data into BESA format,
> and
> > then read those into FieldTrip. This is not optimal, as e.g.
> gradient
> > coils information is not transferred into FieldTrip. We would be
> > grateful for a plugin or a hint enabling us to read the 4D data
> > directly into FieldTrip.
> > 
> >   Best wishes
> >   Andrej Stancak
> > 
> > 
> > Prof. Andrej Stancak, PhD. 
> > The University of Liverpool
> > School of Psychology
> > The Eleanor Rathbone Building
> > Bedford Street South, Room 209
> > Liverpool
> > L69 7ZA
> > 
> > E:mail: a.stancak at liverpool.ac.uk  (primary)
> >            stancak at centrum.cz (secondary)
> > Phone: 0151 7946951
> > Office hours: Monday 10-12, Wednesday 10-12
> > 
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for
> MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From venug001 at BAMA.UA.EDU  Mon Oct  6 16:31:28 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 6 Oct 2008 09:31:28 -0500
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CB0@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <MON.6.OCT.2008.093128.0500.FIELDTRIP@NIC.SURFNET.NL>

Sure will send you those files. Please remember in my files there are
only 146 channel locations as we turned off two channels.I also have a
matlab file from Don Rojas for the 148 channel layout and a file which
he created for the 146 channel layout. Please give some time today, as
I run those programs on a different machine.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopa and Almu,
>
>   do I understand the procedure correctly: we should export data from
> 4D in FIF format (currently we export in native e,... (binary), and
> the text files for the header and the surface points), and then use a
> modified xyz file containing the layout of 148 sensors. I would be
> grateful for one sample xyz file to see whether we can read data this
> way. Naturally, the best would be to incorporate it into the reading
> procedures of FieldTrip.
>
> Best wishes
> Andrej
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 14:12
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>
> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>
> the other users. There was also a discussion about whether the
> systems
> were using third order gradiometers and/or magnetometers as the
> reference. There are mail postings in that thread.
> Everyone: I apologize for the typos in my hastily composed response
> earlier.
> regards
> gopa
>
>
> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>
> > Dear Gopa,
> >
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of
> this
> > system.
> >
> > Best,
> > Almu
> >
> > -----Original Message-----
> > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> On
> > Behalf
> > Of Gopakumar Venugopalan
> > Sent: 06 October 2008 13:22
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> >
> > Hello everyone, I have been wrestling with these problems for a
> while
> >
> > too.
> > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > (.avg,
> > and .eeg), and will read raw data (e,..)from 4D.
> > I believe that EEGLAB/Fieldtrip may not have a template for the
> 148-
> > Channel system co-ordinates. Christian and Don Rojas created one
> for
> > me
> > in early April this year.
> > A FIF export from the 4D system may also solve this problem.
> Stephen
> >
> > Moratti helped me with this a while a ago. It puts out three
> > files .xyz, .4D and the original e,.. file. But, if the .xyz file
> > which
> > has coordinates for 148 channels does not match with the template,
> > then
> > the data will not load. I think for one may have to load a create
> a
> > 148
> > channel template for this purpose. This is my experience with
> EEGLAB,
> >
> > and I think that they underlying engine is the same for both
> EEGLAB
> > and
> > Fieldtrip
> > Then again, I may be completely wrong about everything except the
> > templates that were created for me.
> > regards
> > gopa
> >
> >
> > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> >
> > > Dear all,
> > >
> > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > sensors). For now, we export original 4D data into BESA format,
> > and
> > > then read those into FieldTrip. This is not optimal, as e.g.
> > gradient
> > > coils information is not transferred into FieldTrip. We would be
> > > grateful for a plugin or a hint enabling us to read the 4D data
> > > directly into FieldTrip.
> > >
> > >   Best wishes
> > >   Andrej Stancak
> > >
> > >
> > > Prof. Andrej Stancak, PhD.
> > > The University of Liverpool
> > > School of Psychology
> > > The Eleanor Rathbone Building
> > > Bedford Street South, Room 209
> > > Liverpool
> > > L69 7ZA
> > >
> > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > >            stancak at centrum.cz (secondary)
> > > Phone: 0151 7946951
> > > Office hours: Monday 10-12, Wednesday 10-12
> > >
> > >
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the
> > FieldTrip  toolbox, to share experiences and to discuss new ideas
> for
> > MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From j.schoffelen at PSY.GLA.AC.UK  Mon Oct  6 16:54:57 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Mon, 6 Oct 2008 15:54:57 +0100
Subject: 4D data reading
In-Reply-To: <1223303488.48ea21405717d@bamamail.ua.edu>
Message-ID: <MON.6.OCT.2008.155457.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Andrej, dear Gopa,

Sorry to bother you again, but I tried to make a point in my last
mail that it is not necessary to intermediately convert your raw
epoched or continuous 4D-data into another format, prior to be able
to read it into Fieldtrip. Of course you are free to do so, but the
most natural way to me would seem to work on the raw datafiles
directly. Fieldtrip should support this and it has reading routines
for the raw data-file (beginning with e, or c,), the config-file, and
the file containing the digitized head-surface positions.
You should be able to obtain the header information directly by
calling: hdr = read_header('e,thenameofyourrawdatafile') (give or
take an accidental 'keyboard'-statement in the low-level function
read_4d_hdr, this will be fixed in tonight's release version: if it
occurs now, just type dbcont on the command line when it prompts:
K>>) As far as I know hdr contains a structure grad, which specifies
the sensor-positions. At least it works on our Glaswegian 248-sensor
system.

Yours,

Jan-Mathijs


On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:

> Sure will send you those files. Please remember in my files there are
> only 146 channel locations as we turned off two channels.I also have a
> matlab file from Don Rojas for the 148 channel layout and a file which
> he created for the 146 channel layout. Please give some time today, as
> I run those programs on a different machine.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
>> Dear Gopa and Almu,
>>
>>   do I understand the procedure correctly: we should export data from
>> 4D in FIF format (currently we export in native e,... (binary), and
>> the text files for the header and the surface points), and then use a
>> modified xyz file containing the layout of 148 sensors. I would be
>> grateful for one sample xyz file to see whether we can read data this
>> way. Naturally, the best would be to incorporate it into the reading
>> procedures of FieldTrip.
>>
>> Best wishes
>> Andrej
>>
>>
>> Prof. Andrej Stancak, PhD.
>> The University of Liverpool
>> School of Psychology
>> The Eleanor Rathbone Building
>> Bedford Street South, Room 209
>> Liverpool
>> L69 7ZA
>>
>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>            stancak at centrum.cz (secondary)
>> Phone: 0151 7946951
>> Office hours: Monday 10-12, Wednesday 10-12
>>
>>
>>
>> -----Original Message-----
>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>> Sent: Mon 06/10/2008 14:12
>> To: FIELDTRIP at NIC.SURFNET.NL
>> Subject: Re: [FIELDTRIP] 4D data reading
>>
>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>
>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>
>> the other users. There was also a discussion about whether the
>> systems
>> were using third order gradiometers and/or magnetometers as the
>> reference. There are mail postings in that thread.
>> Everyone: I apologize for the typos in my hastily composed response
>> earlier.
>> regards
>> gopa
>>
>>
>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>
>>> Dear Gopa,
>>>
>>> I have got a template for the 4D - 148 channels system. I could
>> give
>>> it to
>>> the Fieldtrip developers if this is helpful for other users of
>> this
>>> system.
>>>
>>> Best,
>>> Almu
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>> On
>>> Behalf
>>> Of Gopakumar Venugopalan
>>> Sent: 06 October 2008 13:22
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Hello everyone, I have been wrestling with these problems for a
>> while
>>>
>>> too.
>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>> (.avg,
>>> and .eeg), and will read raw data (e,..)from 4D.
>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>> 148-
>>> Channel system co-ordinates. Christian and Don Rojas created one
>> for
>>> me
>>> in early April this year.
>>> A FIF export from the 4D system may also solve this problem.
>> Stephen
>>>
>>> Moratti helped me with this a while a ago. It puts out three
>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>> which
>>> has coordinates for 148 channels does not match with the template,
>>> then
>>> the data will not load. I think for one may have to load a create
>> a
>>> 148
>>> channel template for this purpose. This is my experience with
>> EEGLAB,
>>>
>>> and I think that they underlying engine is the same for both
>> EEGLAB
>>> and
>>> Fieldtrip
>>> Then again, I may be completely wrong about everything except the
>>> templates that were created for me.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>
>>>> Dear all,
>>>>
>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>> sensors). For now, we export original 4D data into BESA format,
>>> and
>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>> gradient
>>>> coils information is not transferred into FieldTrip. We would be
>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>> directly into FieldTrip.
>>>>
>>>>   Best wishes
>>>>   Andrej Stancak
>>>>
>>>>
>>>> Prof. Andrej Stancak, PhD.
>>>> The University of Liverpool
>>>> School of Psychology
>>>> The Eleanor Rathbone Building
>>>> Bedford Street South, Room 209
>>>> Liverpool
>>>> L69 7ZA
>>>>
>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>            stancak at centrum.cz (secondary)
>>>> Phone: 0151 7946951
>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between
>> users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the
>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for
>>> MEG
>>> and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From venug001 at BAMA.UA.EDU  Mon Oct  6 17:03:35 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 6 Oct 2008 10:03:35 -0500
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CB0@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <MON.6.OCT.2008.100335.0500.FIELDTRIP@NIC.SURFNET.NL>

Andrej, I see an error in my mail below. The three files
.xyz, .m4d and the acutal pdf is produced using the command:

pdf2set -u

You post the selection in the propreitary MSI environment, then type in
the command given above. It will put out the three files mentioned for
each data set.
I shall include only the .xyz and .m4d files from grand averaged files,
as they do not contain any identifiable information.
I believe that the .m4d file is also called the header file and
the .xyz is called the location or coordinate file.
Ken Velarde was immensely helpful with this, as were Christian
Weinbruch, and Don Rojas. Don Rojas's colleague Dr. Eugene Kronberg
also has  created an interface that can read 4D data, and he was going
to create such a template as well--as per our last email exchange.
I also have a xls2matlab function that I used to create my own
template, as the sensor location file is usually a product of
individual MEG systems. If I may have mislead anyone it is
unintentional as I am constantly learning.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopa and Almu,
>
>   do I understand the procedure correctly: we should export data from
> 4D in FIF format (currently we export in native e,... (binary), and
> the text files for the header and the surface points), and then use a
> modified xyz file containing the layout of 148 sensors. I would be
> grateful for one sample xyz file to see whether we can read data this
> way. Naturally, the best would be to incorporate it into the reading
> procedures of FieldTrip.
>
> Best wishes
> Andrej
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 14:12
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>
> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>
> the other users. There was also a discussion about whether the
> systems
> were using third order gradiometers and/or magnetometers as the
> reference. There are mail postings in that thread.
> Everyone: I apologize for the typos in my hastily composed response
> earlier.
> regards
> gopa
>
>
> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>
> > Dear Gopa,
> >
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of
> this
> > system.
> >
> > Best,
> > Almu
> >
> > -----Original Message-----
> > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> On
> > Behalf
> > Of Gopakumar Venugopalan
> > Sent: 06 October 2008 13:22
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> >
> > Hello everyone, I have been wrestling with these problems for a
> while
> >
> > too.
> > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > (.avg,
> > and .eeg), and will read raw data (e,..)from 4D.
> > I believe that EEGLAB/Fieldtrip may not have a template for the
> 148-
> > Channel system co-ordinates. Christian and Don Rojas created one
> for
> > me
> > in early April this year.
> > A FIF export from the 4D system may also solve this problem.
> Stephen
> >
> > Moratti helped me with this a while a ago. It puts out three
> > files .xyz, .4D and the original e,.. file. But, if the .xyz file
> > which
> > has coordinates for 148 channels does not match with the template,
> > then
> > the data will not load. I think for one may have to load a create
> a
> > 148
> > channel template for this purpose. This is my experience with
> EEGLAB,
> >
> > and I think that they underlying engine is the same for both
> EEGLAB
> > and
> > Fieldtrip
> > Then again, I may be completely wrong about everything except the
> > templates that were created for me.
> > regards
> > gopa
> >
> >
> > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> >
> > > Dear all,
> > >
> > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > sensors). For now, we export original 4D data into BESA format,
> > and
> > > then read those into FieldTrip. This is not optimal, as e.g.
> > gradient
> > > coils information is not transferred into FieldTrip. We would be
> > > grateful for a plugin or a hint enabling us to read the 4D data
> > > directly into FieldTrip.
> > >
> > >   Best wishes
> > >   Andrej Stancak
> > >
> > >
> > > Prof. Andrej Stancak, PhD.
> > > The University of Liverpool
> > > School of Psychology
> > > The Eleanor Rathbone Building
> > > Bedford Street South, Room 209
> > > Liverpool
> > > L69 7ZA
> > >
> > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > >            stancak at centrum.cz (secondary)
> > > Phone: 0151 7946951
> > > Office hours: Monday 10-12, Wednesday 10-12
> > >
> > >
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the
> > FieldTrip  toolbox, to share experiences and to discuss new ideas
> for
> > MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From A.Stancak at LIVERPOOL.AC.UK  Mon Oct  6 17:45:08 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Mon, 6 Oct 2008 16:45:08 +0100
Subject: 4D data reading
Message-ID: <MON.6.OCT.2008.164508.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Gopa,

 thanks you so much for the files and infomation, I will follow your path, and try what you suggest tomorrow. Jan-Mathijs thinks it should be also possible to read directly from the raw data + config file, and I will try this way too. I will report to the community once I am done as it may be useful for 148-4D researchers.

 Best wishes
 Andrej

Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
Sent: Mon 06/10/2008 16:03
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Andrej, I see an error in my mail below. The three files
.xyz, .m4d and the acutal pdf is produced using the command:

pdf2set -u

You post the selection in the propreitary MSI environment, then type in 
the command given above. It will put out the three files mentioned for 
each data set.
I shall include only the .xyz and .m4d files from grand averaged files, 
as they do not contain any identifiable information.
I believe that the .m4d file is also called the header file and 
the .xyz is called the location or coordinate file.
Ken Velarde was immensely helpful with this, as were Christian 
Weinbruch, and Don Rojas. Don Rojas's colleague Dr. Eugene Kronberg 
also has  created an interface that can read 4D data, and he was going 
to create such a template as well--as per our last email exchange.
I also have a xls2matlab function that I used to create my own 
template, as the sensor location file is usually a product of 
individual MEG systems. If I may have mislead anyone it is 
unintentional as I am constantly learning.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopa and Almu,
> 
>   do I understand the procedure correctly: we should export data from
> 4D in FIF format (currently we export in native e,... (binary), and
> the text files for the header and the surface points), and then use a
> modified xyz file containing the layout of 148 sensors. I would be
> grateful for one sample xyz file to see whether we can read data this
> way. Naturally, the best would be to incorporate it into the reading
> procedures of FieldTrip.
> 
> Best wishes
> Andrej
> 
> 
> Prof. Andrej Stancak, PhD. 
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
> 
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
> 
> 
> 
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 14:12
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>  
> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
> 
> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
> 
> the other users. There was also a discussion about whether the
> systems 
> were using third order gradiometers and/or magnetometers as the 
> reference. There are mail postings in that thread.
> Everyone: I apologize for the typos in my hastily composed response 
> earlier.
> regards
> gopa
> 
> 
> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
> 
> > Dear Gopa,
> > 
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of
> this
> > system.
> > 
> > Best,
> > Almu
> > 
> > -----Original Message-----
> > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> On
> > Behalf
> > Of Gopakumar Venugopalan
> > Sent: 06 October 2008 13:22
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> > 
> > Hello everyone, I have been wrestling with these problems for a
> while
> > 
> > too.
> > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > (.avg, 
> > and .eeg), and will read raw data (e,..)from 4D.
> > I believe that EEGLAB/Fieldtrip may not have a template for the
> 148-
> > Channel system co-ordinates. Christian and Don Rojas created one
> for
> > me 
> > in early April this year.
> > A FIF export from the 4D system may also solve this problem.
> Stephen
> > 
> > Moratti helped me with this a while a ago. It puts out three 
> > files .xyz, .4D and the original e,.. file. But, if the .xyz file
> > which 
> > has coordinates for 148 channels does not match with the template,
> > then 
> > the data will not load. I think for one may have to load a create
> a
> > 148 
> > channel template for this purpose. This is my experience with
> EEGLAB,
> > 
> > and I think that they underlying engine is the same for both
> EEGLAB
> > and 
> > Fieldtrip
> > Then again, I may be completely wrong about everything except the 
> > templates that were created for me.
> > regards
> > gopa
> > 
> > 
> > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> > 
> > > Dear all,
> > > 
> > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > sensors). For now, we export original 4D data into BESA format,
> > and
> > > then read those into FieldTrip. This is not optimal, as e.g.
> > gradient
> > > coils information is not transferred into FieldTrip. We would be
> > > grateful for a plugin or a hint enabling us to read the 4D data
> > > directly into FieldTrip.
> > > 
> > >   Best wishes
> > >   Andrej Stancak
> > > 
> > > 
> > > Prof. Andrej Stancak, PhD. 
> > > The University of Liverpool
> > > School of Psychology
> > > The Eleanor Rathbone Building
> > > Bedford Street South, Room 209
> > > Liverpool
> > > L69 7ZA
> > > 
> > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > >            stancak at centrum.cz (secondary)
> > > Phone: 0151 7946951
> > > Office hours: Monday 10-12, Wednesday 10-12
> > > 
> > > 
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > > 
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the
> > FieldTrip  toolbox, to share experiences and to discuss new ideas
> for
> > MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From A.Stancak at LIVERPOOL.AC.UK  Mon Oct  6 17:50:37 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Mon, 6 Oct 2008 16:50:37 +0100
Subject: 4D data reading
Message-ID: <MON.6.OCT.2008.165037.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs,

  thanks for further information. I need to copy the config file from the MSI server as that is not saved automatically with our
recordings, and then give another try. 

Best wishes
Andrej


Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
Sent: Mon 06/10/2008 15:54
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Dear Andrej, dear Gopa,

Sorry to bother you again, but I tried to make a point in my last  
mail that it is not necessary to intermediately convert your raw  
epoched or continuous 4D-data into another format, prior to be able  
to read it into Fieldtrip. Of course you are free to do so, but the  
most natural way to me would seem to work on the raw datafiles  
directly. Fieldtrip should support this and it has reading routines  
for the raw data-file (beginning with e, or c,), the config-file, and  
the file containing the digitized head-surface positions.
You should be able to obtain the header information directly by  
calling: hdr = read_header('e,thenameofyourrawdatafile') (give or  
take an accidental 'keyboard'-statement in the low-level function  
read_4d_hdr, this will be fixed in tonight's release version: if it  
occurs now, just type dbcont on the command line when it prompts:  
K>>) As far as I know hdr contains a structure grad, which specifies  
the sensor-positions. At least it works on our Glaswegian 248-sensor  
system.

Yours,

Jan-Mathijs


On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:

> Sure will send you those files. Please remember in my files there are
> only 146 channel locations as we turned off two channels.I also have a
> matlab file from Don Rojas for the 148 channel layout and a file which
> he created for the 146 channel layout. Please give some time today, as
> I run those programs on a different machine.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
>> Dear Gopa and Almu,
>>
>>   do I understand the procedure correctly: we should export data from
>> 4D in FIF format (currently we export in native e,... (binary), and
>> the text files for the header and the surface points), and then use a
>> modified xyz file containing the layout of 148 sensors. I would be
>> grateful for one sample xyz file to see whether we can read data this
>> way. Naturally, the best would be to incorporate it into the reading
>> procedures of FieldTrip.
>>
>> Best wishes
>> Andrej
>>
>>
>> Prof. Andrej Stancak, PhD.
>> The University of Liverpool
>> School of Psychology
>> The Eleanor Rathbone Building
>> Bedford Street South, Room 209
>> Liverpool
>> L69 7ZA
>>
>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>            stancak at centrum.cz (secondary)
>> Phone: 0151 7946951
>> Office hours: Monday 10-12, Wednesday 10-12
>>
>>
>>
>> -----Original Message-----
>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>> Sent: Mon 06/10/2008 14:12
>> To: FIELDTRIP at NIC.SURFNET.NL
>> Subject: Re: [FIELDTRIP] 4D data reading
>>
>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>
>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>
>> the other users. There was also a discussion about whether the
>> systems
>> were using third order gradiometers and/or magnetometers as the
>> reference. There are mail postings in that thread.
>> Everyone: I apologize for the typos in my hastily composed response
>> earlier.
>> regards
>> gopa
>>
>>
>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>
>>> Dear Gopa,
>>>
>>> I have got a template for the 4D - 148 channels system. I could
>> give
>>> it to
>>> the Fieldtrip developers if this is helpful for other users of
>> this
>>> system.
>>>
>>> Best,
>>> Almu
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>> On
>>> Behalf
>>> Of Gopakumar Venugopalan
>>> Sent: 06 October 2008 13:22
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Hello everyone, I have been wrestling with these problems for a
>> while
>>>
>>> too.
>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>> (.avg,
>>> and .eeg), and will read raw data (e,..)from 4D.
>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>> 148-
>>> Channel system co-ordinates. Christian and Don Rojas created one
>> for
>>> me
>>> in early April this year.
>>> A FIF export from the 4D system may also solve this problem.
>> Stephen
>>>
>>> Moratti helped me with this a while a ago. It puts out three
>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>> which
>>> has coordinates for 148 channels does not match with the template,
>>> then
>>> the data will not load. I think for one may have to load a create
>> a
>>> 148
>>> channel template for this purpose. This is my experience with
>> EEGLAB,
>>>
>>> and I think that they underlying engine is the same for both
>> EEGLAB
>>> and
>>> Fieldtrip
>>> Then again, I may be completely wrong about everything except the
>>> templates that were created for me.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>
>>>> Dear all,
>>>>
>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>> sensors). For now, we export original 4D data into BESA format,
>>> and
>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>> gradient
>>>> coils information is not transferred into FieldTrip. We would be
>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>> directly into FieldTrip.
>>>>
>>>>   Best wishes
>>>>   Andrej Stancak
>>>>
>>>>
>>>> Prof. Andrej Stancak, PhD.
>>>> The University of Liverpool
>>>> School of Psychology
>>>> The Eleanor Rathbone Building
>>>> Bedford Street South, Room 209
>>>> Liverpool
>>>> L69 7ZA
>>>>
>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>            stancak at centrum.cz (secondary)
>>>> Phone: 0151 7946951
>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between
>> users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the
>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for
>>> MEG
>>> and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users  
> of the FieldTrip  toolbox, to share experiences and to discuss new  
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ 
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From r.oostenveld at FCDONDERS.RU.NL  Tue Oct  7 09:19:29 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Tue, 7 Oct 2008 09:19:29 +0200
Subject: 4D data reading
In-Reply-To: <001001c927b3$e4e14e90$5757d182@DEPT6788A09EF4>
Message-ID: <TUE.7.OCT.2008.091929.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear all,

I have received the layout from Almu and have added the 4D148.lay
layout to the fieldtirp/template directory (where the other layouts
are now also to be found). See attached for how it looks.

thanks,
Robert


On 6 Oct 2008, at 15:02, Almudena Capilla wrote:

> Dear Gopa,
>
> I have got a template for the 4D - 148 channels system. I could give
> it to
> the Fieldtrip developers if this is helpful for other users of this
> system.
>
> Best,
> Almu



----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

From venug001 at BAMA.UA.EDU  Tue Oct  7 13:11:41 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Tue, 7 Oct 2008 06:11:41 -0500
Subject: 4D data reading
In-Reply-To: <5E2A6C3F-3335-4B61-A24E-D608947C471D@fcdonders.ru.nl>
Message-ID: <TUE.7.OCT.2008.061141.0500.FIELDTRIP@NIC.SURFNET.NL>

Dear Almu, Robert, fantastic. Is there anyway this can be incorporated
with EEGLAB? I know that is a separate topic, but as Robert will tell,
EEGLAB uses many Fieldtrip routines. Thanking all of you.
regards
gopa


Quoting Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>:

> Dear all,
>
> I have received the layout from Almu and have added the 4D148.lay
> layout to the fieldtirp/template directory (where the other layouts
>
> are now also to be found). See attached for how it looks.
>
> thanks,
> Robert
>
>
> On 6 Oct 2008, at 15:02, Almudena Capilla wrote:
>
> > Dear Gopa,
> >
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of this
>
> > system.
> >
> > Best,
> > Almu
>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From venug001 at BAMA.UA.EDU  Tue Oct  7 14:26:19 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Tue, 7 Oct 2008 07:26:19 -0500
Subject: 4D data reading
In-Reply-To: <5E2A6C3F-3335-4B61-A24E-D608947C471D@fcdonders.ru.nl>
Message-ID: <TUE.7.OCT.2008.072619.0500.FIELDTRIP@NIC.SURFNET.NL>

Robert, (I know I used to address you more formally than that!), is
there a reason why some channels are a different color than others?
Is there a way that a t-test say NC versus NIC will show up for
significances in Fieldtrip/EEGLAB for all of the 148 channels. I can do
that my dissertation will really look nice. I shall be able to show the
regions where the N400 was significant and contrast it to the regions
where the P600 was significant. Thanks in advance.
regards
gopa

Quoting Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>:

> Dear all,
>
> I have received the layout from Almu and have added the 4D148.lay
> layout to the fieldtirp/template directory (where the other layouts
>
> are now also to be found). See attached for how it looks.
>
> thanks,
> Robert
>
>
> On 6 Oct 2008, at 15:02, Almudena Capilla wrote:
>
> > Dear Gopa,
> >
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of this
>
> > system.
> >
> > Best,
> > Almu
>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From r.oostenveld at FCDONDERS.RU.NL  Tue Oct  7 15:18:47 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Tue, 7 Oct 2008 15:18:47 +0200
Subject: 4D data reading
In-Reply-To: <1223377901.48eb43ed8a08b@bamamail.ua.edu>
Message-ID: <TUE.7.OCT.2008.151847.0200.FIELDTRIP@NIC.SURFNET.NL>

On 7 Oct 2008, at 13:11, Gopakumar Venugopalan wrote:

> Dear Almu, Robert, fantastic. Is there anyway this can be incorporated
> with EEGLAB? I know that is a separate topic, but as Robert will tell,
> EEGLAB uses many Fieldtrip routines. Thanking all of you.
> regards
> gopa

Although EEGLAB also includes a function that goes with the name
"topoplot", just like FIELDTRIP, the two toolboxes do not share any
functionality for plotting. So the answer is no, the 4D148 layout
cannot be used in EEGLAB.

Recent EEGLAB versions (at least the "current" version) do allow to
use the same low level reading functions as used in FieldTrip. That is
done by selecting in eeglab: "file -> import -> from other formats
using fileio". You probably would want to replace the fileio version
included in eeglab with the latest one included in fieldtrip (or
available from http://www2.ru.nl/fcdonders/fieldtrip/doku.php?id=fieldtrip:development:fileio)
.

best regards,
Robert

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From r.oostenveld at FCDONDERS.RU.NL  Tue Oct  7 15:24:45 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Tue, 7 Oct 2008 15:24:45 +0200
Subject: cfg.layout and clusterplot
In-Reply-To: <7F00B6A0D4D0674E80A6C1D6DA873B5701CC652B55@iu-mssg-mbx05.ads.iu.edu>
Message-ID: <TUE.7.OCT.2008.152445.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi

On 6 Oct 2008, at 9:43, Hsu, Shen-Mou wrote:
> I was wondering if someone could help me sort out the following
> problem. I tried to plot significant clusters using clusterplot
> after permutation tests.  When I ran the script as below, it
> returned the message like this:
>
> reverting to 151 channel CTF default

are you working with 151 channel CTF data. If not, then this explains
it.

> ??? Error using ==> topoplotER at 330
> labels in data and labels in layout do not match
>
> Error in ==> clusterplot at 240
>          topoplotER(cfg, stat);
>
> However, I checked both cfg.layout.labels and cfg.layout.pnt.
> Everything seems fine.

You might want to check with the matlab debugger that the COMNT and
SCALE are not messing it up. These two fake channels are included in
the layout files to position the comment and scale. Recently quite
some changes were made to plotting, so you might also want to download
the latest version to test whether the problem persists.

best regards,
Robert

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From A.Stancak at LIVERPOOL.AC.UK  Tue Oct  7 17:44:22 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Tue, 7 Oct 2008 16:44:22 +0100
Subject: 4D data reading
Message-ID: <TUE.7.OCT.2008.164422.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Gopakumar,

  I followed your advice (pdf2set -u), and was almost successful in reading the 4d-148 data into FieldTrip. 
I can read header all right with exception of one line that turns out to be decisive during reading data (read_data):

D=read_data ('d:\data\meg\windup\T1\2\c,rfdc','dataformat','4d');
??? Reference to non-existent field 'ChannelUnitsPerBit'.

Error in ==> read_data at 477
    upb        = hdr.orig.ChannelUnitsPerBit;


Clearly, we miss the field ChannelUnitsPerBit in hdr.orig structure. As read_event.m also calls read_data.m, this problem precludes reading events as well.

To test the rest of the code, I simply put upb = grad (grad is 1 line above in read_data) and then it works all very well (as grad is equal to 1 in all channel fields). So my hope is that if we can sort out the missing field in hdr.orig., we will be able to read all data very well. 
 
I would be grateful for a hint here as have no idea how can we miss that field.

Best wishes
Andrej




Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
Sent: Mon 06/10/2008 16:03
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Andrej, I see an error in my mail below. The three files
.xyz, .m4d and the acutal pdf is produced using the command:

pdf2set -u

You post the selection in the propreitary MSI environment, then type in 
the command given above. It will put out the three files mentioned for 
each data set.
I shall include only the .xyz and .m4d files from grand averaged files, 
as they do not contain any identifiable information.
I believe that the .m4d file is also called the header file and 
the .xyz is called the location or coordinate file.
Ken Velarde was immensely helpful with this, as were Christian 
Weinbruch, and Don Rojas. Don Rojas's colleague Dr. Eugene Kronberg 
also has  created an interface that can read 4D data, and he was going 
to create such a template as well--as per our last email exchange.
I also have a xls2matlab function that I used to create my own 
template, as the sensor location file is usually a product of 
individual MEG systems. If I may have mislead anyone it is 
unintentional as I am constantly learning.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopa and Almu,
> 
>   do I understand the procedure correctly: we should export data from
> 4D in FIF format (currently we export in native e,... (binary), and
> the text files for the header and the surface points), and then use a
> modified xyz file containing the layout of 148 sensors. I would be
> grateful for one sample xyz file to see whether we can read data this
> way. Naturally, the best would be to incorporate it into the reading
> procedures of FieldTrip.
> 
> Best wishes
> Andrej
> 
> 
> Prof. Andrej Stancak, PhD. 
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
> 
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
> 
> 
> 
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 14:12
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>  
> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
> 
> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
> 
> the other users. There was also a discussion about whether the
> systems 
> were using third order gradiometers and/or magnetometers as the 
> reference. There are mail postings in that thread.
> Everyone: I apologize for the typos in my hastily composed response 
> earlier.
> regards
> gopa
> 
> 
> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
> 
> > Dear Gopa,
> > 
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of
> this
> > system.
> > 
> > Best,
> > Almu
> > 
> > -----Original Message-----
> > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> On
> > Behalf
> > Of Gopakumar Venugopalan
> > Sent: 06 October 2008 13:22
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> > 
> > Hello everyone, I have been wrestling with these problems for a
> while
> > 
> > too.
> > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > (.avg, 
> > and .eeg), and will read raw data (e,..)from 4D.
> > I believe that EEGLAB/Fieldtrip may not have a template for the
> 148-
> > Channel system co-ordinates. Christian and Don Rojas created one
> for
> > me 
> > in early April this year.
> > A FIF export from the 4D system may also solve this problem.
> Stephen
> > 
> > Moratti helped me with this a while a ago. It puts out three 
> > files .xyz, .4D and the original e,.. file. But, if the .xyz file
> > which 
> > has coordinates for 148 channels does not match with the template,
> > then 
> > the data will not load. I think for one may have to load a create
> a
> > 148 
> > channel template for this purpose. This is my experience with
> EEGLAB,
> > 
> > and I think that they underlying engine is the same for both
> EEGLAB
> > and 
> > Fieldtrip
> > Then again, I may be completely wrong about everything except the 
> > templates that were created for me.
> > regards
> > gopa
> > 
> > 
> > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> > 
> > > Dear all,
> > > 
> > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > sensors). For now, we export original 4D data into BESA format,
> > and
> > > then read those into FieldTrip. This is not optimal, as e.g.
> > gradient
> > > coils information is not transferred into FieldTrip. We would be
> > > grateful for a plugin or a hint enabling us to read the 4D data
> > > directly into FieldTrip.
> > > 
> > >   Best wishes
> > >   Andrej Stancak
> > > 
> > > 
> > > Prof. Andrej Stancak, PhD. 
> > > The University of Liverpool
> > > School of Psychology
> > > The Eleanor Rathbone Building
> > > Bedford Street South, Room 209
> > > Liverpool
> > > L69 7ZA
> > > 
> > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > >            stancak at centrum.cz (secondary)
> > > Phone: 0151 7946951
> > > Office hours: Monday 10-12, Wednesday 10-12
> > > 
> > > 
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > > 
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the
> > FieldTrip  toolbox, to share experiences and to discuss new ideas
> for
> > MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From venug001 at BAMA.UA.EDU  Tue Oct  7 18:22:23 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Tue, 7 Oct 2008 11:22:23 -0500
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CBF@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <TUE.7.OCT.2008.112223.0500.FIELDTRIP@NIC.SURFNET.NL>

Andrew, I am glad. Thanks to Ken and  and Stephen's assistant. I have
not tweaked around with Cupb settings myself. I would defer that to
folks like Robert, Stephen or Christian. I don't know if Ken is on this
listserv, but I know that he likes to keep up with anything that is 4D
related. I can help with any thing else if I can.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopakumar,
>
>   I followed your advice (pdf2set -u), and was almost successful in
> reading the 4d-148 data into FieldTrip.
> I can read header all right with exception of one line that turns out
> to be decisive during reading data (read_data):
>
> D=read_data ('d:\data\meg\windup\T1\2\c,rfdc','dataformat','4d');
> ??? Reference to non-existent field 'ChannelUnitsPerBit'.
>
> Error in ==> read_data at 477
>     upb        = hdr.orig.ChannelUnitsPerBit;
>
>
> Clearly, we miss the field ChannelUnitsPerBit in hdr.orig structure.
> As read_event.m also calls read_data.m, this problem precludes
> reading events as well.
>
> To test the rest of the code, I simply put upb = grad (grad is 1 line
> above in read_data) and then it works all very well (as grad is equal
> to 1 in all channel fields). So my hope is that if we can sort out
> the missing field in hdr.orig., we will be able to read all data very
> well.
>
> I would be grateful for a hint here as have no idea how can we miss
> that field.
>
> Best wishes
> Andrej
>
>
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 16:03
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Andrej, I see an error in my mail below. The three files
> .xyz, .m4d and the acutal pdf is produced using the command:
>
> pdf2set -u
>
> You post the selection in the propreitary MSI environment, then type
> in
> the command given above. It will put out the three files mentioned
> for
> each data set.
> I shall include only the .xyz and .m4d files from grand averaged
> files,
> as they do not contain any identifiable information.
> I believe that the .m4d file is also called the header file and
> the .xyz is called the location or coordinate file.
> Ken Velarde was immensely helpful with this, as were Christian
> Weinbruch, and Don Rojas. Don Rojas's colleague Dr. Eugene Kronberg
> also has  created an interface that can read 4D data, and he was
> going
> to create such a template as well--as per our last email exchange.
> I also have a xls2matlab function that I used to create my own
> template, as the sensor location file is usually a product of
> individual MEG systems. If I may have mislead anyone it is
> unintentional as I am constantly learning.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
> > Dear Gopa and Almu,
> >
> >   do I understand the procedure correctly: we should export data
> from
> > 4D in FIF format (currently we export in native e,... (binary),
> and
> > the text files for the header and the surface points), and then use
> a
> > modified xyz file containing the layout of 148 sensors. I would be
> > grateful for one sample xyz file to see whether we can read data
> this
> > way. Naturally, the best would be to incorporate it into the
> reading
> > procedures of FieldTrip.
> >
> > Best wishes
> > Andrej
> >
> >
> > Prof. Andrej Stancak, PhD.
> > The University of Liverpool
> > School of Psychology
> > The Eleanor Rathbone Building
> > Bedford Street South, Room 209
> > Liverpool
> > L69 7ZA
> >
> > E:mail: a.stancak at liverpool.ac.uk  (primary)
> >            stancak at centrum.cz (secondary)
> > Phone: 0151 7946951
> > Office hours: Monday 10-12, Wednesday 10-12
> >
> >
> >
> > -----Original Message-----
> > From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> > Sent: Mon 06/10/2008 14:12
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> >
> > Dear Almu (that is a nice name!) thank you  Rob Oostenveld,
> Christian
> >
> > Weinbruch and Arno (EEGLAB) may be the ones who can make it work
> for
> >
> > the other users. There was also a discussion about whether the
> > systems
> > were using third order gradiometers and/or magnetometers as the
> > reference. There are mail postings in that thread.
> > Everyone: I apologize for the typos in my hastily composed response
>
> > earlier.
> > regards
> > gopa
> >
> >
> > Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
> >
> > > Dear Gopa,
> > >
> > > I have got a template for the 4D - 148 channels system. I could
> > give
> > > it to
> > > the Fieldtrip developers if this is helpful for other users of
> > this
> > > system.
> > >
> > > Best,
> > > Almu
> > >
> > > -----Original Message-----
> > > From: FieldTrip discussion list
> [mailto:FIELDTRIP at NIC.SURFNET.NL]
> > On
> > > Behalf
> > > Of Gopakumar Venugopalan
> > > Sent: 06 October 2008 13:22
> > > To: FIELDTRIP at NIC.SURFNET.NL
> > > Subject: Re: [FIELDTRIP] 4D data reading
> > >
> > > Hello everyone, I have been wrestling with these problems for a
> > while
> > >
> > > too.
> > > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > > (.avg,
> > > and .eeg), and will read raw data (e,..)from 4D.
> > > I believe that EEGLAB/Fieldtrip may not have a template for the
> > 148-
> > > Channel system co-ordinates. Christian and Don Rojas created one
> > for
> > > me
> > > in early April this year.
> > > A FIF export from the 4D system may also solve this problem.
> > Stephen
> > >
> > > Moratti helped me with this a while a ago. It puts out three
> > > files .xyz, .4D and the original e,.. file. But, if the .xyz
> file
> > > which
> > > has coordinates for 148 channels does not match with the
> template,
> > > then
> > > the data will not load. I think for one may have to load a
> create
> > a
> > > 148
> > > channel template for this purpose. This is my experience with
> > EEGLAB,
> > >
> > > and I think that they underlying engine is the same for both
> > EEGLAB
> > > and
> > > Fieldtrip
> > > Then again, I may be completely wrong about everything except the
>
> > > templates that were created for me.
> > > regards
> > > gopa
> > >
> > >
> > > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> > >
> > > > Dear all,
> > > >
> > > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > > sensors). For now, we export original 4D data into BESA
> format,
> > > and
> > > > then read those into FieldTrip. This is not optimal, as e.g.
> > > gradient
> > > > coils information is not transferred into FieldTrip. We would
> be
> > > > grateful for a plugin or a hint enabling us to read the 4D
> data
> > > > directly into FieldTrip.
> > > >
> > > >   Best wishes
> > > >   Andrej Stancak
> > > >
> > > >
> > > > Prof. Andrej Stancak, PhD.
> > > > The University of Liverpool
> > > > School of Psychology
> > > > The Eleanor Rathbone Building
> > > > Bedford Street South, Room 209
> > > > Liverpool
> > > > L69 7ZA
> > > >
> > > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > > >            stancak at centrum.cz (secondary)
> > > > Phone: 0151 7946951
> > > > Office hours: Monday 10-12, Wednesday 10-12
> > > >
> > > >
> > > > ----------------------------------
> > > > The aim of this list is to facilitate the discussion between
> > users
> > > of
> > > > the FieldTrip  toolbox, to share experiences and to discuss
> new
> > > ideas
> > > > for MEG and EEG analysis. See also
> > > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > > http://www.ru.nl/fcdonders/fieldtrip.
> > > >
> > >
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the
> > > FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for
> > > MEG
> > > and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > >
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From A.Stancak at LIVERPOOL.AC.UK  Tue Oct  7 18:40:04 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Tue, 7 Oct 2008 17:40:04 +0100
Subject: 4D data reading
Message-ID: <TUE.7.OCT.2008.174004.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs,

  I have followed your path (in parallel to the one suggested by Gopakumar) and it worked. It took me a while to dig out the configuration file in the MSI server and to realise it needs to be renamed and put into the data directory, but it works now. 

  As you write, the procedures change the prompt to K:> and continue after typing dbcont. I do not mind this if it is for once, but what about running batch files? Or is the idea to read data, the header, and the events and then save all for further processing in some different format (e.g. Matlab?). I work with the FieldTrip_20051006 version that I downloaded today, and I do not know whether it has been fixed or whether this feature (K:> dbcont) will stay.

Thank you for your advice. Thanks to you and Gopakumar and few other colleagues we are now close to smooth reading our MEG data into FieldTrip.

 Best wishes
 Andrej

Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
Sent: Mon 06/10/2008 15:54
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Dear Andrej, dear Gopa,

Sorry to bother you again, but I tried to make a point in my last  
mail that it is not necessary to intermediately convert your raw  
epoched or continuous 4D-data into another format, prior to be able  
to read it into Fieldtrip. Of course you are free to do so, but the  
most natural way to me would seem to work on the raw datafiles  
directly. Fieldtrip should support this and it has reading routines  
for the raw data-file (beginning with e, or c,), the config-file, and  
the file containing the digitized head-surface positions.
You should be able to obtain the header information directly by  
calling: hdr = read_header('e,thenameofyourrawdatafile') (give or  
take an accidental 'keyboard'-statement in the low-level function  
read_4d_hdr, this will be fixed in tonight's release version: if it  
occurs now, just type dbcont on the command line when it prompts:  
K>>) As far as I know hdr contains a structure grad, which specifies  
the sensor-positions. At least it works on our Glaswegian 248-sensor  
system.

Yours,

Jan-Mathijs


On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:

> Sure will send you those files. Please remember in my files there are
> only 146 channel locations as we turned off two channels.I also have a
> matlab file from Don Rojas for the 148 channel layout and a file which
> he created for the 146 channel layout. Please give some time today, as
> I run those programs on a different machine.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
>> Dear Gopa and Almu,
>>
>>   do I understand the procedure correctly: we should export data from
>> 4D in FIF format (currently we export in native e,... (binary), and
>> the text files for the header and the surface points), and then use a
>> modified xyz file containing the layout of 148 sensors. I would be
>> grateful for one sample xyz file to see whether we can read data this
>> way. Naturally, the best would be to incorporate it into the reading
>> procedures of FieldTrip.
>>
>> Best wishes
>> Andrej
>>
>>
>> Prof. Andrej Stancak, PhD.
>> The University of Liverpool
>> School of Psychology
>> The Eleanor Rathbone Building
>> Bedford Street South, Room 209
>> Liverpool
>> L69 7ZA
>>
>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>            stancak at centrum.cz (secondary)
>> Phone: 0151 7946951
>> Office hours: Monday 10-12, Wednesday 10-12
>>
>>
>>
>> -----Original Message-----
>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>> Sent: Mon 06/10/2008 14:12
>> To: FIELDTRIP at NIC.SURFNET.NL
>> Subject: Re: [FIELDTRIP] 4D data reading
>>
>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>
>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>
>> the other users. There was also a discussion about whether the
>> systems
>> were using third order gradiometers and/or magnetometers as the
>> reference. There are mail postings in that thread.
>> Everyone: I apologize for the typos in my hastily composed response
>> earlier.
>> regards
>> gopa
>>
>>
>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>
>>> Dear Gopa,
>>>
>>> I have got a template for the 4D - 148 channels system. I could
>> give
>>> it to
>>> the Fieldtrip developers if this is helpful for other users of
>> this
>>> system.
>>>
>>> Best,
>>> Almu
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>> On
>>> Behalf
>>> Of Gopakumar Venugopalan
>>> Sent: 06 October 2008 13:22
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Hello everyone, I have been wrestling with these problems for a
>> while
>>>
>>> too.
>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>> (.avg,
>>> and .eeg), and will read raw data (e,..)from 4D.
>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>> 148-
>>> Channel system co-ordinates. Christian and Don Rojas created one
>> for
>>> me
>>> in early April this year.
>>> A FIF export from the 4D system may also solve this problem.
>> Stephen
>>>
>>> Moratti helped me with this a while a ago. It puts out three
>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>> which
>>> has coordinates for 148 channels does not match with the template,
>>> then
>>> the data will not load. I think for one may have to load a create
>> a
>>> 148
>>> channel template for this purpose. This is my experience with
>> EEGLAB,
>>>
>>> and I think that they underlying engine is the same for both
>> EEGLAB
>>> and
>>> Fieldtrip
>>> Then again, I may be completely wrong about everything except the
>>> templates that were created for me.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>
>>>> Dear all,
>>>>
>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>> sensors). For now, we export original 4D data into BESA format,
>>> and
>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>> gradient
>>>> coils information is not transferred into FieldTrip. We would be
>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>> directly into FieldTrip.
>>>>
>>>>   Best wishes
>>>>   Andrej Stancak
>>>>
>>>>
>>>> Prof. Andrej Stancak, PhD.
>>>> The University of Liverpool
>>>> School of Psychology
>>>> The Eleanor Rathbone Building
>>>> Bedford Street South, Room 209
>>>> Liverpool
>>>> L69 7ZA
>>>>
>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>            stancak at centrum.cz (secondary)
>>>> Phone: 0151 7946951
>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between
>> users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the
>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for
>>> MEG
>>> and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users  
> of the FieldTrip  toolbox, to share experiences and to discuss new  
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ 
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From j.schoffelen at PSY.GLA.AC.UK  Tue Oct  7 19:58:32 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Tue, 7 Oct 2008 18:58:32 +0100
Subject: 4D data reading
Message-ID: <TUE.7.OCT.2008.185832.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Andrej,

I am glad it works now. The keyboard statement in the code (leading to  
K>>) was just to debug some code. I forgot to clear it when I was  
done. I fixed it yesterday, and it should be correct in the latest  
version of fieldtrip (20081007). The idea is certainly not to read the  
events/header/data only once, store it, and refer to it for later use.  
However, depending on what you want, it could be useful (I often save  
my trial definitions after artifact rejection because this is a time  
consuming step). Hopefully you can run batch with the keyboard  
statement removed.
As far as I understood from the formatting of the data coming from our  
248-channel system, each recording is automatically saved with a  
config-file, which is a copy of the system config-file, and which is  
adjusted with run-specific parameters (most importantly weight tables  
for the denoising, and filter setting (I am not entirely sure about  
the filter settings). Anyway, as it is programmed at the moment, the  
code assumes the run-specific config file to be present in the  
run-directory, and it assumes the file to be named 'config'. This of  
course can be made a bit more flexible (for example one could provide  
an explicit path/filename to the system's config file).
Do I understand correctly, that the data you record does not generally  
contain a config-file in the data-directories themselves?

Yours,

Jan-Mathijs


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Jan-Mathijs,
>
>   I have followed your path (in parallel to the one suggested by   
> Gopakumar) and it worked. It took me a while to dig out the   
> configuration file in the MSI server and to realise it needs to be   
> renamed and put into the data directory, but it works now.
>
>   As you write, the procedures change the prompt to K:> and continue  
>  after typing dbcont. I do not mind this if it is for once, but what  
>  about running batch files? Or is the idea to read data, the header,  
>  and the events and then save all for further processing in some   
> different format (e.g. Matlab?). I work with the FieldTrip_20051006   
> version that I downloaded today, and I do not know whether it has   
> been fixed or whether this feature (K:> dbcont) will stay.
>
> Thank you for your advice. Thanks to you and Gopakumar and few other  
>  colleagues we are now close to smooth reading our MEG data into   
> FieldTrip.
>
>  Best wishes
>  Andrej
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
> Sent: Mon 06/10/2008 15:54
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Dear Andrej, dear Gopa,
>
> Sorry to bother you again, but I tried to make a point in my last
> mail that it is not necessary to intermediately convert your raw
> epoched or continuous 4D-data into another format, prior to be able
> to read it into Fieldtrip. Of course you are free to do so, but the
> most natural way to me would seem to work on the raw datafiles
> directly. Fieldtrip should support this and it has reading routines
> for the raw data-file (beginning with e, or c,), the config-file, and
> the file containing the digitized head-surface positions.
> You should be able to obtain the header information directly by
> calling: hdr = read_header('e,thenameofyourrawdatafile') (give or
> take an accidental 'keyboard'-statement in the low-level function
> read_4d_hdr, this will be fixed in tonight's release version: if it
> occurs now, just type dbcont on the command line when it prompts:
> K>>) As far as I know hdr contains a structure grad, which specifies
> the sensor-positions. At least it works on our Glaswegian 248-sensor
> system.
>
> Yours,
>
> Jan-Mathijs
>
>
> On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:
>
>> Sure will send you those files. Please remember in my files there are
>> only 146 channel locations as we turned off two channels.I also have a
>> matlab file from Don Rojas for the 148 channel layout and a file which
>> he created for the 146 channel layout. Please give some time today, as
>> I run those programs on a different machine.
>> regards
>> gopa
>>
>>
>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>
>>> Dear Gopa and Almu,
>>>
>>>   do I understand the procedure correctly: we should export data from
>>> 4D in FIF format (currently we export in native e,... (binary), and
>>> the text files for the header and the surface points), and then use a
>>> modified xyz file containing the layout of 148 sensors. I would be
>>> grateful for one sample xyz file to see whether we can read data this
>>> way. Naturally, the best would be to incorporate it into the reading
>>> procedures of FieldTrip.
>>>
>>> Best wishes
>>> Andrej
>>>
>>>
>>> Prof. Andrej Stancak, PhD.
>>> The University of Liverpool
>>> School of Psychology
>>> The Eleanor Rathbone Building
>>> Bedford Street South, Room 209
>>> Liverpool
>>> L69 7ZA
>>>
>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>            stancak at centrum.cz (secondary)
>>> Phone: 0151 7946951
>>> Office hours: Monday 10-12, Wednesday 10-12
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>>> Sent: Mon 06/10/2008 14:12
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>>
>>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>>
>>> the other users. There was also a discussion about whether the
>>> systems
>>> were using third order gradiometers and/or magnetometers as the
>>> reference. There are mail postings in that thread.
>>> Everyone: I apologize for the typos in my hastily composed response
>>> earlier.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>>
>>>> Dear Gopa,
>>>>
>>>> I have got a template for the 4D - 148 channels system. I could
>>> give
>>>> it to
>>>> the Fieldtrip developers if this is helpful for other users of
>>> this
>>>> system.
>>>>
>>>> Best,
>>>> Almu
>>>>
>>>> -----Original Message-----
>>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>>> On
>>>> Behalf
>>>> Of Gopakumar Venugopalan
>>>> Sent: 06 October 2008 13:22
>>>> To: FIELDTRIP at NIC.SURFNET.NL
>>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>>
>>>> Hello everyone, I have been wrestling with these problems for a
>>> while
>>>>
>>>> too.
>>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>>> (.avg,
>>>> and .eeg), and will read raw data (e,..)from 4D.
>>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>>> 148-
>>>> Channel system co-ordinates. Christian and Don Rojas created one
>>> for
>>>> me
>>>> in early April this year.
>>>> A FIF export from the 4D system may also solve this problem.
>>> Stephen
>>>>
>>>> Moratti helped me with this a while a ago. It puts out three
>>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>>> which
>>>> has coordinates for 148 channels does not match with the template,
>>>> then
>>>> the data will not load. I think for one may have to load a create
>>> a
>>>> 148
>>>> channel template for this purpose. This is my experience with
>>> EEGLAB,
>>>>
>>>> and I think that they underlying engine is the same for both
>>> EEGLAB
>>>> and
>>>> Fieldtrip
>>>> Then again, I may be completely wrong about everything except the
>>>> templates that were created for me.
>>>> regards
>>>> gopa
>>>>
>>>>
>>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>>
>>>>> Dear all,
>>>>>
>>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>>> sensors). For now, we export original 4D data into BESA format,
>>>> and
>>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>>> gradient
>>>>> coils information is not transferred into FieldTrip. We would be
>>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>>> directly into FieldTrip.
>>>>>
>>>>>   Best wishes
>>>>>   Andrej Stancak
>>>>>
>>>>>
>>>>> Prof. Andrej Stancak, PhD.
>>>>> The University of Liverpool
>>>>> School of Psychology
>>>>> The Eleanor Rathbone Building
>>>>> Bedford Street South, Room 209
>>>>> Liverpool
>>>>> L69 7ZA
>>>>>
>>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>>            stancak at centrum.cz (secondary)
>>>>> Phone: 0151 7946951
>>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>>
>>>>>
>>>>> ----------------------------------
>>>>> The aim of this list is to facilitate the discussion between
>>> users
>>>> of
>>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>>> ideas
>>>>> for MEG and EEG analysis. See also
>>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between users
>>> of
>>>> the
>>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for
>>>> MEG
>>>> and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of
>>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of
>>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
>> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users   
> of the FieldTrip  toolbox, to share experiences and to discuss new   
> ideas for MEG and EEG analysis. See also   
> http://listserv.surfnet.nl/archives/fieldtrip.html and   
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users   
> of the FieldTrip  toolbox, to share experiences and to discuss new   
> ideas for MEG and EEG analysis. See also   
> http://listserv.surfnet.nl/archives/fieldtrip.html and   
> http://www.ru.nl/fcdonders/fieldtrip.
>



------------------------------------------------------------------
The University of Glasgow, Department of Psychology WebMail system
------------------------------------------------------------------

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From A.Stancak at LIVERPOOL.AC.UK  Wed Oct  8 15:07:40 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Wed, 8 Oct 2008 14:07:40 +0100
Subject: 4D data reading
Message-ID: <WED.8.OCT.2008.140740.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs,

  thanks for your e-mail and further information. It turned out that the archive data I used for testing the data reading did not have a config file, and neither it is displayed in the MSI window in the list of posted/non-posted files so I was not sure where to find it. Today I have exported data using the MSI disk/tape utilities, and the config file was there as it should be.  

I have now tested reading the 4D files with a correct config file on board and it worked well. I still have to do "dbcont" but this is a small cosmetic issue compared to the way we handled data before. Again many thanks for your advice and information.

 With best wishes
 Andrej

   


  

Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
Sent: Tue 07/10/2008 18:58
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Dear Andrej,

I am glad it works now. The keyboard statement in the code (leading to  
K>>) was just to debug some code. I forgot to clear it when I was  
done. I fixed it yesterday, and it should be correct in the latest  
version of fieldtrip (20081007). The idea is certainly not to read the  
events/header/data only once, store it, and refer to it for later use.  
However, depending on what you want, it could be useful (I often save  
my trial definitions after artifact rejection because this is a time  
consuming step). Hopefully you can run batch with the keyboard  
statement removed.
As far as I understood from the formatting of the data coming from our  
248-channel system, each recording is automatically saved with a  
config-file, which is a copy of the system config-file, and which is  
adjusted with run-specific parameters (most importantly weight tables  
for the denoising, and filter setting (I am not entirely sure about  
the filter settings). Anyway, as it is programmed at the moment, the  
code assumes the run-specific config file to be present in the  
run-directory, and it assumes the file to be named 'config'. This of  
course can be made a bit more flexible (for example one could provide  
an explicit path/filename to the system's config file).
Do I understand correctly, that the data you record does not generally  
contain a config-file in the data-directories themselves?

Yours,

Jan-Mathijs


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Jan-Mathijs,
>
>   I have followed your path (in parallel to the one suggested by   
> Gopakumar) and it worked. It took me a while to dig out the   
> configuration file in the MSI server and to realise it needs to be   
> renamed and put into the data directory, but it works now.
>
>   As you write, the procedures change the prompt to K:> and continue  
>  after typing dbcont. I do not mind this if it is for once, but what  
>  about running batch files? Or is the idea to read data, the header,  
>  and the events and then save all for further processing in some   
> different format (e.g. Matlab?). I work with the FieldTrip_20051006   
> version that I downloaded today, and I do not know whether it has   
> been fixed or whether this feature (K:> dbcont) will stay.
>
> Thank you for your advice. Thanks to you and Gopakumar and few other  
>  colleagues we are now close to smooth reading our MEG data into   
> FieldTrip.
>
>  Best wishes
>  Andrej
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
> Sent: Mon 06/10/2008 15:54
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Dear Andrej, dear Gopa,
>
> Sorry to bother you again, but I tried to make a point in my last
> mail that it is not necessary to intermediately convert your raw
> epoched or continuous 4D-data into another format, prior to be able
> to read it into Fieldtrip. Of course you are free to do so, but the
> most natural way to me would seem to work on the raw datafiles
> directly. Fieldtrip should support this and it has reading routines
> for the raw data-file (beginning with e, or c,), the config-file, and
> the file containing the digitized head-surface positions.
> You should be able to obtain the header information directly by
> calling: hdr = read_header('e,thenameofyourrawdatafile') (give or
> take an accidental 'keyboard'-statement in the low-level function
> read_4d_hdr, this will be fixed in tonight's release version: if it
> occurs now, just type dbcont on the command line when it prompts:
> K>>) As far as I know hdr contains a structure grad, which specifies
> the sensor-positions. At least it works on our Glaswegian 248-sensor
> system.
>
> Yours,
>
> Jan-Mathijs
>
>
> On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:
>
>> Sure will send you those files. Please remember in my files there are
>> only 146 channel locations as we turned off two channels.I also have a
>> matlab file from Don Rojas for the 148 channel layout and a file which
>> he created for the 146 channel layout. Please give some time today, as
>> I run those programs on a different machine.
>> regards
>> gopa
>>
>>
>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>
>>> Dear Gopa and Almu,
>>>
>>>   do I understand the procedure correctly: we should export data from
>>> 4D in FIF format (currently we export in native e,... (binary), and
>>> the text files for the header and the surface points), and then use a
>>> modified xyz file containing the layout of 148 sensors. I would be
>>> grateful for one sample xyz file to see whether we can read data this
>>> way. Naturally, the best would be to incorporate it into the reading
>>> procedures of FieldTrip.
>>>
>>> Best wishes
>>> Andrej
>>>
>>>
>>> Prof. Andrej Stancak, PhD.
>>> The University of Liverpool
>>> School of Psychology
>>> The Eleanor Rathbone Building
>>> Bedford Street South, Room 209
>>> Liverpool
>>> L69 7ZA
>>>
>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>            stancak at centrum.cz (secondary)
>>> Phone: 0151 7946951
>>> Office hours: Monday 10-12, Wednesday 10-12
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>>> Sent: Mon 06/10/2008 14:12
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>>
>>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>>
>>> the other users. There was also a discussion about whether the
>>> systems
>>> were using third order gradiometers and/or magnetometers as the
>>> reference. There are mail postings in that thread.
>>> Everyone: I apologize for the typos in my hastily composed response
>>> earlier.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>>
>>>> Dear Gopa,
>>>>
>>>> I have got a template for the 4D - 148 channels system. I could
>>> give
>>>> it to
>>>> the Fieldtrip developers if this is helpful for other users of
>>> this
>>>> system.
>>>>
>>>> Best,
>>>> Almu
>>>>
>>>> -----Original Message-----
>>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>>> On
>>>> Behalf
>>>> Of Gopakumar Venugopalan
>>>> Sent: 06 October 2008 13:22
>>>> To: FIELDTRIP at NIC.SURFNET.NL
>>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>>
>>>> Hello everyone, I have been wrestling with these problems for a
>>> while
>>>>
>>>> too.
>>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>>> (.avg,
>>>> and .eeg), and will read raw data (e,..)from 4D.
>>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>>> 148-
>>>> Channel system co-ordinates. Christian and Don Rojas created one
>>> for
>>>> me
>>>> in early April this year.
>>>> A FIF export from the 4D system may also solve this problem.
>>> Stephen
>>>>
>>>> Moratti helped me with this a while a ago. It puts out three
>>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>>> which
>>>> has coordinates for 148 channels does not match with the template,
>>>> then
>>>> the data will not load. I think for one may have to load a create
>>> a
>>>> 148
>>>> channel template for this purpose. This is my experience with
>>> EEGLAB,
>>>>
>>>> and I think that they underlying engine is the same for both
>>> EEGLAB
>>>> and
>>>> Fieldtrip
>>>> Then again, I may be completely wrong about everything except the
>>>> templates that were created for me.
>>>> regards
>>>> gopa
>>>>
>>>>
>>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>>
>>>>> Dear all,
>>>>>
>>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>>> sensors). For now, we export original 4D data into BESA format,
>>>> and
>>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>>> gradient
>>>>> coils information is not transferred into FieldTrip. We would be
>>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>>> directly into FieldTrip.
>>>>>
>>>>>   Best wishes
>>>>>   Andrej Stancak
>>>>>
>>>>>
>>>>> Prof. Andrej Stancak, PhD.
>>>>> The University of Liverpool
>>>>> School of Psychology
>>>>> The Eleanor Rathbone Building
>>>>> Bedford Street South, Room 209
>>>>> Liverpool
>>>>> L69 7ZA
>>>>>
>>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>>            stancak at centrum.cz (secondary)
>>>>> Phone: 0151 7946951
>>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>>
>>>>>
>>>>> ----------------------------------
>>>>> The aim of this list is to facilitate the discussion between
>>> users
>>>> of
>>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>>> ideas
>>>>> for MEG and EEG analysis. See also
>>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between users
>>> of
>>>> the
>>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for
>>>> MEG
>>>> and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of
>>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of
>>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
>> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users   
> of the FieldTrip  toolbox, to share experiences and to discuss new   
> ideas for MEG and EEG analysis. See also   
> http://listserv.surfnet.nl/archives/fieldtrip.html and   
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users   
> of the FieldTrip  toolbox, to share experiences and to discuss new   
> ideas for MEG and EEG analysis. See also   
> http://listserv.surfnet.nl/archives/fieldtrip.html and   
> http://www.ru.nl/fcdonders/fieldtrip.
>



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

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.



----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From julian.keil at GMAIL.COM  Wed Oct  8 17:22:14 2008
From: julian.keil at GMAIL.COM (Julian Keil)
Date: Wed, 8 Oct 2008 17:22:14 +0200
Subject: 4D data reading -> 148 channel system
Message-ID: <WED.8.OCT.2008.172214.0200.FIELDTRIP@NIC.SURFNET.NL>

Hello everyone,

i just tried to read 4D raw data as was suggested in the recent
discussion.
Unfortunately, I encountered 2 Problems:

First, Matlab still enters the debug-mode, although I'm using the
latest version of Fieldtrip
Second, though I can read the raw datal, the labels for the MEG
channels are missing. The data.hdr.label contains the 165 recorded
channels but the labels are not the Names but - as I think - the
locations.
(e.g. A3+03).
Could it be, that the definition for the 148-channel 4d-system is
missing?
Does anyone have a hint hw to solve this?

Thanks a lot

Julian Keil


Dipl. Psych. Julian Keil

OBOB-Lab
University of Konstanz
Department of Psychology
P.O. Box D23
78457 Konstanz
Germany

Tel: ++49 - (0)7531 - 88 45 84
Email: julian.keil at uni-konstanz.de
Homepage: http://www.uni-konstanz.de/obob





----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From j.schoffelen at PSY.GLA.AC.UK  Wed Oct  8 17:53:58 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Wed, 8 Oct 2008 16:53:58 +0100
Subject: 4D data reading -> 148 channel system
In-Reply-To: <BD4DCA44-4C7F-4076-9BFA-2531597267A7@GMAIL.COM>
Message-ID: <WED.8.OCT.2008.165358.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Julian,

As of the debugging thingy: sorry about that, I thought I adjusted it
but apparently something went wrong. You can easily fix this yourself
by going to the appropriate function. It's read_4d_hdr and you just
have to remove the keyboard-statement somewhere in the code. I don't
know where the function is located in the release version of
fieldtrip, but it should be somewhere like fieldtrip/private, or
fieldtrip/fileio/private. I hope that as of tomorrow the trailing
keyboard statement is removed from the release version.
Regarding your second point: I tried it out with a 148-channel
dataset I have lying around, and you're absolutely right.
Interestingly, for the 248-system it works just fine. Give me some
time to look into this. I hope to get it working robustly for both
systems. Could you for the time being check whether the field
data.hdr.orig.Channel looks meaningful for your data? A solution for
now would be to replace data.hdr.label (and data.label) with
hdr.orig.Channel.


Yours,

Jan-Mathijs



On Oct 8, 2008, at 4:22 PM, Julian Keil wrote:

> Hello everyone,
>
> i just tried to read 4D raw data as was suggested in the recent
> discussion.
> Unfortunately, I encountered 2 Problems:
>
> First, Matlab still enters the debug-mode, although I'm using the
> latest version of Fieldtrip
> Second, though I can read the raw datal, the labels for the MEG
> channels are missing. The data.hdr.label contains the 165 recorded
> channels but the labels are not the Names but - as I think - the
> locations.
> (e.g. A3+03).
> Could it be, that the definition for the 148-channel 4d-system is
> missing?
> Does anyone have a hint hw to solve this?
>
> Thanks a lot
>
> Julian Keil
>
>
> Dipl. Psych. Julian Keil
>
> OBOB-Lab
> University of Konstanz
> Department of Psychology
> P.O. Box D23
> 78457 Konstanz
> Germany
>
> Tel: ++49 - (0)7531 - 88 45 84
> Email: julian.keil at uni-konstanz.de
> Homepage: http://www.uni-konstanz.de/obob
>
>
>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From julian.keil at GMAIL.COM  Thu Oct  9 12:01:38 2008
From: julian.keil at GMAIL.COM (Julian Keil)
Date: Thu, 9 Oct 2008 12:01:38 +0200
Subject: 4D data reading -> 148 channel system
In-Reply-To: <AAD7D620-D190-4A0E-8649-4F2706ECC5DB@psy.gla.ac.uk>
Message-ID: <THU.9.OCT.2008.120138.0200.FIELDTRIP@NIC.SURFNET.NL>

Hello Jan-Mathijs,

thanks for the fast fix of problem 1.
As for problem 2: the data.hdr.orig.channel indeed looks meaningful
and replacing the files as you mentioned works fine.

Thanks a lot.

Julian

Am 08.10.2008 um 17:53 schrieb jan-mathijs schoffelen:

> Dear Julian,
>
> As of the debugging thingy: sorry about that, I thought I adjusted
> it but apparently something went wrong. You can easily fix this
> yourself by going to the appropriate function. It's read_4d_hdr and
> you just have to remove the keyboard-statement somewhere in the
> code. I don't know where the function is located in the release
> version of fieldtrip, but it should be somewhere like fieldtrip/
> private, or fieldtrip/fileio/private. I hope that as of tomorrow the
> trailing keyboard statement is removed from the release version.
> Regarding your second point: I tried it out with a 148-channel
> dataset I have lying around, and you're absolutely right.
> Interestingly, for the 248-system it works just fine. Give me some
> time to look into this. I hope to get it working robustly for both
> systems. Could you for the time being check whether the field
> data.hdr.orig.Channel looks meaningful for your data? A solution for
> now would be to replace data.hdr.label (and data.label) with
> hdr.orig.Channel.
>
>
> Yours,
>
> Jan-Mathijs
>
>
>
> On Oct 8, 2008, at 4:22 PM, Julian Keil wrote:
>
>> Hello everyone,
>>
>> i just tried to read 4D raw data as was suggested in the recent
>> discussion.
>> Unfortunately, I encountered 2 Problems:
>>
>> First, Matlab still enters the debug-mode, although I'm using the
>> latest version of Fieldtrip
>> Second, though I can read the raw datal, the labels for the MEG
>> channels are missing. The data.hdr.label contains the 165 recorded
>> channels but the labels are not the Names but - as I think - the
>> locations.
>> (e.g. A3+03).
>> Could it be, that the definition for the 148-channel 4d-system is
>> missing?
>> Does anyone have a hint hw to solve this?
>>
>> Thanks a lot
>>
>> Julian Keil
>>
>>
>> Dipl. Psych. Julian Keil
>>
>> OBOB-Lab
>> University of Konstanz
>> Department of Psychology
>> P.O. Box D23
>> 78457 Konstanz
>> Germany
>>
>> Tel: ++49 - (0)7531 - 88 45 84
>> Email: julian.keil at uni-konstanz.de
>> Homepage: http://www.uni-konstanz.de/obob
>>
>>
>>
>>
>> ----------------------------------
>>
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis.
>>
>> http://listserv.surfnet.nl/archives/fieldtrip.html
>>
>> http://www.ru.nl/fcdonders/fieldtrip/
>>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From j.schoffelen at PSY.GLA.AC.UK  Thu Oct  9 12:28:34 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Thu, 9 Oct 2008 11:28:34 +0100
Subject: 4D data reading -> 148 channel system
In-Reply-To: <3423F7AA-91CB-4B9A-81AD-2411538B516C@gmail.com>
Message-ID: <THU.9.OCT.2008.112834.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Julian,

You can easily make this change yourself in the appropriate place of
read_4d_hdr for the time being.
I made the change as well (it seems to look ok for both the 148 and
248 channel systems) and put it in the fieldtrip release.

Yours,

Jan-Mathijs

On Oct 9, 2008, at 11:01 AM, Julian Keil wrote:

> Hello Jan-Mathijs,
>
> thanks for the fast fix of problem 1.
> As for problem 2: the data.hdr.orig.channel indeed looks meaningful
> and replacing the files as you mentioned works fine.
>
> Thanks a lot.
>
> Julian
>
> Am 08.10.2008 um 17:53 schrieb jan-mathijs schoffelen:
>
>> Dear Julian,
>>
>> As of the debugging thingy: sorry about that, I thought I adjusted
>> it but apparently something went wrong. You can easily fix this
>> yourself by going to the appropriate function. It's read_4d_hdr
>> and you just have to remove the keyboard-statement somewhere in
>> the code. I don't know where the function is located in the
>> release version of fieldtrip, but it should be somewhere like
>> fieldtrip/private, or fieldtrip/fileio/private. I hope that as of
>> tomorrow the trailing keyboard statement is removed from the
>> release version.
>> Regarding your second point: I tried it out with a 148-channel
>> dataset I have lying around, and you're absolutely right.
>> Interestingly, for the 248-system it works just fine. Give me some
>> time to look into this. I hope to get it working robustly for both
>> systems. Could you for the time being check whether the field
>> data.hdr.orig.Channel looks meaningful for your data? A solution
>> for now would be to replace data.hdr.label (and data.label) with
>> hdr.orig.Channel.
>>
>>
>> Yours,
>>
>> Jan-Mathijs
>>
>>
>>
>> On Oct 8, 2008, at 4:22 PM, Julian Keil wrote:
>>
>>> Hello everyone,
>>>
>>> i just tried to read 4D raw data as was suggested in the recent
>>> discussion.
>>> Unfortunately, I encountered 2 Problems:
>>>
>>> First, Matlab still enters the debug-mode, although I'm using the
>>> latest version of Fieldtrip
>>> Second, though I can read the raw datal, the labels for the MEG
>>> channels are missing. The data.hdr.label contains the 165
>>> recorded channels but the labels are not the Names but - as I
>>> think - the locations.
>>> (e.g. A3+03).
>>> Could it be, that the definition for the 148-channel 4d-system is
>>> missing?
>>> Does anyone have a hint hw to solve this?
>>>
>>> Thanks a lot
>>>
>>> Julian Keil
>>>
>>>
>>> Dipl. Psych. Julian Keil
>>>
>>> OBOB-Lab
>>> University of Konstanz
>>> Department of Psychology
>>> P.O. Box D23
>>> 78457 Konstanz
>>> Germany
>>>
>>> Tel: ++49 - (0)7531 - 88 45 84
>>> Email: julian.keil at uni-konstanz.de
>>> Homepage: http://www.uni-konstanz.de/obob
>>>
>>>
>>>
>>>
>>> ----------------------------------
>>>
>>> The aim of this list is to facilitate the discussion between
>>> users of the FieldTrip toolbox, to share experiences and to
>>> discuss new ideas for MEG and EEG analysis.
>>>
>>> http://listserv.surfnet.nl/archives/fieldtrip.html
>>>
>>> http://www.ru.nl/fcdonders/fieldtrip/
>>>
>>
>> ----------------------------------
>>
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis.
>>
>> http://listserv.surfnet.nl/archives/fieldtrip.html
>>
>> http://www.ru.nl/fcdonders/fieldtrip/
>>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
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From michelic72 at GMAIL.COM  Fri Oct 10 09:27:28 2008
From: michelic72 at GMAIL.COM (Cristiano Micheli)
Date: Fri, 10 Oct 2008 09:27:28 +0200
Subject: sourceplot - 'surface'
Message-ID: <FRI.10.OCT.2008.092728.0200.FIELDTRIP@NIC.SURFNET.NL>

I am trying to visualize coherence on a 3D surface, after DICS processing,
with a template given in Fieldtrip :

    cfg              = [];
    cfg.parameter    = 'coh'; 
    cfg.downsample = 1;
    cfg.sourceunits  = 'cm';
    cfg.mriunits       = 'mm';
    interp                = sourceinterpolate(cfg, source, mri); 

    cfg                   = [];
    cfg.coordinates = 'ctf';
    cfg.template     = '/home/common/matlab/spm2/templates/T1.mnc'; 
    sourceN  = volumenormalise(cfg, interp);

    sourceN = rmfield(sourceN,'inside'); 
    cfg = [];
    cfg.method = 'surface';
    cfg.funparameter = 'coh';
    cfg.funcolorlim = [0.0 0.5e-3];
    cfg.funcolormap = 'jet';
    cfg.opacitylim = [0.0 0.1]; 
    cfg.opacitymap = 'rampup';  
    cfg.projmethod = 'nearest'; 
    cfg.surffile = 'surface_l4_both.mat';
    cfg.surfdownsample = 10; 
    figure, sourceplot(cfg,sourceN); view ([90 0])

I get stuck at the normalisation when I get this error:

??? Error using ==> spm_create_vol>create_vol at 32
"dim" field is the wrong size (1  4).

Error in ==> spm_create_vol at 16
        v = create_vol(V(i));

Error in ==> fieldtrip-20080729/private/volumewrite_spm at 61
Va         = spm_create_vol(Va);

Error in ==> volumenormalise at 178
VF = volumewrite_spm([cfg.intermediatename,'_anatomy.img'], interp.anatomy,
interp.transform);


I thank you in advance for any suggestion
Cristiano

M.Sc. Ing. Cristiano Micheli
Institute of Medical Psychology and Behavioral Neurobiology MEG-Center
Otfried-Müller-Strasse 47 72076 Tübingen
Phone: +49-7071-29-87689
Fax:   +49-7071-29-5706
Privat: +49-176-26326149
Email: cristiano.micheli at med.uni-tuebingen.de 

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From jlucan at NKI.RFMH.ORG  Tue Oct 14 20:15:33 2008
From: jlucan at NKI.RFMH.ORG (Joshua Lucan)
Date: Tue, 14 Oct 2008 20:15:33 +0200
Subject: within subjects partitioning
Message-ID: <TUE.14.OCT.2008.201533.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi,
  I'm using timelockstatistics to perform a within subjects cluster based non-
parametric test.  I have two conditions and ten subjects.  The data from each 
subject consists of a spatial array of 160 electrodes at one time point.
  My question is how are the data randomly partitioned. Are all samples across 
subjects and conditions put into one group and 20 random drawings (10 
subjects, 2 conditions) of 160 electrodes performed?  Or is data within each 
subject preserved so that there are 10 groups of 320 electrodes from each of 
which two partitions are made?
  Thanks so much,
  Josh

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From e.maris at DONDERS.RU.NL  Tue Oct 14 21:21:08 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Tue, 14 Oct 2008 21:21:08 +0200
Subject: within subjects partitioning
In-Reply-To: <LISTSERV%200810142015333110.139F@NIC.SURFNET.NL>
Message-ID: <TUE.14.OCT.2008.212108.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Josh,


>   I'm using timelockstatistics to perform a within subjects cluster based
non-
> parametric test.  I have two conditions and ten subjects.  The data from
each
> subject consists of a spatial array of 160 electrodes at one time point.
>   My question is how are the data randomly partitioned. Are all samples
across
> subjects and conditions put into one group and 20 random drawings (10
> subjects, 2 conditions) of 160 electrodes performed?  Or is data within
each
> subject preserved so that there are 10 groups of 320 electrodes from each
of
> which two partitions are made?


In a within-subjects design with two conditions, the permutation is
performed as follows: the two spatio-spectral-temporal (possibly with empty
spectral and temporal dimensions) data matrices (one for every condition)
per subject are randomly permuted WITHIN every subject. This is also
described in Maris & Oostenveld (JNM, 2007).


Good luck,

Eric Maris




>   Thanks so much,
>   Josh
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip
> toolbox, to share experiences and to discuss new ideas for MEG and EEG
analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From jlucan at NKI.RFMH.ORG  Tue Oct 14 21:33:09 2008
From: jlucan at NKI.RFMH.ORG (Joshua Lucan)
Date: Tue, 14 Oct 2008 21:33:09 +0200
Subject: within subjects partitioning
Message-ID: <TUE.14.OCT.2008.213309.0200.FIELDTRIP@NIC.SURFNET.NL>

Excellent! Thank you!

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From v.litvak at ION.UCL.AC.UK  Thu Oct 16 09:05:08 2008
From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak)
Date: Thu, 16 Oct 2008 08:05:08 +0100
Subject: Postdoctoral position in neuroimaging
Message-ID: <THU.16.OCT.2008.080508.0100.FIELDTRIP@NIC.SURFNET.NL>

Please contact Prof. Huber directly about this ad.


Title of the advert
Postdoctoral position in neuroimaging

Description
A one year postdoctoral position is available for a first year
post-doc at the University Children's Hospital Zurich, Switzerland.

The group of Prof. Reto Huber is seeking a postdoctoral fellow to
develop and apply advanced MRI techniques, including diffusion tensor
imaging (DTI), in combination with high-density
electroencephalographic recordings in children and adolescents.

The topic of research will be the study of the relationship between
anatomical and electrophysiological markers of brain maturation. Both
MRI and EEG data of healthy children between 8 and 18 years of age are
available.

Education
We are looking for a qualified candidate with research experience in
computational and statistical methods for MRI imaging (e.g. SPM,
MatLab, DTI and gray matter density analysis). Strong image
processing, data analysis and computing skills are essential.
Applicants should have a PhD, preferably in neuroscience. The position
is fully funded for 1 year and is offered to a first year post-doc.

Start
Available now.

Link
http://www.kispi.uzh.ch/sleep


Please send your CV with scientific record, letter of motivation and 2
referees (including e-mail addresses) as a single PDF file by e-mail
to: reto.huber at kispi.uzh.ch

----------------------------------
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From h.leuthold at PSY.GLA.AC.UK  Thu Oct 16 18:44:40 2008
From: h.leuthold at PSY.GLA.AC.UK (Hartmut Leuthold)
Date: Thu, 16 Oct 2008 17:44:40 +0100
Subject: 1-year postdoctoral position
Message-ID: <THU.16.OCT.2008.174440.0100.FIELDTRIP@NIC.SURFNET.NL>

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From florisdelange at GMAIL.COM  Fri Oct 17 16:44:39 2008
From: florisdelange at GMAIL.COM (Floris de Lange)
Date: Fri, 17 Oct 2008 16:44:39 +0200
Subject: cluster statistic on one sample
Message-ID: <FRI.17.OCT.2008.164439.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrippers,

I have a question about statistical analysis on the sensor level.
I would like to make use of the cluster size thresholding of the
clusterrand routine in Fieldtrip. Unfortunately, in the current
wrapper, it seems there is no option for a one-sample T-test? There is
an activation-baseline test, and a (in)dependent samples test between
two conditions, but what I want to do is simply test whether a 14
(subjects) x 275 (channels) matrix is different from zero, taking into
account the spatial relations between adjacent sensors. (The data
points are regression weights from a multiple-regression analysis, so
there's no easy way to split it into two parts.)
I assume this should be easy to tweak, but I couldn't come up with any
smart ideas how to do it.
Anyone any ideas?

Thanks in advance!

Floris

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From ali.mazaheri at FCDONDERS.RU.NL  Fri Oct 17 16:57:09 2008
From: ali.mazaheri at FCDONDERS.RU.NL (Ali Mazaheri)
Date: Fri, 17 Oct 2008 16:57:09 +0200
Subject: cluster statistic on one sample
Message-ID: <FRI.17.OCT.2008.165709.0200.FIELDTRIP@NIC.SURFNET.NL>

Dearest Floris,

Why not just create a zero matrices with a 14 x 275 dimension
 and do a dependent samples test between
your regresion weights and the zero matrices ?



Hope this helps !


best

Ali



----- Original Message -----
From: Floris de Lange <florisdelange at GMAIL.COM>
Date: Friday, October 17, 2008 4:44 pm
Subject: [FIELDTRIP] cluster statistic on one sample

> Dear Fieldtrippers,
>
> I have a question about statistical analysis on the sensor level.
> I would like to make use of the cluster size thresholding of the
> clusterrand routine in Fieldtrip. Unfortunately, in the current
> wrapper, it seems there is no option for a one-sample T-test? There is
> an activation-baseline test, and a (in)dependent samples test between
> two conditions, but what I want to do is simply test whether a 14
> (subjects) x 275 (channels) matrix is different from zero, taking into
> account the spatial relations between adjacent sensors. (The data
> points are regression weights from a multiple-regression analysis, so
> there's no easy way to split it into two parts.)
> I assume this should be easy to tweak, but I couldn't come up with any
> smart ideas how to do it.
> Anyone any ideas?
>
> Thanks in advance!
>
> Floris
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From zanasilva at GMAIL.COM  Fri Oct 17 18:04:14 2008
From: zanasilva at GMAIL.COM (Susana Silva)
Date: Fri, 17 Oct 2008 18:04:14 +0200
Subject: clusterrandanalysis vs timelockstatistics
Message-ID: <FRI.17.OCT.2008.180414.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi all

I have run both clusterrandanalysis and timelockstatistics (with
cfg.correctm=cluster) over the same data.
The t values in clusrand (clusterrandanalysis) are equal to the t values in
stat (timelockstatistics).

However, in timelockstatistics, the number of clusters is much higher and
the prob is much lower than in the clusterrandanalysis procedure.

1-Should I expect it?
2-where can I get some more information on clusrandanalysis function (the
tutorial does not seem to have)?

Thank you
Susana Silva

----------------------------------
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From spike377 at KOREA.COM  Sat Oct 18 22:05:36 2008
From: spike377 at KOREA.COM (=?EUC-KR?B?udrH/LW/?=)
Date: Sun, 19 Oct 2008 05:05:36 +0900
Subject: time-frequency representation of PLV
Message-ID: <SUN.19.OCT.2008.050536.0900.FIELDTRIP@NIC.SURFNET.NL>

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From e.maris at DONDERS.RU.NL  Mon Oct 20 11:17:19 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Mon, 20 Oct 2008 11:17:19 +0200
Subject: cluster statistic on one sample
In-Reply-To: <9fb563140810170744m400d703dkf66c6e6a22145e24@mail.gmail.com>
Message-ID: <MON.20.OCT.2008.111719.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Floris,



> I have a question about statistical analysis on the sensor level.
> I would like to make use of the cluster size thresholding of the
> clusterrand routine in Fieldtrip. Unfortunately, in the current
> wrapper, it seems there is no option for a one-sample T-test? There is
> an activation-baseline test, and a (in)dependent samples test between
> two conditions, but what I want to do is simply test whether a 14
> (subjects) x 275 (channels) matrix is different from zero, taking into
> account the spatial relations between adjacent sensors. (The data
> points are regression weights from a multiple-regression analysis, so
> there's no easy way to split it into two parts.)
> I assume this should be easy to tweak, but I couldn't come up with any
> smart ideas how to do it.
> Anyone any ideas?

I'm afraid that I have to disappoint you, Floris. Your null hypothesis is a
typical parametric null hypothesis; the expected value of some
(matrix-valued) variable being equal to zero. The null hypothesis that is
tested by a nonparametric permutation test is equality across experimental
conditions of the probability distribution from which the
(condition-specific) data are drawn. Since you have single condition only, I
see no way of applying the theory behind nonparametric permutation testing
(of the type described by Maris & Oostenveld, 2007) to your data.

To solve your problem we need a brilliant theoretical insight.


Greetings,

Eric






>
> Thanks in advance!
>
> Floris
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip
> toolbox, to share experiences and to discuss new ideas for MEG and EEG
analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From v.litvak at ION.UCL.AC.UK  Mon Oct 20 12:05:30 2008
From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak)
Date: Mon, 20 Oct 2008 11:05:30 +0100
Subject: cluster statistic on one sample
In-Reply-To: <e1e7c57c0810200304v45bd0061j18c2afce55a16ce@mail.gmail.com>
Message-ID: <MON.20.OCT.2008.110530.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Floris and Eric,

Parametric tests at scalp level taking into account spatial
relationship between sensors can be done in SPM (with RFT correction).
That'll require using some low-level functions to convert
coefficients to images but in principle shouldn't be that difficult.

Best,

Vladimir
>
> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris <e.maris at donders.ru.nl> wrote:
>> Dear Floris,
>>
>>
>>
>>> I have a question about statistical analysis on the sensor level.
>>> I would like to make use of the cluster size thresholding of the
>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
>>> wrapper, it seems there is no option for a one-sample T-test? There is
>>> an activation-baseline test, and a (in)dependent samples test between
>>> two conditions, but what I want to do is simply test whether a 14
>>> (subjects) x 275 (channels) matrix is different from zero, taking into
>>> account the spatial relations between adjacent sensors. (The data
>>> points are regression weights from a multiple-regression analysis, so
>>> there's no easy way to split it into two parts.)
>>> I assume this should be easy to tweak, but I couldn't come up with any
>>> smart ideas how to do it.
>>> Anyone any ideas?
>>
>> I'm afraid that I have to disappoint you, Floris. Your null hypothesis is a
>> typical parametric null hypothesis; the expected value of some
>> (matrix-valued) variable being equal to zero. The null hypothesis that is
>> tested by a nonparametric permutation test is equality across experimental
>> conditions of the probability distribution from which the
>> (condition-specific) data are drawn. Since you have single condition only, I
>> see no way of applying the theory behind nonparametric permutation testing
>> (of the type described by Maris & Oostenveld, 2007) to your data.
>>
>> To solve your problem we need a brilliant theoretical insight.
>>
>>
>> Greetings,
>>
>> Eric
>>
>>
>>
>>
>>
>>
>>>
>>> Thanks in advance!
>>>
>>> Floris
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of the
>> FieldTrip
>>> toolbox, to share experiences and to discuss new ideas for MEG and EEG
>> analysis.
>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>>
>>
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From marco.buiatti at UNITN.IT  Mon Oct 20 14:00:30 2008
From: marco.buiatti at UNITN.IT (Marco Buiatti)
Date: Mon, 20 Oct 2008 14:00:30 +0200
Subject: data format for 'between trials' cluster randomization analysis
Message-ID: <MON.20.OCT.2008.140030.0200.>

Dear Fieldtrippers,

I have data from a single subject with two conditions, and I am trying
to perform the cluster randomization analysis on the statistical
difference between the conditions - therefore a 'between trials'
analysis.

However, my data are not in the fieldtrip format, and I have problems
in converting them in the correct format. Could anyone provide me an
example of such format?

Also, the eeglab2fieldtrip function (which I tried without success) is
not included in the last Fieldtrip release: is it because there are
some problems with that function?

Thank you in advance,

Marco Buiatti

-- 
Marco Buiatti, PhD
Postdoctoral Researcher
Functional NeuroImaging Laboratory
Center for Mind Brain Sciences
Trento University
Via delle Regole, 101
38060, Mattarello (TN) - ITALY
email: marco.buiatti at unitn.it
http://www.cimec.unitn.it
Telephone: +39-0461-88 3077
Fax: +39-0461-88 3066

***********************************************
In occasione del 70° anniversario della promulgazione delle leggi
razziali, LEGGI FIRMA E DIFFONDI IL MANIFESTO ANTIRAZZISTA!
http://www.regione.toscana.it/regione/opencms/RT/sito-RT/MenuUtility/SanRossore-Firma-Manifesto-Antirazzismo
***********************************************

----------------------------------
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From j.schoffelen at PSY.GLA.AC.UK  Mon Oct 20 14:13:11 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Mon, 20 Oct 2008 13:13:11 +0100
Subject: cluster statistic on one sample
In-Reply-To: <e1e7c57c0810200305w7ea38eddt767591636ff2b926@mail.gmail.com>
Message-ID: <MON.20.OCT.2008.131311.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Floris, Eric, Vladimir and all other people reading this message,

What about performing a nonparametric test, based on the bootstrap
distribution of the beta weights under the null-hypothesis?
This problem sounds similar to one I came across recently (and which
I still have to write something about on fieldtrip's wiki-page (sorry
Eric)), which has to do with the testing of the significance of the F-
value for interaction in a 2x2 repeated measure anova. Also in this
case, one also wants to test a parametric null-hypothesis, as Eric
phrased it in his last e-mail. One way to test this (I don't have the
reference at hand), is to test the observed F-statistic against a
null-distribution, obtained from bootstrapping your data, which you
preconditioned as to impose the null-hypothesis (in the case of an
anova it would be to remove from each of the observations the mean of
the cell to which the observation belongs). I don't know yet how to
impose the null-hypothesis in the regression case, but would this
line of thought be a possibility?
As to a potential implementation: Robert and I are pretty close to
have the bootstrapping implemented.

Yours,

Jan-Mathijs


On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:

> Dear Floris and Eric,
>
> Parametric tests at scalp level taking into account spatial
> relationship between sensors can be done in SPM (with RFT correction).
> That'll require using some low-level functions to convert
> coefficients to images but in principle shouldn't be that difficult.
>
> Best,
>
> Vladimir
>>
>> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris
>> <e.maris at donders.ru.nl> wrote:
>>> Dear Floris,
>>>
>>>
>>>
>>>> I have a question about statistical analysis on the sensor level.
>>>> I would like to make use of the cluster size thresholding of the
>>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
>>>> wrapper, it seems there is no option for a one-sample T-test?
>>>> There is
>>>> an activation-baseline test, and a (in)dependent samples test
>>>> between
>>>> two conditions, but what I want to do is simply test whether a 14
>>>> (subjects) x 275 (channels) matrix is different from zero,
>>>> taking into
>>>> account the spatial relations between adjacent sensors. (The data
>>>> points are regression weights from a multiple-regression
>>>> analysis, so
>>>> there's no easy way to split it into two parts.)
>>>> I assume this should be easy to tweak, but I couldn't come up
>>>> with any
>>>> smart ideas how to do it.
>>>> Anyone any ideas?
>>>
>>> I'm afraid that I have to disappoint you, Floris. Your null
>>> hypothesis is a
>>> typical parametric null hypothesis; the expected value of some
>>> (matrix-valued) variable being equal to zero. The null hypothesis
>>> that is
>>> tested by a nonparametric permutation test is equality across
>>> experimental
>>> conditions of the probability distribution from which the
>>> (condition-specific) data are drawn. Since you have single
>>> condition only, I
>>> see no way of applying the theory behind nonparametric
>>> permutation testing
>>> (of the type described by Maris & Oostenveld, 2007) to your data.
>>>
>>> To solve your problem we need a brilliant theoretical insight.
>>>
>>>
>>> Greetings,
>>>
>>> Eric
>>>
>>>
>>>
>>>
>>>
>>>
>>>>
>>>> Thanks in advance!
>>>>
>>>> Floris
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between
>>>> users of the
>>> FieldTrip
>>>> toolbox, to share experiences and to discuss new ideas for MEG
>>>> and EEG
>>> analysis.
>>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between
>>> users of the FieldTrip  toolbox, to share experiences and to
>>> discuss new ideas for MEG and EEG analysis. See also http://
>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/
>>> fcdonders/fieldtrip.
>>>
>>>
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From venug001 at BAMA.UA.EDU  Mon Oct 20 14:27:31 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 20 Oct 2008 07:27:31 -0500
Subject: cluster statistic on one sample
In-Reply-To: <66D7BE2A-86F7-48BA-A94C-0561DF0A568E@psy.gla.ac.uk>
Message-ID: <MON.20.OCT.2008.072731.0500.FIELDTRIP@NIC.SURFNET.NL>

Hello everyone, I just finished testing the null across two conditions
using EEGLAB which puts out t-values at various points on the waveform,
and then by exporting values to excel converting them to RMS and
averaging them over left vs right and post vs ant. I have the SPSS
multivariate code, I have been wondering about this for months now how
to integrate something like this into all the packages. Off course
since MATLAB is very powerful I suspect that adding the required MANOVA
code into those routines will solve the problem.After that is done, the
mathematical formula for generating the F distribution, and the root of
which is the t distribution can be placed in a separate sheet for a
parametric test, even though the data is non-parametric. We can make
parametric assumptions of our data even though it is non-parametric by
nature. I hand did this using a combination of excel, spss, eeglab, and
scan 4.3 which--runs on a matlab engine and is a commercial product.
A paper by Pascual-Marqui (2002) talks about how the F values in the
dipole fit and Current Density Reconstruction is a pseudo-statistic.
That paper also provides a correction so that they can be used as
parametric values. I wonder if such a correction can be applied to the
non-parametric values here, so that they can be treated and interpreted
as parametric values.
 I can see this in my mind by can tweak the c code in MATLAB with some
guidance. Am not a programmer by any strech of imagination.
regards
gopa


Quoting jan-mathijs schoffelen <j.schoffelen at PSY.GLA.AC.UK>:

> Dear Floris, Eric, Vladimir and all other people reading this
> message,
>
> What about performing a nonparametric test, based on the bootstrap
> distribution of the beta weights under the null-hypothesis?
> This problem sounds similar to one I came across recently (and which
>
> I still have to write something about on fieldtrip's wiki-page (sorry
>
> Eric)), which has to do with the testing of the significance of the
> F-
> value for interaction in a 2x2 repeated measure anova. Also in this
>
> case, one also wants to test a parametric null-hypothesis, as Eric
> phrased it in his last e-mail. One way to test this (I don't have the
>
> reference at hand), is to test the observed F-statistic against a
> null-distribution, obtained from bootstrapping your data, which you
>
> preconditioned as to impose the null-hypothesis (in the case of an
> anova it would be to remove from each of the observations the mean of
>
> the cell to which the observation belongs). I don't know yet how to
>
> impose the null-hypothesis in the regression case, but would this
> line of thought be a possibility?
> As to a potential implementation: Robert and I are pretty close to
> have the bootstrapping implemented.
>
> Yours,
>
> Jan-Mathijs
>
>
> On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:
>
> > Dear Floris and Eric,
> >
> > Parametric tests at scalp level taking into account spatial
> > relationship between sensors can be done in SPM (with RFT
> correction).
> > That'll require using some low-level functions to convert
> > coefficients to images but in principle shouldn't be that
> difficult.
> >
> > Best,
> >
> > Vladimir
> >>
> >> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris
> >> <e.maris at donders.ru.nl> wrote:
> >>> Dear Floris,
> >>>
> >>>
> >>>
> >>>> I have a question about statistical analysis on the sensor
> level.
> >>>> I would like to make use of the cluster size thresholding of
> the
> >>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
> >>>> wrapper, it seems there is no option for a one-sample T-test?
> >>>> There is
> >>>> an activation-baseline test, and a (in)dependent samples test
> >>>> between
> >>>> two conditions, but what I want to do is simply test whether a
> 14
> >>>> (subjects) x 275 (channels) matrix is different from zero,
> >>>> taking into
> >>>> account the spatial relations between adjacent sensors. (The
> data
> >>>> points are regression weights from a multiple-regression
> >>>> analysis, so
> >>>> there's no easy way to split it into two parts.)
> >>>> I assume this should be easy to tweak, but I couldn't come up
> >>>> with any
> >>>> smart ideas how to do it.
> >>>> Anyone any ideas?
> >>>
> >>> I'm afraid that I have to disappoint you, Floris. Your null
> >>> hypothesis is a
> >>> typical parametric null hypothesis; the expected value of some
> >>> (matrix-valued) variable being equal to zero. The null hypothesis
>
> >>> that is
> >>> tested by a nonparametric permutation test is equality across
> >>> experimental
> >>> conditions of the probability distribution from which the
> >>> (condition-specific) data are drawn. Since you have single
> >>> condition only, I
> >>> see no way of applying the theory behind nonparametric
> >>> permutation testing
> >>> (of the type described by Maris & Oostenveld, 2007) to your
> data.
> >>>
> >>> To solve your problem we need a brilliant theoretical insight.
> >>>
> >>>
> >>> Greetings,
> >>>
> >>> Eric
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>
> >>>> Thanks in advance!
> >>>>
> >>>> Floris
> >>>>
> >>>> ----------------------------------
> >>>> The aim of this list is to facilitate the discussion between
> >>>> users of the
> >>> FieldTrip
> >>>> toolbox, to share experiences and to discuss new ideas for MEG
>
> >>>> and EEG
> >>> analysis.
> >>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> >>>> http://www.ru.nl/fcdonders/fieldtrip.
> >>>
> >>> ----------------------------------
> >>> The aim of this list is to facilitate the discussion between
> >>> users of the FieldTrip  toolbox, to share experiences and to
> >>> discuss new ideas for MEG and EEG analysis. See also http://
> >>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/
>
> >>> fcdonders/fieldtrip.
> >>>
> >>>
> >>
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
>
> > of the FieldTrip  toolbox, to share experiences and to discuss new
>
> > ideas for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/
> > archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From e.maris at DONDERS.RU.NL  Mon Oct 20 16:02:39 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Mon, 20 Oct 2008 16:02:39 +0200
Subject: cluster statistic on one sample
In-Reply-To: <66D7BE2A-86F7-48BA-A94C-0561DF0A568E@psy.gla.ac.uk>
Message-ID: <MON.20.OCT.2008.160239.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrip-list-readers,


> What about performing a nonparametric test, based on the bootstrap
> distribution of the beta weights under the null-hypothesis?
> This problem sounds similar to one I came across recently (and which
> I still have to write something about on fieldtrip's wiki-page (sorry
> Eric)), which has to do with the testing of the significance of the F-
> value for interaction in a 2x2 repeated measure anova. Also in this
> case, one also wants to test a parametric null-hypothesis, as Eric
> phrased it in his last e-mail. One way to test this (I don't have the
> reference at hand), is to test the observed F-statistic against a
> null-distribution, obtained from bootstrapping your data, which you
> preconditioned as to impose the null-hypothesis (in the case of an
> anova it would be to remove from each of the observations the mean of
> the cell to which the observation belongs). I don't know yet how to
> impose the null-hypothesis in the regression case, but would this
> line of thought be a possibility?
> As to a potential implementation: Robert and I are pretty close to
> have the bootstrapping implemented.

Again, I can only try to clarify some points here. I will not be able to
offer a solution for your problems.

1. Contrary to the permutation test, there is no useful statistical theory
for statistical tests based on the bootstrap distribution. By "useful", I
mean a theory that allows one to specify a scientifically interesting null
hypothesis (such as, "An expected value equal to 0") under which the false
alarm rate of a boostrap-p-value-based test can be controlled.

2. The bootstrap distribution has a nice intuitive appeal, because the
procedure to generate it (sampling with replacement) mimicks the sampling
process behind the sampling distribution (which is the ultimate "thing to
get" if you want to quantify the reliability of some quantity). But that is
not a proof of false alarm rate control!

3. I think the bootstrap distribution can be useful in situations where
parametric statistical tests do not exists, but I know of no rigourous
statistical argument to substantiate this claim.


Greetings,

Eric Maris


>
> Yours,
>
> Jan-Mathijs
>
>
> On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:
>
> > Dear Floris and Eric,
> >
> > Parametric tests at scalp level taking into account spatial
> > relationship between sensors can be done in SPM (with RFT correction).
> > That'll require using some low-level functions to convert
> > coefficients to images but in principle shouldn't be that difficult.
> >
> > Best,
> >
> > Vladimir
> >>
> >> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris
> >> <e.maris at donders.ru.nl> wrote:
> >>> Dear Floris,
> >>>
> >>>
> >>>
> >>>> I have a question about statistical analysis on the sensor level.
> >>>> I would like to make use of the cluster size thresholding of the
> >>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
> >>>> wrapper, it seems there is no option for a one-sample T-test?
> >>>> There is
> >>>> an activation-baseline test, and a (in)dependent samples test
> >>>> between
> >>>> two conditions, but what I want to do is simply test whether a 14
> >>>> (subjects) x 275 (channels) matrix is different from zero,
> >>>> taking into
> >>>> account the spatial relations between adjacent sensors. (The data
> >>>> points are regression weights from a multiple-regression
> >>>> analysis, so
> >>>> there's no easy way to split it into two parts.)
> >>>> I assume this should be easy to tweak, but I couldn't come up
> >>>> with any
> >>>> smart ideas how to do it.
> >>>> Anyone any ideas?
> >>>
> >>> I'm afraid that I have to disappoint you, Floris. Your null
> >>> hypothesis is a
> >>> typical parametric null hypothesis; the expected value of some
> >>> (matrix-valued) variable being equal to zero. The null hypothesis
> >>> that is
> >>> tested by a nonparametric permutation test is equality across
> >>> experimental
> >>> conditions of the probability distribution from which the
> >>> (condition-specific) data are drawn. Since you have single
> >>> condition only, I
> >>> see no way of applying the theory behind nonparametric
> >>> permutation testing
> >>> (of the type described by Maris & Oostenveld, 2007) to your data.
> >>>
> >>> To solve your problem we need a brilliant theoretical insight.
> >>>
> >>>
> >>> Greetings,
> >>>
> >>> Eric
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>
> >>>> Thanks in advance!
> >>>>
> >>>> Floris
> >>>>
> >>>> ----------------------------------
> >>>> The aim of this list is to facilitate the discussion between
> >>>> users of the
> >>> FieldTrip
> >>>> toolbox, to share experiences and to discuss new ideas for MEG
> >>>> and EEG
> >>> analysis.
> >>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> >>>> http://www.ru.nl/fcdonders/fieldtrip.
> >>>
> >>> ----------------------------------
> >>> The aim of this list is to facilitate the discussion between
> >>> users of the FieldTrip  toolbox, to share experiences and to
> >>> discuss new ideas for MEG and EEG analysis. See also http://
> >>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/
> >>> fcdonders/fieldtrip.
> >>>
> >>>
> >>
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> > of the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> > archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip
> toolbox, to share experiences and to discuss new ideas for MEG and EEG
analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From g.rousselet at PSY.GLA.AC.UK  Mon Oct 20 18:00:47 2008
From: g.rousselet at PSY.GLA.AC.UK (Guillaume Rousselet)
Date: Mon, 20 Oct 2008 17:00:47 +0100
Subject: cluster statistic on one sample
In-Reply-To: <20081020140232.D0CA2AA0B6@smtp.ru.nl>
Message-ID: <MON.20.OCT.2008.170047.0100.FIELDTRIP@NIC.SURFNET.NL>

Hey Eric,

I am not sure I understand your point against the bootstrap. My main
source of information about robust statistics is Wilcox, R. R. (2005).
Introduction to Robust Estimation and Hypothesis Testing (2nd Ed.
ed.): Academic Press.
In this book, Wilcox makes an extensive use of the bootstrap
technique. The validation of the technique, when it has been
performed, relies on Monte-Carlo simulations. Also, over almost 600
pages, Wilcox spends only one page on permutations, basically saying
that it is a special case of the bootstrap and that there is no
particular reason to use it.
Do you have references showing validation tests with a direct
comparison of bootstrap and permutation? My understanding is that such
comparisons do not exist for EEG/MEG data.
Also, one must keep in mind that bootstrap is particularly efficient
when applied to robust measures of central tendency, like trimmed
means and M-estimators, see my recent EEG paper for instance (http://www.journalofvision.org/8/12/3/
).
Finally, Wilcox provides a large number of recipes to test
significance of linear regression results, that could be applied to
the problem outlined earlier about the hypothesis test against zero.

Best,

GAR




On 20 Oct 2008, at 15:02, Eric Maris wrote:

> Dear Fieldtrip-list-readers,
>
>
>> What about performing a nonparametric test, based on the bootstrap
>> distribution of the beta weights under the null-hypothesis?
>> This problem sounds similar to one I came across recently (and which
>> I still have to write something about on fieldtrip's wiki-page (sorry
>> Eric)), which has to do with the testing of the significance of the
>> F-
>> value for interaction in a 2x2 repeated measure anova. Also in this
>> case, one also wants to test a parametric null-hypothesis, as Eric
>> phrased it in his last e-mail. One way to test this (I don't have the
>> reference at hand), is to test the observed F-statistic against a
>> null-distribution, obtained from bootstrapping your data, which you
>> preconditioned as to impose the null-hypothesis (in the case of an
>> anova it would be to remove from each of the observations the mean of
>> the cell to which the observation belongs). I don't know yet how to
>> impose the null-hypothesis in the regression case, but would this
>> line of thought be a possibility?
>> As to a potential implementation: Robert and I are pretty close to
>> have the bootstrapping implemented.
>
> Again, I can only try to clarify some points here. I will not be
> able to
> offer a solution for your problems.
>
> 1. Contrary to the permutation test, there is no useful statistical
> theory
> for statistical tests based on the bootstrap distribution. By
> "useful", I
> mean a theory that allows one to specify a scientifically
> interesting null
> hypothesis (such as, "An expected value equal to 0") under which the
> false
> alarm rate of a boostrap-p-value-based test can be controlled.
>
> 2. The bootstrap distribution has a nice intuitive appeal, because the
> procedure to generate it (sampling with replacement) mimicks the
> sampling
> process behind the sampling distribution (which is the ultimate
> "thing to
> get" if you want to quantify the reliability of some quantity). But
> that is
> not a proof of false alarm rate control!
>
> 3. I think the bootstrap distribution can be useful in situations
> where
> parametric statistical tests do not exists, but I know of no rigourous
> statistical argument to substantiate this claim.
>
>
> Greetings,
>
> Eric Maris
>
>
>>
>> Yours,
>>
>> Jan-Mathijs
>>
>>
>> On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:
>>
>>> Dear Floris and Eric,
>>>
>>> Parametric tests at scalp level taking into account spatial
>>> relationship between sensors can be done in SPM (with RFT
>>> correction).
>>> That'll require using some low-level functions to convert
>>> coefficients to images but in principle shouldn't be that difficult.
>>>
>>> Best,
>>>
>>> Vladimir
>>>>
>>>> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris
>>>> <e.maris at donders.ru.nl> wrote:
>>>>> Dear Floris,
>>>>>
>>>>>
>>>>>
>>>>>> I have a question about statistical analysis on the sensor level.
>>>>>> I would like to make use of the cluster size thresholding of the
>>>>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
>>>>>> wrapper, it seems there is no option for a one-sample T-test?
>>>>>> There is
>>>>>> an activation-baseline test, and a (in)dependent samples test
>>>>>> between
>>>>>> two conditions, but what I want to do is simply test whether a 14
>>>>>> (subjects) x 275 (channels) matrix is different from zero,
>>>>>> taking into
>>>>>> account the spatial relations between adjacent sensors. (The data
>>>>>> points are regression weights from a multiple-regression
>>>>>> analysis, so
>>>>>> there's no easy way to split it into two parts.)
>>>>>> I assume this should be easy to tweak, but I couldn't come up
>>>>>> with any
>>>>>> smart ideas how to do it.
>>>>>> Anyone any ideas?
>>>>>
>>>>> I'm afraid that I have to disappoint you, Floris. Your null
>>>>> hypothesis is a
>>>>> typical parametric null hypothesis; the expected value of some
>>>>> (matrix-valued) variable being equal to zero. The null hypothesis
>>>>> that is
>>>>> tested by a nonparametric permutation test is equality across
>>>>> experimental
>>>>> conditions of the probability distribution from which the
>>>>> (condition-specific) data are drawn. Since you have single
>>>>> condition only, I
>>>>> see no way of applying the theory behind nonparametric
>>>>> permutation testing
>>>>> (of the type described by Maris & Oostenveld, 2007) to your data.
>>>>>
>>>>> To solve your problem we need a brilliant theoretical insight.
>>>>>
>>>>>
>>>>> Greetings,
>>>>>
>>>>> Eric
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>> Thanks in advance!
>>>>>>
>>>>>> Floris
>>>>>>
>>>>>> ----------------------------------
>>>>>> The aim of this list is to facilitate the discussion between
>>>>>> users of the
>>>>> FieldTrip
>>>>>> toolbox, to share experiences and to discuss new ideas for MEG
>>>>>> and EEG
>>>>> analysis.
>>>>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>>
>>>>> ----------------------------------
>>>>> The aim of this list is to facilitate the discussion between
>>>>> users of the FieldTrip  toolbox, to share experiences and to
>>>>> discuss new ideas for MEG and EEG analysis. See also http://
>>>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/
>>>>> fcdonders/fieldtrip.
>>>>>
>>>>>
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>>> of the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
>>> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the
> FieldTrip
>> toolbox, to share experiences and to discuss new ideas for MEG and
>> EEG
> analysis.
>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/fcdonders/fieldtrip.






************************************************************************************
Guillaume A. Rousselet, Ph.D.

Lecturer

Centre for Cognitive Neuroimaging (CCNi)
Department of Psychology
Faculty of Information & Mathematical Sciences (FIMS)
University of Glasgow
58 Hillhead Street
Glasgow, UK
G12 8QB

The University of Glasgow, charity number SC004401

http://web.me.com/rousseg/GARs_website/

Email: g.rousselet at psy.gla.ac.uk
Fax. +44 (0)141 330 4606
Tel. +44 (0)141 330 6652
Cell +44 (0)791 779 7833


"no test based upon a theory of probability can by itself
provide any valuable evidence of the truth or falsehood
of a hypothesis.

But we may look at the purpose of tests from another
viewpoint. Without hoping to know whether each separate
hypothesis is true or false, we may search for
rules to govern our behaviour with regard to them, in
following which we insure that, in the long run of
experience, we shall not often be wrong."

	Neyman J & Pearson E, 1933
************************************************************************************







----------------------------------
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From e.maris at DONDERS.RU.NL  Mon Oct 20 21:15:30 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Mon, 20 Oct 2008 21:15:30 +0200
Subject: cluster statistic on one sample
In-Reply-To: <287D1AC6-92F5-466A-BD05-535711CA5AD0@psy.gla.ac.uk>
Message-ID: <MON.20.OCT.2008.211530.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Guillaume,





I am not sure I understand your point against the bootstrap. My main source
of information about robust statistics is Wilcox, R. R. (2005). Introduction
to Robust Estimation and Hypothesis Testing (2nd Ed. ed.): Academic Press.

In this book, Wilcox makes an extensive use of the bootstrap technique. The
validation of the technique, when it has been performed, relies on
Monte-Carlo simulations. Also, over almost 600 pages, Wilcox spends only one
page on permutations, basically saying that it is a special case of the
bootstrap and that there is no particular reason to use it.

Do you have references showing validation tests with a direct comparison of
bootstrap and permutation? My understanding is that such comparisons do not
exist for EEG/MEG data.

Also, one must keep in mind that bootstrap is particularly efficient when
applied to robust measures of central tendency, like trimmed means and
M-estimators, see my recent EEG paper for instance
(http://www.journalofvision.org/8/12/3/).

Finally, Wilcox provides a large number of recipes to test significance of
linear regression results, that could be applied to the problem outlined
earlier about the hypothesis test against zero.





Please do not misunderstand me. I would love to see rigorous mathematical
proofs substantiating the use of the bootstrap distribution for false alarm
rate control under some scientifically interesting null hypothesis. Also, I
am not married to permutation tests (fortunately!). However, I cannot ignore
the fact that a very nice proof exists (which is even very intuitive)
showing that permutation tests control the false alarm rate of any test
statistic and for any correlation pattern in data of arbitrary
dimensionality. Moreover, it does so under a null hypothesis that is
scientifically interesting (data from multiple  experimental conditions
governed by the same probability distribution).



Please forgive for being explicit, but I do not think it is scientifically
appropriate to ask me for "references showing validation tests with a direct
comparison of bootstrap and permutation". The burden of the proof is
completely on the side of the side of the advocates of the bootstrap. They
have to show that a statistical test based on a bootstrap p-value controls
the false alarm rate under a scientifically interesting null hypothesis.
With such a proof on the table, I will become a vigourous defender of the
bootstrap, but until that I will only present it as procedure with an
intuitively appealing rationale.



After showing false alarm rate control by the bootstrap (i.e., under some
null hypothesis), there is the issue of comparing it with permutation tests
with respect to statistical sensitivity (i.e., under the alternative
hypothesis). I have no idea about the relative performance of bootstrap and
permutation tests in this respect, but intuitively I do not expect a big
difference. However, what will make a big difference is the type of test
statistic that is evaluated in under either the permutation or the bootstrap
distribution.







Greetings,



Eric Maris











Best,



GAR









On 20 Oct 2008, at 15:02, Eric Maris wrote:





Dear Fieldtrip-list-readers,





What about performing a nonparametric test, based on the bootstrap

distribution of the beta weights under the null-hypothesis?

This problem sounds similar to one I came across recently (and which

I still have to write something about on fieldtrip's wiki-page (sorry

Eric)), which has to do with the testing of the significance of the F-

value for interaction in a 2x2 repeated measure anova. Also in this

case, one also wants to test a parametric null-hypothesis, as Eric

phrased it in his last e-mail. One way to test this (I don't have the

reference at hand), is to test the observed F-statistic against a

null-distribution, obtained from bootstrapping your data, which you

preconditioned as to impose the null-hypothesis (in the case of an

anova it would be to remove from each of the observations the mean of

the cell to which the observation belongs). I don't know yet how to

impose the null-hypothesis in the regression case, but would this

line of thought be a possibility?

As to a potential implementation: Robert and I are pretty close to

have the bootstrapping implemented.


Again, I can only try to clarify some points here. I will not be able to
offer a solution for your problems.

1. Contrary to the permutation test, there is no useful statistical theory
for statistical tests based on the bootstrap distribution. By "useful", I
mean a theory that allows one to specify a scientifically interesting null
hypothesis (such as, "An expected value equal to 0") under which the false
alarm rate of a boostrap-p-value-based test can be controlled.

2. The bootstrap distribution has a nice intuitive appeal, because the
procedure to generate it (sampling with replacement) mimicks the sampling
process behind the sampling distribution (which is the ultimate "thing to
get" if you want to quantify the reliability of some quantity). But that is
not a proof of false alarm rate control!

3. I think the bootstrap distribution can be useful in situations where
parametric statistical tests do not exists, but I know of no rigourous
statistical argument to substantiate this claim.


Greetings,

Eric Maris







Yours,



Jan-Mathijs





On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:



Dear Floris and Eric,



Parametric tests at scalp level taking into account spatial

relationship between sensors can be done in SPM (with RFT correction).

That'll require using some low-level functions to convert

coefficients to images but in principle shouldn't be that difficult.



Best,



Vladimir



On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris

<e.maris at donders.ru.nl> wrote:

Dear Floris,







I have a question about statistical analysis on the sensor level.

I would like to make use of the cluster size thresholding of the

clusterrand routine in Fieldtrip. Unfortunately, in the current

wrapper, it seems there is no option for a one-sample T-test?

There is

an activation-baseline test, and a (in)dependent samples test

between

two conditions, but what I want to do is simply test whether a 14

(subjects) x 275 (channels) matrix is different from zero,

taking into

account the spatial relations between adjacent sensors. (The data

points are regression weights from a multiple-regression

analysis, so

there's no easy way to split it into two parts.)

I assume this should be easy to tweak, but I couldn't come up

with any

smart ideas how to do it.

Anyone any ideas?



I'm afraid that I have to disappoint you, Floris. Your null

hypothesis is a

typical parametric null hypothesis; the expected value of some

(matrix-valued) variable being equal to zero. The null hypothesis

that is

tested by a nonparametric permutation test is equality across

experimental

conditions of the probability distribution from which the

(condition-specific) data are drawn. Since you have single

condition only, I

see no way of applying the theory behind nonparametric

permutation testing

(of the type described by Maris & Oostenveld, 2007) to your data.



To solve your problem we need a brilliant theoretical insight.





Greetings,



Eric















Thanks in advance!



Floris



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

The aim of this list is to facilitate the discussion between

users of the

FieldTrip

toolbox, to share experiences and to discuss new ideas for MEG

and EEG

analysis.

See also http://listserv.surfnet.nl/archives/fieldtrip.html and

http://www.ru.nl/fcdonders/fieldtrip.



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

The aim of this list is to facilitate the discussion between

users of the FieldTrip  toolbox, to share experiences and to

discuss new ideas for MEG and EEG analysis. See also http://

listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/

fcdonders/fieldtrip.









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

The aim of this list is to facilitate the discussion between users

of the FieldTrip  toolbox, to share experiences and to discuss new

ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/

archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.



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

The aim of this list is to facilitate the discussion between users of the

FieldTrip



toolbox, to share experiences and to discuss new ideas for MEG and EEG

analysis.



See also http://listserv.surfnet.nl/archives/fieldtrip.html and

http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the
FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
and EEG analysis. See also
http://listserv.surfnet.nl/archives/fieldtrip.html and
http://www.ru.nl/fcdonders/fieldtrip.











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

Guillaume A. Rousselet, Ph.D.



Lecturer



Centre for Cognitive Neuroimaging (CCNi)

Department of Psychology

Faculty of Information & Mathematical Sciences (FIMS)

University of Glasgow

58 Hillhead Street

Glasgow, UK

G12 8QB



The University of Glasgow, charity number SC004401



http://web.me.com/rousseg/GARs_website/



Email: g.rousselet at psy.gla.ac.uk

Fax. +44 (0)141 330 4606

Tel. +44 (0)141 330 6652

Cell +44 (0)791 779 7833





"no test based upon a theory of probability can by itself

provide any valuable evidence of the truth or falsehood

of a hypothesis.



But we may look at the purpose of tests from another

viewpoint. Without hoping to know whether each separate

hypothesis is true or false, we may search for

rules to govern our behaviour with regard to them, in

following which we insure that, in the long run of

experience, we shall not often be wrong."



             Neyman J & Pearson E, 1933

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













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From florisdelange at GMAIL.COM  Tue Oct 21 00:33:45 2008
From: florisdelange at GMAIL.COM (Floris de Lange)
Date: Tue, 21 Oct 2008 00:33:45 +0200
Subject: cluster statistic on one sample
Message-ID: <TUE.21.OCT.2008.003345.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Eric and other fieldtrippers,

I am a bit puzzled about your comment that:
"Your null hypothesis is a typical parametric null hypothesis; the
expected value of some
(matrix-valued) variable being equal to zero.The null hypothesis that is
tested by a nonparametric permutation test is equality across experimental
conditions of the probability distribution from which the
(condition-specific) data are drawn."

If I understand what SnPM (for fMRI) does well, it uses a permutation
test on one sample, creating a probability distribution by randomly
changing the sign of the observations. I quote (taken from
http://www.sph.umich.edu/ni-stat/SnPM/)

"Under the null hypothesis we can permute the labels of the effects of
interest. One way of implementing this with contrast images is to
randomly change the sign of each subject's contrast. This
sign-flipping approach can be justified by a symmetric distribution
for each voxel's data under the null hypothesis. While symmetry may
sound like a strong assumption, it is weaker than Normality, and can
be justified by a subtraction of two sample means with the same
(arbitrary) distribution.

Hence the null hypothesis here is:
    H0: The symmetric distribution of (the voxel values of the)
subjects' contrast images have zero mean.

And some more detail on the assumptions:

(..) to analyze a group of subjects for population inference, we need
to only assume exchangeability of subjects. The conventional
assumption of independent subjects implies exchangeability, and hence
a single exchangeability block (EB) consisting of all subjects.

(On a technical note, the assumption of exchangeability can actually
be relaxed for the one-sample case considered here. A sufficient
assumption for the contrast data to have a symmetric distribution, is
for each subject's contrast data to have a symmetric but possibly
different distribution. Such differences between subjects violates
exchangeability of all the data; however, since the null distribution
of the statistic of interest is invariant with respect to
sign-flipping, the test is valid.)

I don't see why this approach wouldn't be applicable for MEG data?
As a side note, comparing my regression weights with a condition of
all zeros with a dependent sample T-test works well, and is
mathematically equivalent to a one-sample T-test as far as I can see,
at least in the parametric domain?


Best wishes,
Floris

--
--
Floris de Lange
http://www.florisdelange.com

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From e.maris at DONDERS.RU.NL  Tue Oct 21 11:03:50 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Tue, 21 Oct 2008 11:03:50 +0200
Subject: cluster statistic on one sample
In-Reply-To: <9fb563140810201533i7e045770n8b88936106ed34b4@mail.gmail.com>
Message-ID: <TUE.21.OCT.2008.110350.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Floris and others,



> If I understand what SnPM (for fMRI) does well, it uses a permutation
> test on one sample, creating a probability distribution by randomly
> changing the sign of the observations. I quote (taken from
> http://www.sph.umich.edu/ni-stat/SnPM/)
>
> "Under the null hypothesis we can permute the labels of the effects of
> interest. One way of implementing this with contrast images is to
> randomly change the sign of each subject's contrast. This
> sign-flipping approach can be justified by a symmetric distribution
> for each voxel's data under the null hypothesis. While symmetry may
> sound like a strong assumption, it is weaker than Normality, and can
> be justified by a subtraction of two sample means with the same
> (arbitrary) distribution.

This quote is about a study involving TWO experimental conditions that are
manipulated within every subject. This is also called a paired-samples
design. So, it is NOT a one-sample study. The confusion probably arises from
the fact that a paired-samples (dependent-samples) T-test is identical to a
one-sample T-test on the difference scores. For a paired-samples T-test it
makes sense to construct a reference distribution by randomly switching the
signs of the difference scores. For a one-sample T-test on the data of a
single condition (e.g., the IQ-scores of a group of students), however, it
does not make sense to think about such an operation. (This is a brief,
intuitive explanation, which could be made more precise, but only at the
expense of more text.)

In your quote, also the concepts "symmetry of the distribution" and
"exchangeability" are mentioned. To keep things clear in our minds, it is
good to know that

1. Some statisticians (e.g., Tom Nichols, the author of your quote) motivate
permutation tests from considerations involving the shape of the probability
distribution (such as symmetry). Other statisticians (like Fortunato
Pesarin, and I) motivate permutation tests from considerations about
exchangeability between experimental conditions.

2. "Exchangeability" is a very general concept that can be used in very
different contexts. Some statisticians (e.g., Tom Nichols) use the term
"exchangeability" to denote a property of the probability distribution from
which the subjects are drawn, not mentioning the fact that these subjects
were observed in two experimental conditions. Other statisticians (like I)
use "exchangeability" with explicit reference to the data observed in the
two experimental conditions. For me, exchangeability involves that the
probability distribution of paired observations is invariant under random
permutations of the members of these pairs. This assumption of
exchangeability implies that the data in the two experimental conditions
have the same marginal probability distribution.


(If you like this explanation, Floris, you could join Jan-Mathijs in his
effort to make a Wiki-tutorial about the statistical rationale of
permutation tests.)




Don't start cursing the statisticians now!


Eric Maris

>
> Hence the null hypothesis here is:
>     H0: The symmetric distribution of (the voxel values of the)
> subjects' contrast images have zero mean.
>
> And some more detail on the assumptions:
>
> (..) to analyze a group of subjects for population inference, we need
> to only assume exchangeability of subjects. The conventional
> assumption of independent subjects implies exchangeability, and hence
> a single exchangeability block (EB) consisting of all subjects.
>
> (On a technical note, the assumption of exchangeability can actually
> be relaxed for the one-sample case considered here. A sufficient
> assumption for the contrast data to have a symmetric distribution, is
> for each subject's contrast data to have a symmetric but possibly
> different distribution. Such differences between subjects violates
> exchangeability of all the data; however, since the null distribution
> of the statistic of interest is invariant with respect to
> sign-flipping, the test is valid.)
>
> I don't see why this approach wouldn't be applicable for MEG data?
> As a side note, comparing my regression weights with a condition of
> all zeros with a dependent sample T-test works well, and is
> mathematically equivalent to a one-sample T-test as far as I can see,
> at least in the parametric domain?
>
>
> Best wishes,
> Floris
>
> --
> --
> Floris de Lange
> http://www.florisdelange.com
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip
> toolbox, to share experiences and to discuss new ideas for MEG and EEG
analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From florisdelange at GMAIL.COM  Tue Oct 21 17:47:30 2008
From: florisdelange at GMAIL.COM (Floris de Lange)
Date: Tue, 21 Oct 2008 17:47:30 +0200
Subject: cluster statistic on one sample
Message-ID: <TUE.21.OCT.2008.174730.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Eric,

>This quote is about a study involving TWO experimental conditions that are
>manipulated within every subject. This is also called a paired-samples
>design. So, it is NOT a one-sample study. 

I agree. Note that in my original question I didn't ask about a one-sample
*study*, but a one-sample *T-test* (on regression weights, which reflect a
weighted difference between several conditions, so not a one-sample study).
Ali's suggestion of simply comparing the regression weights against a matrix
of zeros, using paired samples T-test is excellent I think, and amounts to
the same as sign-flipping in a one-sample T-test. 

Thanks at any rate for your clarification, and best wishes from Paris
Floris

>In your quote, also the concepts "symmetry of the distribution" and
>"exchangeability" are mentioned. To keep things clear in our minds, it is
>good to know that
>
>1. Some statisticians (e.g., Tom Nichols, the author of your quote) motivate
>permutation tests from considerations involving the shape of the probability
>distribution (such as symmetry). Other statisticians (like Fortunato
>Pesarin, and I) motivate permutation tests from considerations about
>exchangeability between experimental conditions.
>
>2. "Exchangeability" is a very general concept that can be used in very
>different contexts. Some statisticians (e.g., Tom Nichols) use the term
>"exchangeability" to denote a property of the probability distribution from
>which the subjects are drawn, not mentioning the fact that these subjects
>were observed in two experimental conditions. Other statisticians (like I)
>use "exchangeability" with explicit reference to the data observed in the
>two experimental conditions. For me, exchangeability involves that the
>probability distribution of paired observations is invariant under random
>permutations of the members of these pairs. This assumption of
>exchangeability implies that the data in the two experimental conditions
>have the same marginal probability distribution.
>
>
>(If you like this explanation, Floris, you could join Jan-Mathijs in his
>effort to make a Wiki-tutorial about the statistical rationale of
>permutation tests.)
>
>
>
>
>Don't start cursing the statisticians now!
>
>
>Eric Maris
>
>>
>> Hence the null hypothesis here is:
>>     H0: The symmetric distribution of (the voxel values of the)
>> subjects' contrast images have zero mean.
>>
>> And some more detail on the assumptions:
>>
>> (..) to analyze a group of subjects for population inference, we need
>> to only assume exchangeability of subjects. The conventional
>> assumption of independent subjects implies exchangeability, and hence
>> a single exchangeability block (EB) consisting of all subjects.
>>
>> (On a technical note, the assumption of exchangeability can actually
>> be relaxed for the one-sample case considered here. A sufficient
>> assumption for the contrast data to have a symmetric distribution, is
>> for each subject's contrast data to have a symmetric but possibly
>> different distribution. Such differences between subjects violates
>> exchangeability of all the data; however, since the null distribution
>> of the statistic of interest is invariant with respect to
>> sign-flipping, the test is valid.)
>>
>> I don't see why this approach wouldn't be applicable for MEG data?
>> As a side note, comparing my regression weights with a condition of
>> all zeros with a dependent sample T-test works well, and is
>> mathematically equivalent to a one-sample T-test as far as I can see,
>> at least in the parametric domain?
>>
>>
>> Best wishes,
>> Floris
>>
>> --
>> --
>> Floris de Lange
>> http://www.florisdelange.com
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of the
>FieldTrip
>> toolbox, to share experiences and to discuss new ideas for MEG and EEG
>analysis.
>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>
>----------------------------------
>The aim of this list is to facilitate the discussion between users of the
FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
and EEG analysis. See also
http://listserv.surfnet.nl/archives/fieldtrip.html and
http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From spike377 at KOREA.COM  Wed Oct 22 04:01:15 2008
From: spike377 at KOREA.COM (=?EUC-KR?B?aHlvdW5nZG9uZy5wYXJr?=)
Date: Wed, 22 Oct 2008 11:01:15 +0900
Subject: question about topoplot
Message-ID: <WED.22.OCT.2008.110115.0900.FIELDTRIP@NIC.SURFNET.NL>

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From e.maris at DONDERS.RU.NL  Wed Oct 22 11:22:44 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Wed, 22 Oct 2008 11:22:44 +0200
Subject: cluster statistic on one sample
In-Reply-To: <LISTSERV%200810211747300670.67ED@NIC.SURFNET.NL>
Message-ID: <WED.22.OCT.2008.112244.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Floris,



> >This quote is about a study involving TWO experimental conditions that
are
> >manipulated within every subject. This is also called a paired-samples
> >design. So, it is NOT a one-sample study.
>
> I agree. Note that in my original question I didn't ask about a one-sample
> *study*, but a one-sample *T-test* (on regression weights, which reflect a
> weighted difference between several conditions, so not a one-sample
study).
> Ali's suggestion of simply comparing the regression weights against a
matrix
> of zeros, using paired samples T-test is excellent I think, and amounts to
> the same as sign-flipping in a one-sample T-test.


I do not agree. If your regression weights are calculated over multiple
conditions (each indexed by some number), then the appropriate permutation
is permutation across these multiple conditions. The appropriate "statfun"
(this is Fieldtrip terminology) is "indepsamplesregrT" for a between-units
design (typically, between-trials) and "depsamplesregrT" for a within-units
design (typically, within-subjects).


Good luck,

Eric






>
> Thanks at any rate for your clarification, and best wishes from Paris
> Floris
>
> >In your quote, also the concepts "symmetry of the distribution" and
> >"exchangeability" are mentioned. To keep things clear in our minds, it is
> >good to know that
> >
> >1. Some statisticians (e.g., Tom Nichols, the author of your quote)
motivate
> >permutation tests from considerations involving the shape of the
probability
> >distribution (such as symmetry). Other statisticians (like Fortunato
> >Pesarin, and I) motivate permutation tests from considerations about
> >exchangeability between experimental conditions.
> >
> >2. "Exchangeability" is a very general concept that can be used in very
> >different contexts. Some statisticians (e.g., Tom Nichols) use the term
> >"exchangeability" to denote a property of the probability distribution
from
> >which the subjects are drawn, not mentioning the fact that these subjects
> >were observed in two experimental conditions. Other statisticians (like
I)
> >use "exchangeability" with explicit reference to the data observed in the
> >two experimental conditions. For me, exchangeability involves that the
> >probability distribution of paired observations is invariant under random
> >permutations of the members of these pairs. This assumption of
> >exchangeability implies that the data in the two experimental conditions
> >have the same marginal probability distribution.
> >
> >
> >(If you like this explanation, Floris, you could join Jan-Mathijs in his
> >effort to make a Wiki-tutorial about the statistical rationale of
> >permutation tests.)
> >
> >
> >
> >
> >Don't start cursing the statisticians now!
> >
> >
> >Eric Maris
> >
> >>
> >> Hence the null hypothesis here is:
> >>     H0: The symmetric distribution of (the voxel values of the)
> >> subjects' contrast images have zero mean.
> >>
> >> And some more detail on the assumptions:
> >>
> >> (..) to analyze a group of subjects for population inference, we need
> >> to only assume exchangeability of subjects. The conventional
> >> assumption of independent subjects implies exchangeability, and hence
> >> a single exchangeability block (EB) consisting of all subjects.
> >>
> >> (On a technical note, the assumption of exchangeability can actually
> >> be relaxed for the one-sample case considered here. A sufficient
> >> assumption for the contrast data to have a symmetric distribution, is
> >> for each subject's contrast data to have a symmetric but possibly
> >> different distribution. Such differences between subjects violates
> >> exchangeability of all the data; however, since the null distribution
> >> of the statistic of interest is invariant with respect to
> >> sign-flipping, the test is valid.)
> >>
> >> I don't see why this approach wouldn't be applicable for MEG data?
> >> As a side note, comparing my regression weights with a condition of
> >> all zeros with a dependent sample T-test works well, and is
> >> mathematically equivalent to a one-sample T-test as far as I can see,
> >> at least in the parametric domain?
> >>
> >>
> >> Best wishes,
> >> Floris
> >>
> >> --
> >> --
> >> Floris de Lange
> >> http://www.florisdelange.com
> >>
> >> ----------------------------------
> >> The aim of this list is to facilitate the discussion between users of
the
> >FieldTrip
> >> toolbox, to share experiences and to discuss new ideas for MEG and EEG
> >analysis.
> >> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> >> http://www.ru.nl/fcdonders/fieldtrip.
> >
> >----------------------------------
> >The aim of this list is to facilitate the discussion between users of the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From olga at GRAPHICMIND.INFO  Wed Oct 22 13:10:01 2008
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Wed, 22 Oct 2008 12:10:01 +0100
Subject: Fwd: RE: clusterrandomization for 2 epochs separately
Message-ID: <WED.22.OCT.2008.121001.0100.>

> Dear Eric, 
> I would like to consult with you about some our ERP data and
> application of the clusterrandomization to it. 
> 
> I am writing now the article about ERP signs of visual change
> detection. 
> 
> We have ERP to the "deviant" and "standard" stimuli sampling rate
> 512 Hz, 64 channels (Biosemi), 12 subjects. 
> 
> If we use the paired-wise t-test to compare the ERPs' amplitudes in
> response to standard and deviant stimuli separately for each
> electrode and time point (and plot it see the picture at the end of
> the letter) we can see 2 (4) time regions of differences. But
> application of clusterrandomization analysis to these data (latency
> 0-500 ms) reveal only late cluster as significant, the early cluster
> is marginally significant (p=0.1). But I really believe in this early
> effect (120-160 ms), it is very important for our paper. When I run
> the clusterrandomization analysis on the narrowed epoch (0-300 ms) I
> got the early cluster significant. But the problem than that I loose
> the late effect, which is also worth mentioning in the paper. 
> 
> Therefore, I would like you opinion about the possibility to use the
> clusterrandomization analysis separately on the 2 epochs of interest,
> let say first 250 ms post-stimulus (0-250 ms) and next (250-500 ms). 
> 
> In this case there would be two significant clusters...  
> Best Regards, 
> 
> Olga Sysoeva 
> P.S. 
> 
> I also used different parameters for clusterrandomization (ndis,
> nchannels) but this does not change the results much.  
> P.P.S. 
> 
> Additional material 
> The paired-wise t-test was used to compare the ERPs' amplitudes in
> response to standard and deviant stimuli separately for each
> electrode and time point. 
> 
> The standard and deviant ERPs comparison reveals 2(4) intervals of
> significant differences:  
> 
> Fig.1. At this weird J picture we see the boxes of significant
> differences between standard and deviant ERPs for each time point (x
> axis) and electrode (y axis). 
> Olga Sysoeva, PhD
> Institute of Higher Nervous 
> Activity and Neurophysiology
> Russian Academy of Sciences
> 5a Butlerova str.
> Moscow 117485
> RUSSIA
> tel.: (7-095)-3347011, 
> fax:(7-095)-338-85-00.    
> 
> Links:
> ------
> [2] http://www.ru.nl/master/cns/
> 
> 

----------------------------------
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From enteka at HOTMAIL.COM  Wed Oct 22 15:24:15 2008
From: enteka at HOTMAIL.COM (Nicolas Robitaille)
Date: Wed, 22 Oct 2008 13:24:15 +0000
Subject: Fwd: RE: clusterrandomization for 2 epochs separately
In-Reply-To: <49214.1224673801@graphicmind.info>
Message-ID: <WED.22.OCT.2008.132415.0000.FIELDTRIP@NIC.SURFNET.NL>


Dear Olga,

I have a quick answer for you, and would be please to heard people's comment on it. If you had a priori reason to belive something would happen for these electrodes and time-window, you don't need cluster analysis at all. All the solutions to the multiple-comparison problem are to be used in exploratory situation, when you don't know what to expect. If you had specific hypothesis, don't be shy: test them directy with a T-Test on the average voltage for a pre-determined time-window. 

Think about it, if you did expect these effects to be there, you could had create a montage with only one or two electrodes, and the multiple-comparison problem would not apply at all.

Hope this help,

Nic

************************************
Nicolas Robitaille, candidat Ph.D
Département de Psychologie
Université de Montréal
C.P. 6128, succursale Centre-ville
Montréal, Québec H3C 3J7
Tel.: 514-343-6111 x2631
Fax: 514-343-5787
************************************


> Date: Wed, 22 Oct 2008 12:10:01 +0100
> From: olga at GRAPHICMIND.INFO
> Subject: [FIELDTRIP] Fwd: RE: clusterrandomization for 2 epochs separately
> To: FIELDTRIP at NIC.SURFNET.NL
> 
> > Dear Eric, 
> > I would like to consult with you about some our ERP data and
> > application of the clusterrandomization to it. 
> > 
> > I am writing now the article about ERP signs of visual change
> > detection. 
> > 
> > We have ERP to the "deviant" and "standard" stimuli sampling rate
> > 512 Hz, 64 channels (Biosemi), 12 subjects. 
> > 
> > If we use the paired-wise t-test to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point (and plot it see the picture at the end of
> > the letter) we can see 2 (4) time regions of differences. But
> > application of clusterrandomization analysis to these data (latency
> > 0-500 ms) reveal only late cluster as significant, the early cluster
> > is marginally significant (p=0.1). But I really believe in this early
> > effect (120-160 ms), it is very important for our paper. When I run
> > the clusterrandomization analysis on the narrowed epoch (0-300 ms) I
> > got the early cluster significant. But the problem than that I loose
> > the late effect, which is also worth mentioning in the paper. 
> > 
> > Therefore, I would like you opinion about the possibility to use the
> > clusterrandomization analysis separately on the 2 epochs of interest,
> > let say first 250 ms post-stimulus (0-250 ms) and next (250-500 ms). 
> > 
> > In this case there would be two significant clusters...  
> > Best Regards, 
> > 
> > Olga Sysoeva 
> > P.S. 
> > 
> > I also used different parameters for clusterrandomization (ndis,
> > nchannels) but this does not change the results much.  
> > P.P.S. 
> > 
> > Additional material 
> > The paired-wise t-test was used to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point. 
> > 
> > The standard and deviant ERPs comparison reveals 2(4) intervals of
> > significant differences:  
> > 
> > Fig.1. At this weird J picture we see the boxes of significant
> > differences between standard and deviant ERPs for each time point (x
> > axis) and electrode (y axis). 
> > Olga Sysoeva, PhD
> > Institute of Higher Nervous 
> > Activity and Neurophysiology
> > Russian Academy of Sciences
> > 5a Butlerova str.
> > Moscow 117485
> > RUSSIA
> > tel.: (7-095)-3347011, 
> > fax:(7-095)-338-85-00.    
> > 
> > Links:
> > ------
> > [2] http://www.ru.nl/master/cns/
> > 
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

_________________________________________________________________


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From e.maris at DONDERS.RU.NL  Wed Oct 22 15:43:01 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Wed, 22 Oct 2008 15:43:01 +0200
Subject: Fwd: RE: clusterrandomization for 2 epochs separately
In-Reply-To: <BAY136-W214848AC17B1ADB18F421EDF290@phx.gbl>
Message-ID: <WED.22.OCT.2008.154301.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Nic,

 

 

I have a quick answer for you, and would be please to heard people's comment
on it. If you had a priori reason to belive something would happen for these
electrodes and time-window, you don't need cluster analysis at all. All the
solutions to the multiple-comparison problem are to be used in exploratory
situation, when you don't know what to expect. If you had specific
hypothesis, don't be shy: test them directy with a T-Test on the average
voltage for a pre-determined time-window. 

Think about it, if you did expect these effects to be there, you could had
create a montage with only one or two electrodes, and the
multiple-comparison problem would not apply at all.



Your understanding makes me happy! I couldn’t have formulated it any better.

 

Eric Maris

 

 

 

 

 

 


Hope this help,

Nic

************************************
Nicolas Robitaille, candidat Ph.D
Département de Psychologie
Université de Montréal
C.P. 6128, succursale Centre-ville
Montréal, Québec H3C 3J7
Tel.: 514-343-6111 x2631
Fax: 514-343-5787
************************************


> Date: Wed, 22 Oct 2008 12:10:01 +0100
> From: olga at GRAPHICMIND.INFO
> Subject: [FIELDTRIP] Fwd: RE: clusterrandomization for 2 epochs separately
> To: FIELDTRIP at NIC.SURFNET.NL
> 
> > Dear Eric, 
> > I would like to consult with you about some our ERP data and
> > application of the clusterrandomization to it. 
> > 
> > I am writing now the article about ERP signs of visual change
> > detection. 
> > 
> > We have ERP to the "deviant" and "standard" stimuli sampling rate
> > 512 Hz, 64 channels (Biosemi), 12 subjects. 
> > 
> > If we use the paired-wise t-test to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point (and plot it see the picture at the end of
> > the letter) we can see 2 (4) time regions of differences. But
> > application of clusterrandomization analysis to these data (latency
> > 0-500 ms) reveal only late cluster as significant, the early cluster
> > is marginally significant (p=0.1). But I really believe in this early
> > effect (120-160 ms), it is very important for our paper. When I run
> > the clusterrandomization analysis on the narrowed epoch (0-300 ms) I
> > got the early cluster significant. But the problem than that I loose
> > the late effect, which is also worth mentioning in the paper. 
> > 
> > Therefore, I would like you opinion about the possibility to use the
> > clusterrandomization analysis separately on the 2 epochs of interest,
> > let say first 250 ms post-stimulus (0-250 ms) and next (250-500 ms). 
> > 
> > In this case there would be two significant clusters... 
> > Best Regards, 
> > 
> > Olga Sysoeva 
> > P.S. 
> > 
> > I also used different parameters for clusterrandomization (ndis,
> > nchannels) but this does not change the results much. 
> > P.P.S. 
> > 
> > Additional material 
> > The paired-wise t-test was used to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point. 
> > 
> > The standard and deviant ERPs comparison reveals 2(4) intervals of
> > significant differences: 
> > 
> > Fig.1. At this weird J picture we see the boxes of significant
> > differences between standard and deviant ERPs for each time point (x
> > axis) and electrode (y axis). 
> > Olga Sysoeva, PhD
> > Institute of Higher Nervous 
> > Activity and Neurophysiology
> > Russian Academy of Sciences
> > 5a Butlerova str.
> > Moscow 117485
> > RUSSIA
> > tel.: (7-095)-3347011, 
> > fax:(7-095)-338-85-00. 
> > 
> > Links:
> > ------
> > [2] http://www.ru.nl/master/cns/
> > 
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/fcdonders/fieldtrip.

  _____  

Obtenez votre dose d'information sur votre cellulaire. Avec MSN Mobile,
obtenez des mises à jour régulières sur l'actualité, les sports et les
finances Essayez-le aujourd'hui
<http://info.mobile.ca.msn.com/fr-ca/default.aspx>  !

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

The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/fieldtrip/


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From olga at GRAPHICMIND.INFO  Wed Oct 22 17:12:27 2008
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Wed, 22 Oct 2008 19:12:27 +0400
Subject: Fwd: RE: clusterrandomization for 2 epochs separately
In-Reply-To: <20081022134258.CECC8A9FDE@smtp.ru.nl>
Message-ID: <WED.22.OCT.2008.191227.0400.FIELDTRIP@NIC.SURFNET.NL>

Thank you all for your answer. I perfectly understand what you wrote.

Unfortunately early effect I believe in is what only our group is found
therefore we could not use the former study and take the electrode and
latency from them.

I also know the way how I can represent our data using the conventional
t-test analysis.

I just want to use here the clusterrandomization analysis for more logical
and tense description of the results.

My question is does the usage of clusterrandomization on the 2 epochs
separately make sense here. If you think that the conventional t-test is
more suitable here, I’ll stand on it.

 

Best Regards,

Olga.

 

  _____  

From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Eric Maris
Sent: Wednesday, October 22, 2008 5:43 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] Fwd: RE: clusterrandomization for 2 epochs
separately

 

Dear Nic,

 

 

I have a quick answer for you, and would be please to heard people's comment
on it. If you had a priori reason to belive something would happen for these
electrodes and time-window, you don't need cluster analysis at all. All the
solutions to the multiple-comparison problem are to be used in exploratory
situation, when you don't know what to expect. If you had specific
hypothesis, don't be shy: test them directy with a T-Test on the average
voltage for a pre-determined time-window. 

Think about it, if you did expect these effects to be there, you could had
create a montage with only one or two electrodes, and the
multiple-comparison problem would not apply at all.

Your understanding makes me happy! I couldn’t have formulated it any better.

 

Eric Maris

 

 

 

 

 

 


Hope this help,

Nic

************************************
Nicolas Robitaille, candidat Ph.D
Département de Psychologie
Université de Montréal
C.P. 6128, succursale Centre-ville
Montréal, Québec H3C 3J7
Tel.: 514-343-6111 x2631
Fax: 514-343-5787
************************************


> Date: Wed, 22 Oct 2008 12:10:01 +0100
> From: olga at GRAPHICMIND.INFO
> Subject: [FIELDTRIP] Fwd: RE: clusterrandomization for 2 epochs separately
> To: FIELDTRIP at NIC.SURFNET.NL
> 
> > Dear Eric, 
> > I would like to consult with you about some our ERP data and
> > application of the clusterrandomization to it. 
> > 
> > I am writing now the article about ERP signs of visual change
> > detection. 
> > 
> > We have ERP to the "deviant" and "standard" stimuli sampling rate
> > 512 Hz, 64 channels (Biosemi), 12 subjects. 
> > 
> > If we use the paired-wise t-test to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point (and plot it see the picture at the end of
> > the letter) we can see 2 (4) time regions of differences. But
> > application of clusterrandomization analysis to these data (latency
> > 0-500 ms) reveal only late cluster as significant, the early cluster
> > is marginally significant (p=0.1). But I really believe in this early
> > effect (120-160 ms), it is very important for our paper. When I run
> > the clusterrandomization analysis on the narrowed epoch (0-300 ms) I
> > got the early cluster significant. But the problem than that I loose
> > the late effect, which is also worth mentioning in the paper. 
> > 
> > Therefore, I would like you opinion about the possibility to use the
> > clusterrandomization analysis separately on the 2 epochs of interest,
> > let say first 250 ms post-stimulus (0-250 ms) and next (250-500 ms). 
> > 
> > In this case there would be two significant clusters... 
> > Best Regards, 
> > 
> > Olga Sysoeva 
> > P.S. 
> > 
> > I also used different parameters for clusterrandomization (ndis,
> > nchannels) but this does not change the results much. 
> > P.P.S. 
> > 
> > Additional material 
> > The paired-wise t-test was used to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point. 
> > 
> > The standard and deviant ERPs comparison reveals 2(4) intervals of
> > significant differences: 
> > 
> > Fig.1. At this weird J picture we see the boxes of significant
> > differences between standard and deviant ERPs for each time point (x
> > axis) and electrode (y axis). 
> > Olga Sysoeva, PhD
> > Institute of Higher Nervous 
> > Activity and Neurophysiology
> > Russian Academy of Sciences
> > 5a Butlerova str.
> > Moscow 117485
> > RUSSIA
> > tel.: (7-095)-3347011, 
> > fax:(7-095)-338-85-00. 
> > 
> > Links:
> > ------
> > [2] http://www.ru.nl/master/cns/
> > 
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/fcdonders/fieldtrip.

  _____  

Obtenez votre dose d'information sur votre cellulaire. Avec MSN Mobile,
obtenez des mises à jour régulières sur l'actualité, les sports et les
finances Essayez-le <http://info.mobile.ca.msn.com/fr-ca/default.aspx>
aujourd'hui !



__________ NOD32 3536 (20081019) Information __________

This message was checked by NOD32 antivirus system.
http://www.eset.com

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

The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/fieldtrip/

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

The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/fieldtrip/


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From g.rousselet at PSY.GLA.AC.UK  Fri Oct 24 18:40:44 2008
From: g.rousselet at PSY.GLA.AC.UK (Guillaume Rousselet)
Date: Fri, 24 Oct 2008 17:40:44 +0100
Subject: Launch of CCNi and SI project
Message-ID: <FRI.24.OCT.2008.174044.0100.FIELDTRIP@NIC.SURFNET.NL>

The Department of Psychology at University of Glasgow is pleased to  
announce a Joint Event to launch the Centre for Cognitive Neuroimaging  
(CCNi) and  to officially launch our project: Social Interaction: a  
Cognitive Neurosciences Approach.
Date: Friday 28th November 2008; Venue: Kelvin Gallery, Gilbert Scott  
Building, University Avenue & the Department of Psychology / CCNi,  
University of Glasgow, UK.

The Event, starting at 10am, will include presentations by Professor  
Philippe Schyns (CCNi Director), Professor Nikos Logothetis (MPI  
Tübingen, Germany), Professor Riitta Hari (Low Temperature Laboratory,  
Helsinki, Finland), Professor Alvaro Pascual-Leone (Harvard Medical  
School, Boston, USA), Professor Paula Niedenthal (Université Blaise  
Pascal, Clermont-Ferrand, France), Professor Rainer Goebel (Univeridty  
of Maastricht, The Netherlands).

A drinks reception and a Tour of CCNi with poster presentation will be  
held from 5pm onwards in the Department of Psychology. Contact:  
Heather Robertson, CCNi Administrator, Department of Psychology (Room  
519) University of Glasgow, 58 Hillhead Street, Glasgow G12 8QB. tel:  
+44 (0)141 330 6173. Email: h.robertson at psy.gla.ac.uk. Web: www.ccni.gla.ac.uk 
,www.socialinteraction.gla.ac.uk




************************************************************************************
Guillaume A. Rousselet, Ph.D.

Lecturer

Centre for Cognitive Neuroimaging (CCNi)
Department of Psychology
Faculty of Information & Mathematical Sciences (FIMS)
University of Glasgow
58 Hillhead Street
Glasgow, UK
G12 8QB

The University of Glasgow, charity number SC004401

http://web.me.com/rousseg/GARs_website/

Email: g.rousselet at psy.gla.ac.uk
Fax. +44 (0)141 330 4606
Tel. +44 (0)141 330 6652
Cell +44 (0)791 779 7833


“Computers in the future may weigh no more than 1.5 tons.”
	
	Popular Mechanics, 1949
************************************************************************************




----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From r.oostenveld at FCDONDERS.RU.NL  Mon Oct 27 10:03:39 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Mon, 27 Oct 2008 10:03:39 +0100
Subject: time-frequency representation of PLV
In-Reply-To: <1224360344780798.0.outsmtp04@outsmtp04>
Message-ID: <MON.27.OCT.2008.100339.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi Hyoungdong

On 18 Oct 2008, at 22:05, 박형동 wrote:
> Is it possible to draw a time-frequency representation of PLV using  
> singleplotTFR ?
>
> It looks like that i can only draw TFR of power spectra with  
> singleplotTFR, even though multiplotTFR and topoplotTFR supports PLV.

You can specify xparam/yparam and zparam in the singleplotTFR  
configuration. Assuming that you have something like

freq = freqanalysis(...)

cfg.cohmethod = 'plv'
fd = freqdescriptives(cfg, freq)

then your fd structure contains
   fd.time
   fd.freq
   fd.plvspctrm
which are to be specified as x, y and z params for singleplotTFR.

best regards,
Robert

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From spil at OKWF.FUW.EDU.PL  Mon Oct 27 15:12:12 2008
From: spil at OKWF.FUW.EDU.PL (=?ISO-8859-2?Q?Szymon_Pi=B3at?=)
Date: Mon, 27 Oct 2008 15:12:12 +0100
Subject: Dipolefitting output coordinates
Message-ID: <MON.27.OCT.2008.151212.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi everyone!

For several days I have been trying to figure out the "dipolefitting"
script output.

I guess its output is in xyz coordinates. But is this in MNI space or
Talairach space?

BTW: How to visualise the dipole I found? I use "dipplot" from EEGLAB
but I am looking for other simple way to visualise a dipole.

Thank you in advance for your help.
Best regards,
Szymon Pilat
--
spil at okwf.fuw.edu.pl
Department of Biomedical Physics
University of Warsaw

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From a.maye at UKE.DE  Mon Oct 27 16:04:56 2008
From: a.maye at UKE.DE (Alexander Maye)
Date: Mon, 27 Oct 2008 16:04:56 +0100
Subject: Preproc - thresholding negative z-scores too?
Message-ID: <MON.27.OCT.2008.160456.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear List!

In my dataset I have a nice EOG signal, in which the respective artifact detection routines 
nonetheless do not detect artifacts,since its polarity is negative. Consequently the 
z-scores also deviate towards negative, and are always below (the positive) threshold 
value. So, shouldn't artifact_zvalue threshold the *absolute* z-value instead of the raw 
z-score? I know this has been asked last year, but couldn't find an answer. Any 
opinions/preferred solutions? Ah, and yes, I played with hilbert and rectify, but hilbert does 
not change the polarity (what does it anyway?), and rectify rectifies the data, not the 
z-scores.

Best,

                       ALEX.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From v.litvak at ION.UCL.AC.UK  Mon Oct 27 19:26:50 2008
From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak)
Date: Mon, 27 Oct 2008 18:26:50 +0000
Subject: Dipolefitting output coordinates
In-Reply-To: <8834c95d0810270712j6941eb08xf29d3ca5881fcb98@mail.gmail.com>
Message-ID: <MON.27.OCT.2008.182650.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Szymon,

Fieldtrip can work in any coordinate system so the coordinates of the
output are determined by coordinates of the input (i.e. the sensors
and the volume model that you provided). MNI space and Talairach space
are exactly the same. The only thing different is the template brain
i.e. anatomical interpretation of the coordinates.  But the
coordinates Fieldtrip outputs can be neither unless your sensor
locations are given in MNI coordinates.

You can use headmodelplot to plot your volume and sensors and then
plot3 to add the dipole locations to that plot.

Best,

Vladimir


On Mon, Oct 27, 2008 at 2:12 PM, Szymon Piłat <spil at okwf.fuw.edu.pl> wrote:
> Hi everyone!
>
> For several days I have been trying to figure out the "dipolefitting"
> script output.
>
> I guess its output is in xyz coordinates. But is this in MNI space or
> Talairach space?
>
> BTW: How to visualise the dipole I found? I use "dipplot" from EEGLAB
> but I am looking for other simple way to visualise a dipole.
>
> Thank you in advance for your help.
> Best regards,
> Szymon Pilat
> --
> spil at okwf.fuw.edu.pl
> Department of Biomedical Physics
> University of Warsaw
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
>

From j.schoffelen at PSY.GLA.AC.UK  Tue Oct 28 10:47:06 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Tue, 28 Oct 2008 09:47:06 +0000
Subject: Preproc - thresholding negative z-scores too?
In-Reply-To: <LISTSERV%200810271604560250.00C5@NIC.SURFNET.NL>
Message-ID: <TUE.28.OCT.2008.094706.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Alex,

As far as I remember, the default settings for artifact_eog (the
'higher' level function which calls artifact_zvalue later on) contain
the (absolute of the) hilbert transform.
The hilbert-transform of a bandpass filtered signal is an estimate of
the instantaneous amplitude. Since it is an absolute value, it is
always positive and should reverse
the polarity of the EOG, as would rectification.
I do not really understand your statement that the polarity is not
changed by either rectification of hilbert transformation. Could it
be that you specified your options in
cfg.artfctdef.eog, and then called artifact_zvalue? or
cfg.artfctdef.zvalue and called artifact_eog?

I guess specifying cfg.artfctdef.XXX. rectify/hilbert = 'yes', and
subsequently calling artifact_XXX (eog or zvalue) should do the
trick. Of course, specifying cfg.artfctdef.XXX.feedback = 'yes',
gives you an idea how the data look.

Good luck

Jan-Mathijs


On Oct 27, 2008, at 3:04 PM, Alexander Maye wrote:

> Dear List!
>
> In my dataset I have a nice EOG signal, in which the respective
> artifact detection routines
> nonetheless do not detect artifacts,since its polarity is negative.
> Consequently the
> z-scores also deviate towards negative, and are always below (the
> positive) threshold
> value. So, shouldn't artifact_zvalue threshold the *absolute* z-
> value instead of the raw
> z-score? I know this has been asked last year, but couldn't find an
> answer. Any
> opinions/preferred solutions? Ah, and yes, I played with hilbert
> and rectify, but hilbert does
> not change the polarity (what does it anyway?), and rectify
> rectifies the data, not the
> z-scores.
>
> Best,
>
>                        ALEX.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From a.maye at UKE.DE  Tue Oct 28 14:14:08 2008
From: a.maye at UKE.DE (Alexander Maye)
Date: Tue, 28 Oct 2008 14:14:08 +0100
Subject: Preproc - thresholding negative z-scores too?
Message-ID: <TUE.28.OCT.2008.141408.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs and All!

Thank you for the quick response. Hilbert indeed flips my eye blinks towards positive 
z-values - at the cost of reduced discriminability. That is to say that the amplitude of the 
z-score of the eye blink is twice as high without Hilbert (but in the "wrong" direction). Apart 
from that I still would like to know the rationale behind considering deviations of the z-value 
towards +Inf as artifacts, while those towards -Inf not. This is the same concern as in 
#Item001386 of this list exactly one year ago. Any opinions?

Best,

                         ALEX.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From bps231 at NYU.EDU  Thu Oct 30 18:19:30 2008
From: bps231 at NYU.EDU (Bernhard Staresina)
Date: Thu, 30 Oct 2008 18:19:30 +0100
Subject: stats on single subject coherence
Message-ID: <THU.30.OCT.2008.181930.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear FieldTrip experts,

I was wondering if there is a way to test the significance of coherence
values between two channels across two different conditions within a single
subject (assuming, for simplicity, equal number of trials in both
conditions). As far as I know this is not implemented in the neat
randomization/cluster stats methods for now, but any advice would be greatly
appreciated.

Thanks,
Bernhard



----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From g.rousselet at PSY.GLA.AC.UK  Thu Oct 30 18:36:09 2008
From: g.rousselet at PSY.GLA.AC.UK (Guillaume Rousselet)
Date: Thu, 30 Oct 2008 17:36:09 +0000
Subject: stats on single subject coherence
In-Reply-To: <LISTSERV%200810301819306620.3CDB@NIC.SURFNET.NL>
Message-ID: <THU.30.OCT.2008.173609.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Bernhard,

what you want to do is the same as comparing 2 independent groups of
subjects. Thanks to the modular architecture of Filedtrip you can plug-
in a T-statistic for independent samples when you do the permutation +
clustering. The general procedure is described in Eric Maris' 2007 J.
Neurosci. Meth. paper.

Best,

GAR



On 30 Oct 2008, at 17:19, Bernhard Staresina wrote:

> Dear FieldTrip experts,
>
> I was wondering if there is a way to test the significance of
> coherence
> values between two channels across two different conditions within a
> single
> subject (assuming, for simplicity, equal number of trials in both
> conditions). As far as I know this is not implemented in the neat
> randomization/cluster stats methods for now, but any advice would be
> greatly
> appreciated.
>
> Thanks,
> Bernhard
>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/fcdonders/fieldtrip.



************************************************************************************
Guillaume A. Rousselet, Ph.D.

Lecturer

Centre for Cognitive Neuroimaging (CCNi)
Department of Psychology
Faculty of Information & Mathematical Sciences (FIMS)
University of Glasgow
58 Hillhead Street
Glasgow, UK
G12 8QB

The University of Glasgow, charity number SC004401

http://web.me.com/rousseg/GARs_website/

Email: g.rousselet at psy.gla.ac.uk
Fax. +44 (0)141 330 4606
Tel. +44 (0)141 330 6652
Cell +44 (0)791 779 7833


"There is, in short, a huge tacit conspiracy between the U.S.
government, its
agencies and its multinational corporations, on the one hand, and local
business and military cliques in the Third World, on the other, to
assume
complete control of these countries and "develop" them on a joint
venture
basis. The military leaders of the Third World were carefully nurtured
by the
U.S. security establishment to serve as the "enforcers" of this joint
venture
partnership, and they have been duly supplied with machine guns and the
latest data on methods of interrogation of subversives."

	Edward S. Herman - The Real terror network - 1982
************************************************************************************






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From j.schoffelen at PSY.GLA.AC.UK  Fri Oct 31 10:30:09 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Fri, 31 Oct 2008 09:30:09 +0000
Subject: Preproc - thresholding negative z-scores too?
In-Reply-To: <LISTSERV%200810281414088160.05C0@NIC.SURFNET.NL>
Message-ID: <FRI.31.OCT.2008.093009.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Alex,

The answer to you question would be in this case: it's a historical
thing. The Z-value thresholding was conceived to be done on filtered-
and-subsequently-rectified/hilberted data. No need to look for low
Zvalues in that case. In itself, there's no reason not to build in an
option to look for negative Z-values as well. I would gladly help to
build it into the release version for you. I would think of an
option: cfg.artfctdef.zvalue.tail, which will be 1 by default (that
is: only looking at high positive deviations), but could be -1 (for
the large negative ones), or 0 (for both sided). Could you propose an
adjusted version of artifact_zvalue to me, and I'll check it and
build it in.
As for the reduced discriminability: I still don't understand why
this is the case. I assume you have more than 1 EOG channel?
Probably, one of these guys is picking up most of the artifacts, but
if you use both channels in a single run of artifact_eog, the same
threshold is applied to both channels, which indeed would affect the
sensitivity. An alternative would be to call artifact_eog twice, with
the different EOG in cfg.artfctdef.eog.channel, so that you can use
channel-specific thresholds.

Yours,

Jan-Mathijs

On Oct 28, 2008, at 1:14 PM, Alexander Maye wrote:

> Dear Jan-Mathijs and All!
>
> Thank you for the quick response. Hilbert indeed flips my eye
> blinks towards positive
> z-values - at the cost of reduced discriminability. That is to say
> that the amplitude of the
> z-score of the eye blink is twice as high without Hilbert (but in
> the "wrong" direction). Apart
> from that I still would like to know the rationale behind
> considering deviations of the z-value
> towards +Inf as artifacts, while those towards -Inf not. This is
> the same concern as in
> #Item001386 of this list exactly one year ago. Any opinions?
>
> Best,
>
>                          ALEX.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From miguelconstante at GMAIL.COM  Fri Oct 31 18:23:09 2008
From: miguelconstante at GMAIL.COM (Miguel Constante)
Date: Fri, 31 Oct 2008 18:23:09 +0100
Subject: low frequency cut-off and filtfilt
Message-ID: <FRI.31.OCT.2008.182309.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi
I have been trying to high-pass filter my EEG data, 
cfg.hpfilter = 'yes';
cfg.hpfreq = 0.03;
data = preprocessing(cfg);

using cut offs under 1Hz (e.g. 0.03Hz) and systematically get this type of 
error:

Warning: Matrix is close to singular or badly scaled.
         Results may be inaccurate. RCOND = 2.221255e-017.

Can someone advise on how to overcome this?
Thanks
Miguel

----------------------------------
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From r.oostenveld at FCDONDERS.RU.NL  Wed Oct  1 10:50:03 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Wed, 1 Oct 2008 10:50:03 +0200
Subject: changed default reading functions for CTF
In-Reply-To: <1222808946.17803.63.camel@kurage.nimh.nih.gov>
Message-ID: <WED.1.OCT.2008.105003.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Tom,

On 30 Sep 2008, at 23:09, Tom Holroyd wrote:
> Two questions. 1) We record data with 3rd gradient turned on by
> default.
> That is, the MEG channels have already had the background noise
> subtracted. So our datasets contain only balanced data. No further
> processing is required. Does your code take care of this case?

Hmmm, good question... I cannot immediately answer confirmative. The
data that is read will be balanced, that won't be the problem. What I
don't immediately oversee is whether the leadfield computation will
match the balanced data. In the old case it was sure not to match the
data. In the new case the reading routine should take care of that.

I don't have any 3rd order data lying around right now, so would you
please check the following
   data = preprocessing(cfg)  % with your standard config
and then look into the field
   data.grad
There should be a
   data.grad.balance
structure and
   data.grad.balance.current
string. In your case current should be G3BR.

Subsequently please check the weighing of the gradiometer coils to
channels using
   imagesc(data.grad.tra)
You should more or less see two identity matrices concatenated with
some small non-zero numbers in the rightmost part of thaht figure.
This matrix is used in the forward computation: first the field at
every individual coil is computed (keeping the coil orientation in
mind), and then the "coils" are combined to form "channels". The two
identity matrices represent the bottom and top coil, and the small
numbers in the rightmost part represent the small corrections to the
forward model required to mimic the balancing (in which also a small
part of the dipole field is subtracted from the data).

Please let us know whether those two fields are as I expect them to
be. Perhaps you could also send me (not through this email list!) a
3rd gradient dataset (preverably averaged, i.e. small MB size) for
your system, so that I can use that for testing.  You can use ftp.fcdonders.nl/pub/incoming
  or something like yousendit.com.

> 2) Why is
> the code closed source?

We discussed the release of the code in the joined context of SPM8 and
Fieldtrip with the CTF support. See below for their statement

>> ---------- Forwarded message ----------
>> From: MEG Customer Support <support at megservice.com>
>> Date: Thu, Apr 24, 2008 at 1:00 AM
>> Subject: RE: MATLAB Import/Export Routines
>> To: David Bradbury <d.bradbury at fil.ion.ucl.ac.uk>, MEG Customer
>> Support <support at megservice.com>
>> Cc: litvak.vladimir at gmail.com
>>
>>
>> Dear David (& Vladimir),
>>
>> We're most glad to hear that the issue with the stim codes may have
>> been
>> resolved.  As you say please keep us informed if it is not.
>>
>> Thank you very much for your request regarding the VSM MatLab codes.
>> Because we consider them to be covered under the systems' general
>> non-disclosure agreements you are free to use these algorithms
>> internally (i.e. by all MEG users at UCL and F.C. Donders Centre)
>> without restriction however we would like to request that you only
>> distribute these functions external to your labs in a pre-compiled
>> form.
>> Thank you for your consideration in this matter.
>>
>> With best regards,
>>
>> Brent


So I have the m-files but am not allowed to distribute them, hence the
p-files in the fieldtrip/external/ctf directory (and in spm8/external/
ctf). I guess that you as CTF user should be able to get your own copy
of the m-files from CTF support.

best regards,
Robert





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From r.oostenveld at FCDONDERS.RU.NL  Wed Oct  1 12:42:40 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Wed, 1 Oct 2008 12:42:40 +0200
Subject: problem reading old CTF data
In-Reply-To: <f7392e897f60b.48e27315@ru.nl>
Message-ID: <WED.1.OCT.2008.124240.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Barbara (CC fieldtrip list)

The problem that you have with your CTF dataset is due to a bug in the
dataset itself. Since other people might encounter the same problem,
I'll forward the information to the FT mailing list as well.

The dataset that you are trying to read has a bug in the
headcoordinates (*.hc) file. The 5th line in the file is
   stadard left ear coil position relative to dewar (cm):
but should be
   standard left ear coil position relative to dewar (cm):
Note the missing "n" in the buggy headcoordinates file.

In the previous reading routines (read_ctf_hc, see line 182) that bug
was known and the code explicitely tested for that bug. In the new
reading routines (i.e. the ones supplied to us by CTF to handle
synthetic gradients) that bug in the HC file causes a problem.

The only solution for now that I can think of is to edit the HC file
(in a text editor) and to fix the typo by adding the "n" to "stadard".

best regards,
Robert


On 30 Sep 2008, at 18:42, Barbara Haendel wrote:

> I'm not sure what happened but I can't read in my old files anymore
> (something which already had worked about two weeks go). I also
> can't make much sense out of the error message (see below). The
> problem seems to be that FT can't read the trial definition because
> cfg.trialdef.eventtype = '?'; does not give any event information
> anymore. Could it be that something has changed lately since it was
> already working before?
> It would be great if you could help me,
> Thanks,
> Barbara
>
> cfg=[];
>    cfg.dataset='AxLiPERCEPT390405.ds';
>    cfg.continuous = 'no';
>    cfg.trialdef.eventtype = 'trial';
>    cfg = definetrial(cfg);
> evaluating trialfunction 'trialfun_general'
>
> readCTFds: You are reading CTF data for use with a software-
> application tool
> 	that is not manufactured by VSM MedTech Ltd. and has not received
> marketing
> 	clearance for clinical applications.  If CTF MEG data are processed
> by this tool,
> 	they should not be later employed for clinical and/or diagnostic
> purposes.
>
> readCPersist: Stop strings (EndOfParameters) do not balance start
> strings (WS1_).
>              (No. of start strings)-(No. of stop strings)=1.
> ??? Index exceeds matrix dimensions.
>
> Error in ==> /home/common/matlab/fieldtrip/external/ctf/
> readCTFds.p>readHc at 599
>
> Error in ==> /home/common/matlab/fieldtrip/external/ctf/
> readCTFds.p>readCTFds at 203

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From michael.wibral at WEB.DE  Thu Oct  2 16:02:18 2008
From: michael.wibral at WEB.DE (Michael Wibral)
Date: Thu, 2 Oct 2008 16:02:18 +0200
Subject: Missing dim filed after source analysis.
Message-ID: <THU.2.OCT.2008.160218.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Listuser,

I am having a little problem with the beamformer (dics) tutorial. If I run first sourceanalysis on 'data' like this:

SourceDataSingleTrial=sourceanalysis(cfg, data)

applying precomputed filters to single trials (as in the tutorial) and then feed SourceDataSingleTrial to sourcestatistics like this:

SourceStats=sourceanalysis(cfg,SourceDataSingleTrial )

Then sourcestatistics complains about a missing filed 'dim'. I can fix this problem by creating the field SourceStats.dim by hand, giving the voxel conuts in each dimension [voxX voxY voxZ] and the code runs. However, the function might also need the number of trials or the like ???

Any idea what could be the reason for sourceanalysis not producing the dim field?

Michael

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From r.oostenveld at FCDONDERS.RU.NL  Thu Oct  2 17:39:32 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 2 Oct 2008 17:39:32 +0200
Subject: Missing dim filed after source analysis.
In-Reply-To: <794538785@web.de>
Message-ID: <THU.2.OCT.2008.173932.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Michael,

On 2 Oct 2008, at 16:02, Michael Wibral wrote:
> I am having a little problem with the beamformer (dics) tutorial. If
> I run first sourceanalysis on 'data' like this:
>
> SourceDataSingleTrial=sourceanalysis(cfg, data)
>
> applying precomputed filters to single trials (as in the tutorial)
> and then feed SourceDataSingleTrial to sourcestatistics like this:
>
> SourceStats=sourceanalysis(cfg,SourceDataSingleTrial )
>
> Then sourcestatistics complains about a missing filed 'dim'.

Are you working wih the latest copy of fieldtirp? If not, please see
whether that fixes the problem.

> I can fix this problem by creating the field SourceStats.dim by hand,

I presume you mean that you add dim to SourceDataSingleTrial and not
to SourceStats?

> giving the voxel conuts in each dimension [voxX voxY voxZ] and the
> code runs. However, the function might also need the number of
> trials or the like ???

The number of trials is determined in the code as
length(SourceDataSingleTrial.trial) and equals size(cfg.design,2).

> Any idea what could be the reason for sourceanalysis not producing
> the dim field?

We recently started cleaning up the representation of source data. In
the FT code there was a possible confusion about sources being
represented as a "random set of points", where each point is specified
by its position, or represented as a nicely arranged 3D volume. In the
latter case you can also specify the position of each voxel, but the
latter case is more conveniently represented using a homogenous
transformation matrix in combination with voxel indices.

This cleanup was realized in the "checkdata" function, which ensures
that the input to each FT function is as what the function expects.
The checkdata function manages backward compatibility of data
structures (i.e. still allowing to work with data that was sitting in
a mat file for a long time, and not requiring to compute the data
every time) and it tries to convert data between different
representations (i.e. volume->source_positions and the other way
around if the positions are arranged in a 3D grid).

I'll try to reproduce the problem and get back to you. For the moment
you can just add the dim field, that won't break anything.

best regards,
Robert

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From wibral at BIC.UNI-FRANKFURT.DE  Thu Oct  2 17:41:58 2008
From: wibral at BIC.UNI-FRANKFURT.DE (Michael Wibral)
Date: Thu, 2 Oct 2008 17:41:58 +0200
Subject: fix pow=pow' still necessary
Message-ID: <THU.2.OCT.2008.174158.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Listusers,

a question related to my last one. In the beamformer tutorial, the pow matrix gets transposed for each trial when going form sourceanalysis to sourcestatistics. Is that still necessary at the moment (i.e. FT20081001)?

Best Regards,
Michael

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From r.oostenveld at FCDONDERS.RU.NL  Thu Oct  2 18:07:33 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 2 Oct 2008 18:07:33 +0200
Subject: fix pow=pow' still necessary
In-Reply-To: <794649790@web.de>
Message-ID: <THU.2.OCT.2008.180733.0200.FIELDTRIP@NIC.SURFNET.NL>

On 2 Oct 2008, at 17:41, Michael Wibral wrote:

> Dear Listusers,
>
> a question related to my last one. In the beamformer tutorial, the
> pow matrix gets transposed for each trial when going form
> sourceanalysis to sourcestatistics. Is that still necessary at the
> moment (i.e. FT20081001)?

Hmm, I though that I had removed the transposing of the pow just a few
days ago on the wiki, because that is indeed not needed any more in
recent versions. Could you check the wiki once more (maybe you are
working from a cached version or from a printout)...

Robert

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From j.schoffelen at PSY.GLA.AC.UK  Fri Oct  3 22:11:49 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Fri, 3 Oct 2008 21:11:49 +0100
Subject: cross-spectrum to cross-correlogram
In-Reply-To: <200809290754.m8T7sv6F002791@ns1.intern.nin.knaw.nl>
Message-ID: <FRI.3.OCT.2008.211149.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jasper,

I did not yet completely think it through, but I see two problems
here. Obviously, you would like to verify whether multiplication in
the frequency domain is equivalent to convolution in the time
domain ;o),
actually that conjugate multiplication is equivalent to cross-
covariancing (shouldn't you use xcov, instead of xcorr?)

1 you apply a hanning taper in your frequency analysis; to make a
fair comparison you probably should specify cfg.taper='rectwin',
because your time domain data is not tapered in the xcorr-analysis
2 mathematically the convolution vs. multiplication holds when you
also take into account the 'negative frequencies' in your ifft.
However, freqanalysis does not output these in the first place
3 (sorry there's a third thing): probably you should specify the
additional option 'unbiased' when calling xcorr (or xcov), because
fft assumes circular data so the ifft'ed csd does not taper off at
the edges (which in the xcov/xcorr is due to a decrease in the number
of overlapping samples).

Hopefully these thoughts help.

Yours,

Jan-Mathijs



On Sep 29, 2008, at 8:54 AM, Jasper Poort wrote:

> CS=freq.fourierspctrm(:,1,:).*conj(freq.fourierspctrm(:,2,:));
> y = real((squeeze(mean(CS))));
> figure;plot(y)
>
> % inverse fft of cross-spectrum
> y = real(ifft(squeeze(mean(CS))));
> figure;plot(y)
>
> % compare to cross-correlation function
> [c,lags] = xcorr(mean(squeeze(wav(:,:,1)),2),mean(squeeze(wav(:,:,
> 2)),2));
> figure;plot(lags,c)


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From shehsu at INDIANA.EDU  Mon Oct  6 09:43:15 2008
From: shehsu at INDIANA.EDU (Hsu, Shen-Mou)
Date: Mon, 6 Oct 2008 03:43:15 -0400
Subject: cfg.layout and clusterplot
Message-ID: <MON.6.OCT.2008.034315.0400.FIELDTRIP@NIC.SURFNET.NL>

Dear users,

I was wondering if someone could help me sort out the following problem. I tried to plot significant clusters using clusterplot after permutation tests.  When I ran the script as below, it returned the message like this:

reverting to 151 channel CTF default
??? Error using ==> topoplotER at 330
labels in data and labels in layout do not match

Error in ==> clusterplot at 240
          topoplotER(cfg, stat);

However, I checked both cfg.layout.labels and cfg.layout.pnt. Everything seems fine.

Many thanks in advance.



My script:

%load data
load GA_N_HV_base; load GA_N_LV_base;
%load statistics
load stat_N_HVvsLV_400;
%load layout
load Sub19_ERP_HVN;

GA_N_HVvsLV = GA_N_HV_base;
GA_N_HVvsLV.avg = GA_N_HV_base.avg - GA_N_LV_base.avg;

% clusterplot
cfg = [];
cfg.alpha = 0.05;
cfg.layout = ERPdata.elec
clusterplot(cfg,stat_N_HVvsLV)

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From shehsu at INDIANA.EDU  Mon Oct  6 10:02:56 2008
From: shehsu at INDIANA.EDU (Hsu, Shen-Mou)
Date: Mon, 6 Oct 2008 04:02:56 -0400
Subject: plot the raw effects
Message-ID: <MON.6.OCT.2008.040256.0400.FIELDTRIP@NIC.SURFNET.NL>

Dear users,

I was wondering if someone could help me sort out the another problem. I tried to plot the raw effect (the difference between two conditions using the script like this

%load data
load GA_N_HV_base; load GA_N_LV_base;

GA_N_HVvsLV = GA_N_HV_base;
GA_N_HVvsLV.avg = GA_N_HV_base.avg - GA_N_LV_base.avg;

cfg = [];
cfg.xlim = [0 0.5];
cfg.channel = 'P3';
clf;
singleplotER(cfg,GA_N_HVvsLV);

However, I noticed that the graph is exactly the same as the graph from GA_N_HV_base. In other words, the singleplotER did not plot the raw effect, GA_N_HVvsLV.avg.

I am indebted to your kindness in this matter.

Shen-Mou Hsu

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From j.lange at FCDONDERS.RU.NL  Mon Oct  6 10:21:45 2008
From: j.lange at FCDONDERS.RU.NL (Jo Lange)
Date: Mon, 6 Oct 2008 10:21:45 +0200
Subject: postdoctoral position
Message-ID: <MON.6.OCT.2008.102145.0200.FIELDTRIP@NIC.SURFNET.NL>

A three-year postdoctoral position is available in the lab of Prof. Schnitzler in 
the Institute of Clinical Neuroscience and Medical Psychology at Heinrich-
Heine-University Düsseldorf, Germany. The position is available from February 
2009, funded by the European Commision (ERAT-NET NEURON). 

The successful candidate will conduct MEG experiments to study the effects 
of Deep Brain Stimulation on cortico-subcortical pathways in Parkinson’s 
disease. The project is part of an international collaboration with partners in 
Germany, Scotland, and Italy. The lab of Prof. Schnitzler offers outstanding 
experience with Deep Brain Stimulation and a whole-head MEG system.

Applicants should have a doctoral degree (PhD) in Neuroscience, Physics, 
Psychology, or related disciplines, experience with MEG recordings and an 
outstanding academic record, including publications. Expertise in Matlab and 
time-frequency analysis (FieldTrip) is desirable.

Salary follows the German Public Service Regulations. To apply, please submit 
your applications with full CV, list of publications, and three references. 
Submission deadline is the 15th of November. For more information about the 
position, contact Prof. A. Schnitzler (alfons.schnitzler at uni-duesseldorf.de) or 
Dr. J. Lange (joachim.lange at med.uni-duesseldorf.de). 

Contact Information
Prof. Dr. Alfons Schnitzler
Institute of Clinical Neuroscience and Medical Psychology
Heinrich-Heine University Düsseldorf
Universitätstr. 1
40225 Düsseldorf
Germany  
Phone: +49-211-81-13014 
Fax: +49-211-81-13015 
E-mail: alfons.schnitzler at uni-duesseldorf.de 

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From A.Stancak at LIVERPOOL.AC.UK  Mon Oct  6 12:31:12 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Mon, 6 Oct 2008 11:31:12 +0100
Subject: 4D data reading
Message-ID: <MON.6.OCT.2008.113112.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear all,

  we have some problems reading 4D Neuroimaging MEG data (148 sensors). For now, we export original 4D data into BESA format, and then read those into FieldTrip. This is not optimal, as e.g. gradient coils information is not transferred into FieldTrip. We would be grateful for a plugin or a hint enabling us to read the 4D data directly into FieldTrip.

  Best wishes
  Andrej Stancak


Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From j.schoffelen at PSY.GLA.AC.UK  Mon Oct  6 12:44:54 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Mon, 6 Oct 2008 11:44:54 +0100
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CAF@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <MON.6.OCT.2008.114454.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Andrej,

As far as I know, 4D data can be read in directly into fieldtrip. At
least it works with our 248-channel system.
There is no need to convert the data into whatever format, meaning
you should be able to read from the raw
datafiles directly. Please let me know if this does not work for you.

Yours,

Jan-Mathijs



On Oct 6, 2008, at 11:31 AM, Stancak, Andrej wrote:

> Dear all,
>
>   we have some problems reading 4D Neuroimaging MEG data (148
> sensors). For now, we export original 4D data into BESA format, and
> then read those into FieldTrip. This is not optimal, as e.g.
> gradient coils information is not transferred into FieldTrip. We
> would be grateful for a plugin or a hint enabling us to read the 4D
> data directly into FieldTrip.
>
>   Best wishes
>   Andrej Stancak
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From venug001 at BAMA.UA.EDU  Mon Oct  6 14:22:17 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 6 Oct 2008 07:22:17 -0500
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CAF@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <MON.6.OCT.2008.072217.0500.FIELDTRIP@NIC.SURFNET.NL>

Hello everyone, I have been wrestling with these problems for a while
too.
Here is what I found: Fieldtrip/EEGLAB will read neuroscan files (.avg,
and .eeg), and will read raw data (e,..)from 4D.
I believe that EEGLAB/Fieldtrip may not have a template for the 148-
Channel system co-ordinates. Christian and Don Rojas created one for me
in early April this year.
A FIF export from the 4D system may also solve this problem. Stephen
Moratti helped me with this a while a ago. It puts out three
files .xyz, .4D and the original e,.. file. But, if the .xyz file which
has coordinates for 148 channels does not match with the template, then
the data will not load. I think for one may have to load a create a 148
channel template for this purpose. This is my experience with EEGLAB,
and I think that they underlying engine is the same for both EEGLAB and
Fieldtrip
Then again, I may be completely wrong about everything except the
templates that were created for me.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear all,
>
>   we have some problems reading 4D Neuroimaging MEG data (148
> sensors). For now, we export original 4D data into BESA format, and
> then read those into FieldTrip. This is not optimal, as e.g. gradient
> coils information is not transferred into FieldTrip. We would be
> grateful for a plugin or a hint enabling us to read the 4D data
> directly into FieldTrip.
>
>   Best wishes
>   Andrej Stancak
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From a.capilla at PSY.GLA.AC.UK  Mon Oct  6 15:02:44 2008
From: a.capilla at PSY.GLA.AC.UK (Almudena Capilla)
Date: Mon, 6 Oct 2008 14:02:44 +0100
Subject: 4D data reading
In-Reply-To: <1223295737.48ea02f9caab1@bamamail.ua.edu>
Message-ID: <MON.6.OCT.2008.140244.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Gopa,

I have got a template for the 4D - 148 channels system. I could give it to
the Fieldtrip developers if this is helpful for other users of this system.

Best,
Almu

-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Gopakumar Venugopalan
Sent: 06 October 2008 13:22
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading

Hello everyone, I have been wrestling with these problems for a while
too.
Here is what I found: Fieldtrip/EEGLAB will read neuroscan files (.avg,
and .eeg), and will read raw data (e,..)from 4D.
I believe that EEGLAB/Fieldtrip may not have a template for the 148-
Channel system co-ordinates. Christian and Don Rojas created one for me
in early April this year.
A FIF export from the 4D system may also solve this problem. Stephen
Moratti helped me with this a while a ago. It puts out three
files .xyz, .4D and the original e,.. file. But, if the .xyz file which
has coordinates for 148 channels does not match with the template, then
the data will not load. I think for one may have to load a create a 148
channel template for this purpose. This is my experience with EEGLAB,
and I think that they underlying engine is the same for both EEGLAB and
Fieldtrip
Then again, I may be completely wrong about everything except the
templates that were created for me.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear all,
>
>   we have some problems reading 4D Neuroimaging MEG data (148
> sensors). For now, we export original 4D data into BESA format, and
> then read those into FieldTrip. This is not optimal, as e.g. gradient
> coils information is not transferred into FieldTrip. We would be
> grateful for a plugin or a hint enabling us to read the 4D data
> directly into FieldTrip.
>
>   Best wishes
>   Andrej Stancak
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the
FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
and EEG analysis. See also
http://listserv.surfnet.nl/archives/fieldtrip.html and
http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From venug001 at BAMA.UA.EDU  Mon Oct  6 15:12:33 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 6 Oct 2008 08:12:33 -0500
Subject: 4D data reading
In-Reply-To: <001001c927b3$e4e14e90$5757d182@DEPT6788A09EF4>
Message-ID: <MON.6.OCT.2008.081233.0500.FIELDTRIP@NIC.SURFNET.NL>

Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
the other users. There was also a discussion about whether the systems
were using third order gradiometers and/or magnetometers as the
reference. There are mail postings in that thread.
Everyone: I apologize for the typos in my hastily composed response
earlier.
regards
gopa


Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:

> Dear Gopa,
>
> I have got a template for the 4D - 148 channels system. I could give
> it to
> the Fieldtrip developers if this is helpful for other users of this
> system.
>
> Best,
> Almu
>
> -----Original Message-----
> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf
> Of Gopakumar Venugopalan
> Sent: 06 October 2008 13:22
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Hello everyone, I have been wrestling with these problems for a while
>
> too.
> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> (.avg,
> and .eeg), and will read raw data (e,..)from 4D.
> I believe that EEGLAB/Fieldtrip may not have a template for the 148-
> Channel system co-ordinates. Christian and Don Rojas created one for
> me
> in early April this year.
> A FIF export from the 4D system may also solve this problem. Stephen
>
> Moratti helped me with this a while a ago. It puts out three
> files .xyz, .4D and the original e,.. file. But, if the .xyz file
> which
> has coordinates for 148 channels does not match with the template,
> then
> the data will not load. I think for one may have to load a create a
> 148
> channel template for this purpose. This is my experience with EEGLAB,
>
> and I think that they underlying engine is the same for both EEGLAB
> and
> Fieldtrip
> Then again, I may be completely wrong about everything except the
> templates that were created for me.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
> > Dear all,
> >
> >   we have some problems reading 4D Neuroimaging MEG data (148
> > sensors). For now, we export original 4D data into BESA format,
> and
> > then read those into FieldTrip. This is not optimal, as e.g.
> gradient
> > coils information is not transferred into FieldTrip. We would be
> > grateful for a plugin or a hint enabling us to read the 4D data
> > directly into FieldTrip.
> >
> >   Best wishes
> >   Andrej Stancak
> >
> >
> > Prof. Andrej Stancak, PhD.
> > The University of Liverpool
> > School of Psychology
> > The Eleanor Rathbone Building
> > Bedford Street South, Room 209
> > Liverpool
> > L69 7ZA
> >
> > E:mail: a.stancak at liverpool.ac.uk  (primary)
> >            stancak at centrum.cz (secondary)
> > Phone: 0151 7946951
> > Office hours: Monday 10-12, Wednesday 10-12
> >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for
> MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From A.Stancak at LIVERPOOL.AC.UK  Mon Oct  6 16:11:20 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Mon, 6 Oct 2008 15:11:20 +0100
Subject: 4D data reading
Message-ID: <MON.6.OCT.2008.151120.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Gopa and Almu,

  do I understand the procedure correctly: we should export data from 4D in FIF format (currently we export in native e,... (binary), and the text files for the header and the surface points), and then use a modified xyz file containing the layout of 148 sensors. I would be grateful for one sample xyz file to see whether we can read data this way. Naturally, the best would be to incorporate it into the reading procedures of FieldTrip.

Best wishes
Andrej


Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
Sent: Mon 06/10/2008 14:12
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian 
Weinbruch and Arno (EEGLAB) may be the ones who can make it work for 
the other users. There was also a discussion about whether the systems 
were using third order gradiometers and/or magnetometers as the 
reference. There are mail postings in that thread.
Everyone: I apologize for the typos in my hastily composed response 
earlier.
regards
gopa


Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:

> Dear Gopa,
> 
> I have got a template for the 4D - 148 channels system. I could give
> it to
> the Fieldtrip developers if this is helpful for other users of this
> system.
> 
> Best,
> Almu
> 
> -----Original Message-----
> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf
> Of Gopakumar Venugopalan
> Sent: 06 October 2008 13:22
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
> 
> Hello everyone, I have been wrestling with these problems for a while
> 
> too.
> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> (.avg, 
> and .eeg), and will read raw data (e,..)from 4D.
> I believe that EEGLAB/Fieldtrip may not have a template for the 148-
> Channel system co-ordinates. Christian and Don Rojas created one for
> me 
> in early April this year.
> A FIF export from the 4D system may also solve this problem. Stephen
> 
> Moratti helped me with this a while a ago. It puts out three 
> files .xyz, .4D and the original e,.. file. But, if the .xyz file
> which 
> has coordinates for 148 channels does not match with the template,
> then 
> the data will not load. I think for one may have to load a create a
> 148 
> channel template for this purpose. This is my experience with EEGLAB,
> 
> and I think that they underlying engine is the same for both EEGLAB
> and 
> Fieldtrip
> Then again, I may be completely wrong about everything except the 
> templates that were created for me.
> regards
> gopa
> 
> 
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> 
> > Dear all,
> > 
> >   we have some problems reading 4D Neuroimaging MEG data (148
> > sensors). For now, we export original 4D data into BESA format,
> and
> > then read those into FieldTrip. This is not optimal, as e.g.
> gradient
> > coils information is not transferred into FieldTrip. We would be
> > grateful for a plugin or a hint enabling us to read the 4D data
> > directly into FieldTrip.
> > 
> >   Best wishes
> >   Andrej Stancak
> > 
> > 
> > Prof. Andrej Stancak, PhD. 
> > The University of Liverpool
> > School of Psychology
> > The Eleanor Rathbone Building
> > Bedford Street South, Room 209
> > Liverpool
> > L69 7ZA
> > 
> > E:mail: a.stancak at liverpool.ac.uk  (primary)
> >            stancak at centrum.cz (secondary)
> > Phone: 0151 7946951
> > Office hours: Monday 10-12, Wednesday 10-12
> > 
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for
> MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From venug001 at BAMA.UA.EDU  Mon Oct  6 16:31:28 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 6 Oct 2008 09:31:28 -0500
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CB0@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <MON.6.OCT.2008.093128.0500.FIELDTRIP@NIC.SURFNET.NL>

Sure will send you those files. Please remember in my files there are
only 146 channel locations as we turned off two channels.I also have a
matlab file from Don Rojas for the 148 channel layout and a file which
he created for the 146 channel layout. Please give some time today, as
I run those programs on a different machine.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopa and Almu,
>
>   do I understand the procedure correctly: we should export data from
> 4D in FIF format (currently we export in native e,... (binary), and
> the text files for the header and the surface points), and then use a
> modified xyz file containing the layout of 148 sensors. I would be
> grateful for one sample xyz file to see whether we can read data this
> way. Naturally, the best would be to incorporate it into the reading
> procedures of FieldTrip.
>
> Best wishes
> Andrej
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 14:12
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>
> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>
> the other users. There was also a discussion about whether the
> systems
> were using third order gradiometers and/or magnetometers as the
> reference. There are mail postings in that thread.
> Everyone: I apologize for the typos in my hastily composed response
> earlier.
> regards
> gopa
>
>
> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>
> > Dear Gopa,
> >
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of
> this
> > system.
> >
> > Best,
> > Almu
> >
> > -----Original Message-----
> > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> On
> > Behalf
> > Of Gopakumar Venugopalan
> > Sent: 06 October 2008 13:22
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> >
> > Hello everyone, I have been wrestling with these problems for a
> while
> >
> > too.
> > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > (.avg,
> > and .eeg), and will read raw data (e,..)from 4D.
> > I believe that EEGLAB/Fieldtrip may not have a template for the
> 148-
> > Channel system co-ordinates. Christian and Don Rojas created one
> for
> > me
> > in early April this year.
> > A FIF export from the 4D system may also solve this problem.
> Stephen
> >
> > Moratti helped me with this a while a ago. It puts out three
> > files .xyz, .4D and the original e,.. file. But, if the .xyz file
> > which
> > has coordinates for 148 channels does not match with the template,
> > then
> > the data will not load. I think for one may have to load a create
> a
> > 148
> > channel template for this purpose. This is my experience with
> EEGLAB,
> >
> > and I think that they underlying engine is the same for both
> EEGLAB
> > and
> > Fieldtrip
> > Then again, I may be completely wrong about everything except the
> > templates that were created for me.
> > regards
> > gopa
> >
> >
> > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> >
> > > Dear all,
> > >
> > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > sensors). For now, we export original 4D data into BESA format,
> > and
> > > then read those into FieldTrip. This is not optimal, as e.g.
> > gradient
> > > coils information is not transferred into FieldTrip. We would be
> > > grateful for a plugin or a hint enabling us to read the 4D data
> > > directly into FieldTrip.
> > >
> > >   Best wishes
> > >   Andrej Stancak
> > >
> > >
> > > Prof. Andrej Stancak, PhD.
> > > The University of Liverpool
> > > School of Psychology
> > > The Eleanor Rathbone Building
> > > Bedford Street South, Room 209
> > > Liverpool
> > > L69 7ZA
> > >
> > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > >            stancak at centrum.cz (secondary)
> > > Phone: 0151 7946951
> > > Office hours: Monday 10-12, Wednesday 10-12
> > >
> > >
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the
> > FieldTrip  toolbox, to share experiences and to discuss new ideas
> for
> > MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From j.schoffelen at PSY.GLA.AC.UK  Mon Oct  6 16:54:57 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Mon, 6 Oct 2008 15:54:57 +0100
Subject: 4D data reading
In-Reply-To: <1223303488.48ea21405717d@bamamail.ua.edu>
Message-ID: <MON.6.OCT.2008.155457.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Andrej, dear Gopa,

Sorry to bother you again, but I tried to make a point in my last
mail that it is not necessary to intermediately convert your raw
epoched or continuous 4D-data into another format, prior to be able
to read it into Fieldtrip. Of course you are free to do so, but the
most natural way to me would seem to work on the raw datafiles
directly. Fieldtrip should support this and it has reading routines
for the raw data-file (beginning with e, or c,), the config-file, and
the file containing the digitized head-surface positions.
You should be able to obtain the header information directly by
calling: hdr = read_header('e,thenameofyourrawdatafile') (give or
take an accidental 'keyboard'-statement in the low-level function
read_4d_hdr, this will be fixed in tonight's release version: if it
occurs now, just type dbcont on the command line when it prompts:
K>>) As far as I know hdr contains a structure grad, which specifies
the sensor-positions. At least it works on our Glaswegian 248-sensor
system.

Yours,

Jan-Mathijs


On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:

> Sure will send you those files. Please remember in my files there are
> only 146 channel locations as we turned off two channels.I also have a
> matlab file from Don Rojas for the 148 channel layout and a file which
> he created for the 146 channel layout. Please give some time today, as
> I run those programs on a different machine.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
>> Dear Gopa and Almu,
>>
>>   do I understand the procedure correctly: we should export data from
>> 4D in FIF format (currently we export in native e,... (binary), and
>> the text files for the header and the surface points), and then use a
>> modified xyz file containing the layout of 148 sensors. I would be
>> grateful for one sample xyz file to see whether we can read data this
>> way. Naturally, the best would be to incorporate it into the reading
>> procedures of FieldTrip.
>>
>> Best wishes
>> Andrej
>>
>>
>> Prof. Andrej Stancak, PhD.
>> The University of Liverpool
>> School of Psychology
>> The Eleanor Rathbone Building
>> Bedford Street South, Room 209
>> Liverpool
>> L69 7ZA
>>
>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>            stancak at centrum.cz (secondary)
>> Phone: 0151 7946951
>> Office hours: Monday 10-12, Wednesday 10-12
>>
>>
>>
>> -----Original Message-----
>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>> Sent: Mon 06/10/2008 14:12
>> To: FIELDTRIP at NIC.SURFNET.NL
>> Subject: Re: [FIELDTRIP] 4D data reading
>>
>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>
>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>
>> the other users. There was also a discussion about whether the
>> systems
>> were using third order gradiometers and/or magnetometers as the
>> reference. There are mail postings in that thread.
>> Everyone: I apologize for the typos in my hastily composed response
>> earlier.
>> regards
>> gopa
>>
>>
>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>
>>> Dear Gopa,
>>>
>>> I have got a template for the 4D - 148 channels system. I could
>> give
>>> it to
>>> the Fieldtrip developers if this is helpful for other users of
>> this
>>> system.
>>>
>>> Best,
>>> Almu
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>> On
>>> Behalf
>>> Of Gopakumar Venugopalan
>>> Sent: 06 October 2008 13:22
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Hello everyone, I have been wrestling with these problems for a
>> while
>>>
>>> too.
>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>> (.avg,
>>> and .eeg), and will read raw data (e,..)from 4D.
>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>> 148-
>>> Channel system co-ordinates. Christian and Don Rojas created one
>> for
>>> me
>>> in early April this year.
>>> A FIF export from the 4D system may also solve this problem.
>> Stephen
>>>
>>> Moratti helped me with this a while a ago. It puts out three
>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>> which
>>> has coordinates for 148 channels does not match with the template,
>>> then
>>> the data will not load. I think for one may have to load a create
>> a
>>> 148
>>> channel template for this purpose. This is my experience with
>> EEGLAB,
>>>
>>> and I think that they underlying engine is the same for both
>> EEGLAB
>>> and
>>> Fieldtrip
>>> Then again, I may be completely wrong about everything except the
>>> templates that were created for me.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>
>>>> Dear all,
>>>>
>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>> sensors). For now, we export original 4D data into BESA format,
>>> and
>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>> gradient
>>>> coils information is not transferred into FieldTrip. We would be
>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>> directly into FieldTrip.
>>>>
>>>>   Best wishes
>>>>   Andrej Stancak
>>>>
>>>>
>>>> Prof. Andrej Stancak, PhD.
>>>> The University of Liverpool
>>>> School of Psychology
>>>> The Eleanor Rathbone Building
>>>> Bedford Street South, Room 209
>>>> Liverpool
>>>> L69 7ZA
>>>>
>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>            stancak at centrum.cz (secondary)
>>>> Phone: 0151 7946951
>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between
>> users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the
>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for
>>> MEG
>>> and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From venug001 at BAMA.UA.EDU  Mon Oct  6 17:03:35 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 6 Oct 2008 10:03:35 -0500
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CB0@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <MON.6.OCT.2008.100335.0500.FIELDTRIP@NIC.SURFNET.NL>

Andrej, I see an error in my mail below. The three files
.xyz, .m4d and the acutal pdf is produced using the command:

pdf2set -u

You post the selection in the propreitary MSI environment, then type in
the command given above. It will put out the three files mentioned for
each data set.
I shall include only the .xyz and .m4d files from grand averaged files,
as they do not contain any identifiable information.
I believe that the .m4d file is also called the header file and
the .xyz is called the location or coordinate file.
Ken Velarde was immensely helpful with this, as were Christian
Weinbruch, and Don Rojas. Don Rojas's colleague Dr. Eugene Kronberg
also has  created an interface that can read 4D data, and he was going
to create such a template as well--as per our last email exchange.
I also have a xls2matlab function that I used to create my own
template, as the sensor location file is usually a product of
individual MEG systems. If I may have mislead anyone it is
unintentional as I am constantly learning.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopa and Almu,
>
>   do I understand the procedure correctly: we should export data from
> 4D in FIF format (currently we export in native e,... (binary), and
> the text files for the header and the surface points), and then use a
> modified xyz file containing the layout of 148 sensors. I would be
> grateful for one sample xyz file to see whether we can read data this
> way. Naturally, the best would be to incorporate it into the reading
> procedures of FieldTrip.
>
> Best wishes
> Andrej
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 14:12
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>
> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>
> the other users. There was also a discussion about whether the
> systems
> were using third order gradiometers and/or magnetometers as the
> reference. There are mail postings in that thread.
> Everyone: I apologize for the typos in my hastily composed response
> earlier.
> regards
> gopa
>
>
> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>
> > Dear Gopa,
> >
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of
> this
> > system.
> >
> > Best,
> > Almu
> >
> > -----Original Message-----
> > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> On
> > Behalf
> > Of Gopakumar Venugopalan
> > Sent: 06 October 2008 13:22
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> >
> > Hello everyone, I have been wrestling with these problems for a
> while
> >
> > too.
> > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > (.avg,
> > and .eeg), and will read raw data (e,..)from 4D.
> > I believe that EEGLAB/Fieldtrip may not have a template for the
> 148-
> > Channel system co-ordinates. Christian and Don Rojas created one
> for
> > me
> > in early April this year.
> > A FIF export from the 4D system may also solve this problem.
> Stephen
> >
> > Moratti helped me with this a while a ago. It puts out three
> > files .xyz, .4D and the original e,.. file. But, if the .xyz file
> > which
> > has coordinates for 148 channels does not match with the template,
> > then
> > the data will not load. I think for one may have to load a create
> a
> > 148
> > channel template for this purpose. This is my experience with
> EEGLAB,
> >
> > and I think that they underlying engine is the same for both
> EEGLAB
> > and
> > Fieldtrip
> > Then again, I may be completely wrong about everything except the
> > templates that were created for me.
> > regards
> > gopa
> >
> >
> > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> >
> > > Dear all,
> > >
> > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > sensors). For now, we export original 4D data into BESA format,
> > and
> > > then read those into FieldTrip. This is not optimal, as e.g.
> > gradient
> > > coils information is not transferred into FieldTrip. We would be
> > > grateful for a plugin or a hint enabling us to read the 4D data
> > > directly into FieldTrip.
> > >
> > >   Best wishes
> > >   Andrej Stancak
> > >
> > >
> > > Prof. Andrej Stancak, PhD.
> > > The University of Liverpool
> > > School of Psychology
> > > The Eleanor Rathbone Building
> > > Bedford Street South, Room 209
> > > Liverpool
> > > L69 7ZA
> > >
> > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > >            stancak at centrum.cz (secondary)
> > > Phone: 0151 7946951
> > > Office hours: Monday 10-12, Wednesday 10-12
> > >
> > >
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the
> > FieldTrip  toolbox, to share experiences and to discuss new ideas
> for
> > MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From A.Stancak at LIVERPOOL.AC.UK  Mon Oct  6 17:45:08 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Mon, 6 Oct 2008 16:45:08 +0100
Subject: 4D data reading
Message-ID: <MON.6.OCT.2008.164508.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Gopa,

 thanks you so much for the files and infomation, I will follow your path, and try what you suggest tomorrow. Jan-Mathijs thinks it should be also possible to read directly from the raw data + config file, and I will try this way too. I will report to the community once I am done as it may be useful for 148-4D researchers.

 Best wishes
 Andrej

Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
Sent: Mon 06/10/2008 16:03
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Andrej, I see an error in my mail below. The three files
.xyz, .m4d and the acutal pdf is produced using the command:

pdf2set -u

You post the selection in the propreitary MSI environment, then type in 
the command given above. It will put out the three files mentioned for 
each data set.
I shall include only the .xyz and .m4d files from grand averaged files, 
as they do not contain any identifiable information.
I believe that the .m4d file is also called the header file and 
the .xyz is called the location or coordinate file.
Ken Velarde was immensely helpful with this, as were Christian 
Weinbruch, and Don Rojas. Don Rojas's colleague Dr. Eugene Kronberg 
also has  created an interface that can read 4D data, and he was going 
to create such a template as well--as per our last email exchange.
I also have a xls2matlab function that I used to create my own 
template, as the sensor location file is usually a product of 
individual MEG systems. If I may have mislead anyone it is 
unintentional as I am constantly learning.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopa and Almu,
> 
>   do I understand the procedure correctly: we should export data from
> 4D in FIF format (currently we export in native e,... (binary), and
> the text files for the header and the surface points), and then use a
> modified xyz file containing the layout of 148 sensors. I would be
> grateful for one sample xyz file to see whether we can read data this
> way. Naturally, the best would be to incorporate it into the reading
> procedures of FieldTrip.
> 
> Best wishes
> Andrej
> 
> 
> Prof. Andrej Stancak, PhD. 
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
> 
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
> 
> 
> 
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 14:12
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>  
> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
> 
> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
> 
> the other users. There was also a discussion about whether the
> systems 
> were using third order gradiometers and/or magnetometers as the 
> reference. There are mail postings in that thread.
> Everyone: I apologize for the typos in my hastily composed response 
> earlier.
> regards
> gopa
> 
> 
> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
> 
> > Dear Gopa,
> > 
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of
> this
> > system.
> > 
> > Best,
> > Almu
> > 
> > -----Original Message-----
> > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> On
> > Behalf
> > Of Gopakumar Venugopalan
> > Sent: 06 October 2008 13:22
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> > 
> > Hello everyone, I have been wrestling with these problems for a
> while
> > 
> > too.
> > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > (.avg, 
> > and .eeg), and will read raw data (e,..)from 4D.
> > I believe that EEGLAB/Fieldtrip may not have a template for the
> 148-
> > Channel system co-ordinates. Christian and Don Rojas created one
> for
> > me 
> > in early April this year.
> > A FIF export from the 4D system may also solve this problem.
> Stephen
> > 
> > Moratti helped me with this a while a ago. It puts out three 
> > files .xyz, .4D and the original e,.. file. But, if the .xyz file
> > which 
> > has coordinates for 148 channels does not match with the template,
> > then 
> > the data will not load. I think for one may have to load a create
> a
> > 148 
> > channel template for this purpose. This is my experience with
> EEGLAB,
> > 
> > and I think that they underlying engine is the same for both
> EEGLAB
> > and 
> > Fieldtrip
> > Then again, I may be completely wrong about everything except the 
> > templates that were created for me.
> > regards
> > gopa
> > 
> > 
> > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> > 
> > > Dear all,
> > > 
> > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > sensors). For now, we export original 4D data into BESA format,
> > and
> > > then read those into FieldTrip. This is not optimal, as e.g.
> > gradient
> > > coils information is not transferred into FieldTrip. We would be
> > > grateful for a plugin or a hint enabling us to read the 4D data
> > > directly into FieldTrip.
> > > 
> > >   Best wishes
> > >   Andrej Stancak
> > > 
> > > 
> > > Prof. Andrej Stancak, PhD. 
> > > The University of Liverpool
> > > School of Psychology
> > > The Eleanor Rathbone Building
> > > Bedford Street South, Room 209
> > > Liverpool
> > > L69 7ZA
> > > 
> > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > >            stancak at centrum.cz (secondary)
> > > Phone: 0151 7946951
> > > Office hours: Monday 10-12, Wednesday 10-12
> > > 
> > > 
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > > 
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the
> > FieldTrip  toolbox, to share experiences and to discuss new ideas
> for
> > MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From A.Stancak at LIVERPOOL.AC.UK  Mon Oct  6 17:50:37 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Mon, 6 Oct 2008 16:50:37 +0100
Subject: 4D data reading
Message-ID: <MON.6.OCT.2008.165037.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs,

  thanks for further information. I need to copy the config file from the MSI server as that is not saved automatically with our
recordings, and then give another try. 

Best wishes
Andrej


Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
Sent: Mon 06/10/2008 15:54
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Dear Andrej, dear Gopa,

Sorry to bother you again, but I tried to make a point in my last  
mail that it is not necessary to intermediately convert your raw  
epoched or continuous 4D-data into another format, prior to be able  
to read it into Fieldtrip. Of course you are free to do so, but the  
most natural way to me would seem to work on the raw datafiles  
directly. Fieldtrip should support this and it has reading routines  
for the raw data-file (beginning with e, or c,), the config-file, and  
the file containing the digitized head-surface positions.
You should be able to obtain the header information directly by  
calling: hdr = read_header('e,thenameofyourrawdatafile') (give or  
take an accidental 'keyboard'-statement in the low-level function  
read_4d_hdr, this will be fixed in tonight's release version: if it  
occurs now, just type dbcont on the command line when it prompts:  
K>>) As far as I know hdr contains a structure grad, which specifies  
the sensor-positions. At least it works on our Glaswegian 248-sensor  
system.

Yours,

Jan-Mathijs


On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:

> Sure will send you those files. Please remember in my files there are
> only 146 channel locations as we turned off two channels.I also have a
> matlab file from Don Rojas for the 148 channel layout and a file which
> he created for the 146 channel layout. Please give some time today, as
> I run those programs on a different machine.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
>> Dear Gopa and Almu,
>>
>>   do I understand the procedure correctly: we should export data from
>> 4D in FIF format (currently we export in native e,... (binary), and
>> the text files for the header and the surface points), and then use a
>> modified xyz file containing the layout of 148 sensors. I would be
>> grateful for one sample xyz file to see whether we can read data this
>> way. Naturally, the best would be to incorporate it into the reading
>> procedures of FieldTrip.
>>
>> Best wishes
>> Andrej
>>
>>
>> Prof. Andrej Stancak, PhD.
>> The University of Liverpool
>> School of Psychology
>> The Eleanor Rathbone Building
>> Bedford Street South, Room 209
>> Liverpool
>> L69 7ZA
>>
>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>            stancak at centrum.cz (secondary)
>> Phone: 0151 7946951
>> Office hours: Monday 10-12, Wednesday 10-12
>>
>>
>>
>> -----Original Message-----
>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>> Sent: Mon 06/10/2008 14:12
>> To: FIELDTRIP at NIC.SURFNET.NL
>> Subject: Re: [FIELDTRIP] 4D data reading
>>
>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>
>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>
>> the other users. There was also a discussion about whether the
>> systems
>> were using third order gradiometers and/or magnetometers as the
>> reference. There are mail postings in that thread.
>> Everyone: I apologize for the typos in my hastily composed response
>> earlier.
>> regards
>> gopa
>>
>>
>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>
>>> Dear Gopa,
>>>
>>> I have got a template for the 4D - 148 channels system. I could
>> give
>>> it to
>>> the Fieldtrip developers if this is helpful for other users of
>> this
>>> system.
>>>
>>> Best,
>>> Almu
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>> On
>>> Behalf
>>> Of Gopakumar Venugopalan
>>> Sent: 06 October 2008 13:22
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Hello everyone, I have been wrestling with these problems for a
>> while
>>>
>>> too.
>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>> (.avg,
>>> and .eeg), and will read raw data (e,..)from 4D.
>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>> 148-
>>> Channel system co-ordinates. Christian and Don Rojas created one
>> for
>>> me
>>> in early April this year.
>>> A FIF export from the 4D system may also solve this problem.
>> Stephen
>>>
>>> Moratti helped me with this a while a ago. It puts out three
>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>> which
>>> has coordinates for 148 channels does not match with the template,
>>> then
>>> the data will not load. I think for one may have to load a create
>> a
>>> 148
>>> channel template for this purpose. This is my experience with
>> EEGLAB,
>>>
>>> and I think that they underlying engine is the same for both
>> EEGLAB
>>> and
>>> Fieldtrip
>>> Then again, I may be completely wrong about everything except the
>>> templates that were created for me.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>
>>>> Dear all,
>>>>
>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>> sensors). For now, we export original 4D data into BESA format,
>>> and
>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>> gradient
>>>> coils information is not transferred into FieldTrip. We would be
>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>> directly into FieldTrip.
>>>>
>>>>   Best wishes
>>>>   Andrej Stancak
>>>>
>>>>
>>>> Prof. Andrej Stancak, PhD.
>>>> The University of Liverpool
>>>> School of Psychology
>>>> The Eleanor Rathbone Building
>>>> Bedford Street South, Room 209
>>>> Liverpool
>>>> L69 7ZA
>>>>
>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>            stancak at centrum.cz (secondary)
>>>> Phone: 0151 7946951
>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between
>> users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the
>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for
>>> MEG
>>> and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users  
> of the FieldTrip  toolbox, to share experiences and to discuss new  
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ 
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From r.oostenveld at FCDONDERS.RU.NL  Tue Oct  7 09:19:29 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Tue, 7 Oct 2008 09:19:29 +0200
Subject: 4D data reading
In-Reply-To: <001001c927b3$e4e14e90$5757d182@DEPT6788A09EF4>
Message-ID: <TUE.7.OCT.2008.091929.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear all,

I have received the layout from Almu and have added the 4D148.lay
layout to the fieldtirp/template directory (where the other layouts
are now also to be found). See attached for how it looks.

thanks,
Robert


On 6 Oct 2008, at 15:02, Almudena Capilla wrote:

> Dear Gopa,
>
> I have got a template for the 4D - 148 channels system. I could give
> it to
> the Fieldtrip developers if this is helpful for other users of this
> system.
>
> Best,
> Almu



----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

From venug001 at BAMA.UA.EDU  Tue Oct  7 13:11:41 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Tue, 7 Oct 2008 06:11:41 -0500
Subject: 4D data reading
In-Reply-To: <5E2A6C3F-3335-4B61-A24E-D608947C471D@fcdonders.ru.nl>
Message-ID: <TUE.7.OCT.2008.061141.0500.FIELDTRIP@NIC.SURFNET.NL>

Dear Almu, Robert, fantastic. Is there anyway this can be incorporated
with EEGLAB? I know that is a separate topic, but as Robert will tell,
EEGLAB uses many Fieldtrip routines. Thanking all of you.
regards
gopa


Quoting Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>:

> Dear all,
>
> I have received the layout from Almu and have added the 4D148.lay
> layout to the fieldtirp/template directory (where the other layouts
>
> are now also to be found). See attached for how it looks.
>
> thanks,
> Robert
>
>
> On 6 Oct 2008, at 15:02, Almudena Capilla wrote:
>
> > Dear Gopa,
> >
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of this
>
> > system.
> >
> > Best,
> > Almu
>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From venug001 at BAMA.UA.EDU  Tue Oct  7 14:26:19 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Tue, 7 Oct 2008 07:26:19 -0500
Subject: 4D data reading
In-Reply-To: <5E2A6C3F-3335-4B61-A24E-D608947C471D@fcdonders.ru.nl>
Message-ID: <TUE.7.OCT.2008.072619.0500.FIELDTRIP@NIC.SURFNET.NL>

Robert, (I know I used to address you more formally than that!), is
there a reason why some channels are a different color than others?
Is there a way that a t-test say NC versus NIC will show up for
significances in Fieldtrip/EEGLAB for all of the 148 channels. I can do
that my dissertation will really look nice. I shall be able to show the
regions where the N400 was significant and contrast it to the regions
where the P600 was significant. Thanks in advance.
regards
gopa

Quoting Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>:

> Dear all,
>
> I have received the layout from Almu and have added the 4D148.lay
> layout to the fieldtirp/template directory (where the other layouts
>
> are now also to be found). See attached for how it looks.
>
> thanks,
> Robert
>
>
> On 6 Oct 2008, at 15:02, Almudena Capilla wrote:
>
> > Dear Gopa,
> >
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of this
>
> > system.
> >
> > Best,
> > Almu
>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From r.oostenveld at FCDONDERS.RU.NL  Tue Oct  7 15:18:47 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Tue, 7 Oct 2008 15:18:47 +0200
Subject: 4D data reading
In-Reply-To: <1223377901.48eb43ed8a08b@bamamail.ua.edu>
Message-ID: <TUE.7.OCT.2008.151847.0200.FIELDTRIP@NIC.SURFNET.NL>

On 7 Oct 2008, at 13:11, Gopakumar Venugopalan wrote:

> Dear Almu, Robert, fantastic. Is there anyway this can be incorporated
> with EEGLAB? I know that is a separate topic, but as Robert will tell,
> EEGLAB uses many Fieldtrip routines. Thanking all of you.
> regards
> gopa

Although EEGLAB also includes a function that goes with the name
"topoplot", just like FIELDTRIP, the two toolboxes do not share any
functionality for plotting. So the answer is no, the 4D148 layout
cannot be used in EEGLAB.

Recent EEGLAB versions (at least the "current" version) do allow to
use the same low level reading functions as used in FieldTrip. That is
done by selecting in eeglab: "file -> import -> from other formats
using fileio". You probably would want to replace the fileio version
included in eeglab with the latest one included in fieldtrip (or
available from http://www2.ru.nl/fcdonders/fieldtrip/doku.php?id=fieldtrip:development:fileio)
.

best regards,
Robert

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From r.oostenveld at FCDONDERS.RU.NL  Tue Oct  7 15:24:45 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Tue, 7 Oct 2008 15:24:45 +0200
Subject: cfg.layout and clusterplot
In-Reply-To: <7F00B6A0D4D0674E80A6C1D6DA873B5701CC652B55@iu-mssg-mbx05.ads.iu.edu>
Message-ID: <TUE.7.OCT.2008.152445.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi

On 6 Oct 2008, at 9:43, Hsu, Shen-Mou wrote:
> I was wondering if someone could help me sort out the following
> problem. I tried to plot significant clusters using clusterplot
> after permutation tests.  When I ran the script as below, it
> returned the message like this:
>
> reverting to 151 channel CTF default

are you working with 151 channel CTF data. If not, then this explains
it.

> ??? Error using ==> topoplotER at 330
> labels in data and labels in layout do not match
>
> Error in ==> clusterplot at 240
>          topoplotER(cfg, stat);
>
> However, I checked both cfg.layout.labels and cfg.layout.pnt.
> Everything seems fine.

You might want to check with the matlab debugger that the COMNT and
SCALE are not messing it up. These two fake channels are included in
the layout files to position the comment and scale. Recently quite
some changes were made to plotting, so you might also want to download
the latest version to test whether the problem persists.

best regards,
Robert

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From A.Stancak at LIVERPOOL.AC.UK  Tue Oct  7 17:44:22 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Tue, 7 Oct 2008 16:44:22 +0100
Subject: 4D data reading
Message-ID: <TUE.7.OCT.2008.164422.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Gopakumar,

  I followed your advice (pdf2set -u), and was almost successful in reading the 4d-148 data into FieldTrip. 
I can read header all right with exception of one line that turns out to be decisive during reading data (read_data):

D=read_data ('d:\data\meg\windup\T1\2\c,rfdc','dataformat','4d');
??? Reference to non-existent field 'ChannelUnitsPerBit'.

Error in ==> read_data at 477
    upb        = hdr.orig.ChannelUnitsPerBit;


Clearly, we miss the field ChannelUnitsPerBit in hdr.orig structure. As read_event.m also calls read_data.m, this problem precludes reading events as well.

To test the rest of the code, I simply put upb = grad (grad is 1 line above in read_data) and then it works all very well (as grad is equal to 1 in all channel fields). So my hope is that if we can sort out the missing field in hdr.orig., we will be able to read all data very well. 
 
I would be grateful for a hint here as have no idea how can we miss that field.

Best wishes
Andrej




Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
Sent: Mon 06/10/2008 16:03
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Andrej, I see an error in my mail below. The three files
.xyz, .m4d and the acutal pdf is produced using the command:

pdf2set -u

You post the selection in the propreitary MSI environment, then type in 
the command given above. It will put out the three files mentioned for 
each data set.
I shall include only the .xyz and .m4d files from grand averaged files, 
as they do not contain any identifiable information.
I believe that the .m4d file is also called the header file and 
the .xyz is called the location or coordinate file.
Ken Velarde was immensely helpful with this, as were Christian 
Weinbruch, and Don Rojas. Don Rojas's colleague Dr. Eugene Kronberg 
also has  created an interface that can read 4D data, and he was going 
to create such a template as well--as per our last email exchange.
I also have a xls2matlab function that I used to create my own 
template, as the sensor location file is usually a product of 
individual MEG systems. If I may have mislead anyone it is 
unintentional as I am constantly learning.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopa and Almu,
> 
>   do I understand the procedure correctly: we should export data from
> 4D in FIF format (currently we export in native e,... (binary), and
> the text files for the header and the surface points), and then use a
> modified xyz file containing the layout of 148 sensors. I would be
> grateful for one sample xyz file to see whether we can read data this
> way. Naturally, the best would be to incorporate it into the reading
> procedures of FieldTrip.
> 
> Best wishes
> Andrej
> 
> 
> Prof. Andrej Stancak, PhD. 
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
> 
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
> 
> 
> 
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 14:12
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>  
> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
> 
> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
> 
> the other users. There was also a discussion about whether the
> systems 
> were using third order gradiometers and/or magnetometers as the 
> reference. There are mail postings in that thread.
> Everyone: I apologize for the typos in my hastily composed response 
> earlier.
> regards
> gopa
> 
> 
> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
> 
> > Dear Gopa,
> > 
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of
> this
> > system.
> > 
> > Best,
> > Almu
> > 
> > -----Original Message-----
> > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> On
> > Behalf
> > Of Gopakumar Venugopalan
> > Sent: 06 October 2008 13:22
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> > 
> > Hello everyone, I have been wrestling with these problems for a
> while
> > 
> > too.
> > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > (.avg, 
> > and .eeg), and will read raw data (e,..)from 4D.
> > I believe that EEGLAB/Fieldtrip may not have a template for the
> 148-
> > Channel system co-ordinates. Christian and Don Rojas created one
> for
> > me 
> > in early April this year.
> > A FIF export from the 4D system may also solve this problem.
> Stephen
> > 
> > Moratti helped me with this a while a ago. It puts out three 
> > files .xyz, .4D and the original e,.. file. But, if the .xyz file
> > which 
> > has coordinates for 148 channels does not match with the template,
> > then 
> > the data will not load. I think for one may have to load a create
> a
> > 148 
> > channel template for this purpose. This is my experience with
> EEGLAB,
> > 
> > and I think that they underlying engine is the same for both
> EEGLAB
> > and 
> > Fieldtrip
> > Then again, I may be completely wrong about everything except the 
> > templates that were created for me.
> > regards
> > gopa
> > 
> > 
> > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> > 
> > > Dear all,
> > > 
> > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > sensors). For now, we export original 4D data into BESA format,
> > and
> > > then read those into FieldTrip. This is not optimal, as e.g.
> > gradient
> > > coils information is not transferred into FieldTrip. We would be
> > > grateful for a plugin or a hint enabling us to read the 4D data
> > > directly into FieldTrip.
> > > 
> > >   Best wishes
> > >   Andrej Stancak
> > > 
> > > 
> > > Prof. Andrej Stancak, PhD. 
> > > The University of Liverpool
> > > School of Psychology
> > > The Eleanor Rathbone Building
> > > Bedford Street South, Room 209
> > > Liverpool
> > > L69 7ZA
> > > 
> > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > >            stancak at centrum.cz (secondary)
> > > Phone: 0151 7946951
> > > Office hours: Monday 10-12, Wednesday 10-12
> > > 
> > > 
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > > 
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the
> > FieldTrip  toolbox, to share experiences and to discuss new ideas
> for
> > MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
> 


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From venug001 at BAMA.UA.EDU  Tue Oct  7 18:22:23 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Tue, 7 Oct 2008 11:22:23 -0500
Subject: 4D data reading
In-Reply-To: <45FEBCBE11DAC142A421BF00CBC7349D01831CBF@EVSSTAFF2.livad.liv.ac.uk>
Message-ID: <TUE.7.OCT.2008.112223.0500.FIELDTRIP@NIC.SURFNET.NL>

Andrew, I am glad. Thanks to Ken and  and Stephen's assistant. I have
not tweaked around with Cupb settings myself. I would defer that to
folks like Robert, Stephen or Christian. I don't know if Ken is on this
listserv, but I know that he likes to keep up with anything that is 4D
related. I can help with any thing else if I can.
regards
gopa


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Gopakumar,
>
>   I followed your advice (pdf2set -u), and was almost successful in
> reading the 4d-148 data into FieldTrip.
> I can read header all right with exception of one line that turns out
> to be decisive during reading data (read_data):
>
> D=read_data ('d:\data\meg\windup\T1\2\c,rfdc','dataformat','4d');
> ??? Reference to non-existent field 'ChannelUnitsPerBit'.
>
> Error in ==> read_data at 477
>     upb        = hdr.orig.ChannelUnitsPerBit;
>
>
> Clearly, we miss the field ChannelUnitsPerBit in hdr.orig structure.
> As read_event.m also calls read_data.m, this problem precludes
> reading events as well.
>
> To test the rest of the code, I simply put upb = grad (grad is 1 line
> above in read_data) and then it works all very well (as grad is equal
> to 1 in all channel fields). So my hope is that if we can sort out
> the missing field in hdr.orig., we will be able to read all data very
> well.
>
> I would be grateful for a hint here as have no idea how can we miss
> that field.
>
> Best wishes
> Andrej
>
>
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 16:03
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Andrej, I see an error in my mail below. The three files
> .xyz, .m4d and the acutal pdf is produced using the command:
>
> pdf2set -u
>
> You post the selection in the propreitary MSI environment, then type
> in
> the command given above. It will put out the three files mentioned
> for
> each data set.
> I shall include only the .xyz and .m4d files from grand averaged
> files,
> as they do not contain any identifiable information.
> I believe that the .m4d file is also called the header file and
> the .xyz is called the location or coordinate file.
> Ken Velarde was immensely helpful with this, as were Christian
> Weinbruch, and Don Rojas. Don Rojas's colleague Dr. Eugene Kronberg
> also has  created an interface that can read 4D data, and he was
> going
> to create such a template as well--as per our last email exchange.
> I also have a xls2matlab function that I used to create my own
> template, as the sensor location file is usually a product of
> individual MEG systems. If I may have mislead anyone it is
> unintentional as I am constantly learning.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
> > Dear Gopa and Almu,
> >
> >   do I understand the procedure correctly: we should export data
> from
> > 4D in FIF format (currently we export in native e,... (binary),
> and
> > the text files for the header and the surface points), and then use
> a
> > modified xyz file containing the layout of 148 sensors. I would be
> > grateful for one sample xyz file to see whether we can read data
> this
> > way. Naturally, the best would be to incorporate it into the
> reading
> > procedures of FieldTrip.
> >
> > Best wishes
> > Andrej
> >
> >
> > Prof. Andrej Stancak, PhD.
> > The University of Liverpool
> > School of Psychology
> > The Eleanor Rathbone Building
> > Bedford Street South, Room 209
> > Liverpool
> > L69 7ZA
> >
> > E:mail: a.stancak at liverpool.ac.uk  (primary)
> >            stancak at centrum.cz (secondary)
> > Phone: 0151 7946951
> > Office hours: Monday 10-12, Wednesday 10-12
> >
> >
> >
> > -----Original Message-----
> > From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> > Sent: Mon 06/10/2008 14:12
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> >
> > Dear Almu (that is a nice name!) thank you  Rob Oostenveld,
> Christian
> >
> > Weinbruch and Arno (EEGLAB) may be the ones who can make it work
> for
> >
> > the other users. There was also a discussion about whether the
> > systems
> > were using third order gradiometers and/or magnetometers as the
> > reference. There are mail postings in that thread.
> > Everyone: I apologize for the typos in my hastily composed response
>
> > earlier.
> > regards
> > gopa
> >
> >
> > Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
> >
> > > Dear Gopa,
> > >
> > > I have got a template for the 4D - 148 channels system. I could
> > give
> > > it to
> > > the Fieldtrip developers if this is helpful for other users of
> > this
> > > system.
> > >
> > > Best,
> > > Almu
> > >
> > > -----Original Message-----
> > > From: FieldTrip discussion list
> [mailto:FIELDTRIP at NIC.SURFNET.NL]
> > On
> > > Behalf
> > > Of Gopakumar Venugopalan
> > > Sent: 06 October 2008 13:22
> > > To: FIELDTRIP at NIC.SURFNET.NL
> > > Subject: Re: [FIELDTRIP] 4D data reading
> > >
> > > Hello everyone, I have been wrestling with these problems for a
> > while
> > >
> > > too.
> > > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > > (.avg,
> > > and .eeg), and will read raw data (e,..)from 4D.
> > > I believe that EEGLAB/Fieldtrip may not have a template for the
> > 148-
> > > Channel system co-ordinates. Christian and Don Rojas created one
> > for
> > > me
> > > in early April this year.
> > > A FIF export from the 4D system may also solve this problem.
> > Stephen
> > >
> > > Moratti helped me with this a while a ago. It puts out three
> > > files .xyz, .4D and the original e,.. file. But, if the .xyz
> file
> > > which
> > > has coordinates for 148 channels does not match with the
> template,
> > > then
> > > the data will not load. I think for one may have to load a
> create
> > a
> > > 148
> > > channel template for this purpose. This is my experience with
> > EEGLAB,
> > >
> > > and I think that they underlying engine is the same for both
> > EEGLAB
> > > and
> > > Fieldtrip
> > > Then again, I may be completely wrong about everything except the
>
> > > templates that were created for me.
> > > regards
> > > gopa
> > >
> > >
> > > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> > >
> > > > Dear all,
> > > >
> > > >   we have some problems reading 4D Neuroimaging MEG data (148
> > > > sensors). For now, we export original 4D data into BESA
> format,
> > > and
> > > > then read those into FieldTrip. This is not optimal, as e.g.
> > > gradient
> > > > coils information is not transferred into FieldTrip. We would
> be
> > > > grateful for a plugin or a hint enabling us to read the 4D
> data
> > > > directly into FieldTrip.
> > > >
> > > >   Best wishes
> > > >   Andrej Stancak
> > > >
> > > >
> > > > Prof. Andrej Stancak, PhD.
> > > > The University of Liverpool
> > > > School of Psychology
> > > > The Eleanor Rathbone Building
> > > > Bedford Street South, Room 209
> > > > Liverpool
> > > > L69 7ZA
> > > >
> > > > E:mail: a.stancak at liverpool.ac.uk  (primary)
> > > >            stancak at centrum.cz (secondary)
> > > > Phone: 0151 7946951
> > > > Office hours: Monday 10-12, Wednesday 10-12
> > > >
> > > >
> > > > ----------------------------------
> > > > The aim of this list is to facilitate the discussion between
> > users
> > > of
> > > > the FieldTrip  toolbox, to share experiences and to discuss
> new
> > > ideas
> > > > for MEG and EEG analysis. See also
> > > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > > http://www.ru.nl/fcdonders/fieldtrip.
> > > >
> > >
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the
> > > FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for
> > > MEG
> > > and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > >
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip  toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From A.Stancak at LIVERPOOL.AC.UK  Tue Oct  7 18:40:04 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Tue, 7 Oct 2008 17:40:04 +0100
Subject: 4D data reading
Message-ID: <TUE.7.OCT.2008.174004.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs,

  I have followed your path (in parallel to the one suggested by Gopakumar) and it worked. It took me a while to dig out the configuration file in the MSI server and to realise it needs to be renamed and put into the data directory, but it works now. 

  As you write, the procedures change the prompt to K:> and continue after typing dbcont. I do not mind this if it is for once, but what about running batch files? Or is the idea to read data, the header, and the events and then save all for further processing in some different format (e.g. Matlab?). I work with the FieldTrip_20051006 version that I downloaded today, and I do not know whether it has been fixed or whether this feature (K:> dbcont) will stay.

Thank you for your advice. Thanks to you and Gopakumar and few other colleagues we are now close to smooth reading our MEG data into FieldTrip.

 Best wishes
 Andrej

Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
Sent: Mon 06/10/2008 15:54
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Dear Andrej, dear Gopa,

Sorry to bother you again, but I tried to make a point in my last  
mail that it is not necessary to intermediately convert your raw  
epoched or continuous 4D-data into another format, prior to be able  
to read it into Fieldtrip. Of course you are free to do so, but the  
most natural way to me would seem to work on the raw datafiles  
directly. Fieldtrip should support this and it has reading routines  
for the raw data-file (beginning with e, or c,), the config-file, and  
the file containing the digitized head-surface positions.
You should be able to obtain the header information directly by  
calling: hdr = read_header('e,thenameofyourrawdatafile') (give or  
take an accidental 'keyboard'-statement in the low-level function  
read_4d_hdr, this will be fixed in tonight's release version: if it  
occurs now, just type dbcont on the command line when it prompts:  
K>>) As far as I know hdr contains a structure grad, which specifies  
the sensor-positions. At least it works on our Glaswegian 248-sensor  
system.

Yours,

Jan-Mathijs


On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:

> Sure will send you those files. Please remember in my files there are
> only 146 channel locations as we turned off two channels.I also have a
> matlab file from Don Rojas for the 148 channel layout and a file which
> he created for the 146 channel layout. Please give some time today, as
> I run those programs on a different machine.
> regards
> gopa
>
>
> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>
>> Dear Gopa and Almu,
>>
>>   do I understand the procedure correctly: we should export data from
>> 4D in FIF format (currently we export in native e,... (binary), and
>> the text files for the header and the surface points), and then use a
>> modified xyz file containing the layout of 148 sensors. I would be
>> grateful for one sample xyz file to see whether we can read data this
>> way. Naturally, the best would be to incorporate it into the reading
>> procedures of FieldTrip.
>>
>> Best wishes
>> Andrej
>>
>>
>> Prof. Andrej Stancak, PhD.
>> The University of Liverpool
>> School of Psychology
>> The Eleanor Rathbone Building
>> Bedford Street South, Room 209
>> Liverpool
>> L69 7ZA
>>
>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>            stancak at centrum.cz (secondary)
>> Phone: 0151 7946951
>> Office hours: Monday 10-12, Wednesday 10-12
>>
>>
>>
>> -----Original Message-----
>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>> Sent: Mon 06/10/2008 14:12
>> To: FIELDTRIP at NIC.SURFNET.NL
>> Subject: Re: [FIELDTRIP] 4D data reading
>>
>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>
>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>
>> the other users. There was also a discussion about whether the
>> systems
>> were using third order gradiometers and/or magnetometers as the
>> reference. There are mail postings in that thread.
>> Everyone: I apologize for the typos in my hastily composed response
>> earlier.
>> regards
>> gopa
>>
>>
>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>
>>> Dear Gopa,
>>>
>>> I have got a template for the 4D - 148 channels system. I could
>> give
>>> it to
>>> the Fieldtrip developers if this is helpful for other users of
>> this
>>> system.
>>>
>>> Best,
>>> Almu
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>> On
>>> Behalf
>>> Of Gopakumar Venugopalan
>>> Sent: 06 October 2008 13:22
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Hello everyone, I have been wrestling with these problems for a
>> while
>>>
>>> too.
>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>> (.avg,
>>> and .eeg), and will read raw data (e,..)from 4D.
>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>> 148-
>>> Channel system co-ordinates. Christian and Don Rojas created one
>> for
>>> me
>>> in early April this year.
>>> A FIF export from the 4D system may also solve this problem.
>> Stephen
>>>
>>> Moratti helped me with this a while a ago. It puts out three
>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>> which
>>> has coordinates for 148 channels does not match with the template,
>>> then
>>> the data will not load. I think for one may have to load a create
>> a
>>> 148
>>> channel template for this purpose. This is my experience with
>> EEGLAB,
>>>
>>> and I think that they underlying engine is the same for both
>> EEGLAB
>>> and
>>> Fieldtrip
>>> Then again, I may be completely wrong about everything except the
>>> templates that were created for me.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>
>>>> Dear all,
>>>>
>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>> sensors). For now, we export original 4D data into BESA format,
>>> and
>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>> gradient
>>>> coils information is not transferred into FieldTrip. We would be
>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>> directly into FieldTrip.
>>>>
>>>>   Best wishes
>>>>   Andrej Stancak
>>>>
>>>>
>>>> Prof. Andrej Stancak, PhD.
>>>> The University of Liverpool
>>>> School of Psychology
>>>> The Eleanor Rathbone Building
>>>> Bedford Street South, Room 209
>>>> Liverpool
>>>> L69 7ZA
>>>>
>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>            stancak at centrum.cz (secondary)
>>>> Phone: 0151 7946951
>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between
>> users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the
>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for
>>> MEG
>>> and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>> of
>>> the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of
>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users  
> of the FieldTrip  toolbox, to share experiences and to discuss new  
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ 
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From j.schoffelen at PSY.GLA.AC.UK  Tue Oct  7 19:58:32 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Tue, 7 Oct 2008 18:58:32 +0100
Subject: 4D data reading
Message-ID: <TUE.7.OCT.2008.185832.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Andrej,

I am glad it works now. The keyboard statement in the code (leading to  
K>>) was just to debug some code. I forgot to clear it when I was  
done. I fixed it yesterday, and it should be correct in the latest  
version of fieldtrip (20081007). The idea is certainly not to read the  
events/header/data only once, store it, and refer to it for later use.  
However, depending on what you want, it could be useful (I often save  
my trial definitions after artifact rejection because this is a time  
consuming step). Hopefully you can run batch with the keyboard  
statement removed.
As far as I understood from the formatting of the data coming from our  
248-channel system, each recording is automatically saved with a  
config-file, which is a copy of the system config-file, and which is  
adjusted with run-specific parameters (most importantly weight tables  
for the denoising, and filter setting (I am not entirely sure about  
the filter settings). Anyway, as it is programmed at the moment, the  
code assumes the run-specific config file to be present in the  
run-directory, and it assumes the file to be named 'config'. This of  
course can be made a bit more flexible (for example one could provide  
an explicit path/filename to the system's config file).
Do I understand correctly, that the data you record does not generally  
contain a config-file in the data-directories themselves?

Yours,

Jan-Mathijs


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Jan-Mathijs,
>
>   I have followed your path (in parallel to the one suggested by   
> Gopakumar) and it worked. It took me a while to dig out the   
> configuration file in the MSI server and to realise it needs to be   
> renamed and put into the data directory, but it works now.
>
>   As you write, the procedures change the prompt to K:> and continue  
>  after typing dbcont. I do not mind this if it is for once, but what  
>  about running batch files? Or is the idea to read data, the header,  
>  and the events and then save all for further processing in some   
> different format (e.g. Matlab?). I work with the FieldTrip_20051006   
> version that I downloaded today, and I do not know whether it has   
> been fixed or whether this feature (K:> dbcont) will stay.
>
> Thank you for your advice. Thanks to you and Gopakumar and few other  
>  colleagues we are now close to smooth reading our MEG data into   
> FieldTrip.
>
>  Best wishes
>  Andrej
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
> Sent: Mon 06/10/2008 15:54
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Dear Andrej, dear Gopa,
>
> Sorry to bother you again, but I tried to make a point in my last
> mail that it is not necessary to intermediately convert your raw
> epoched or continuous 4D-data into another format, prior to be able
> to read it into Fieldtrip. Of course you are free to do so, but the
> most natural way to me would seem to work on the raw datafiles
> directly. Fieldtrip should support this and it has reading routines
> for the raw data-file (beginning with e, or c,), the config-file, and
> the file containing the digitized head-surface positions.
> You should be able to obtain the header information directly by
> calling: hdr = read_header('e,thenameofyourrawdatafile') (give or
> take an accidental 'keyboard'-statement in the low-level function
> read_4d_hdr, this will be fixed in tonight's release version: if it
> occurs now, just type dbcont on the command line when it prompts:
> K>>) As far as I know hdr contains a structure grad, which specifies
> the sensor-positions. At least it works on our Glaswegian 248-sensor
> system.
>
> Yours,
>
> Jan-Mathijs
>
>
> On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:
>
>> Sure will send you those files. Please remember in my files there are
>> only 146 channel locations as we turned off two channels.I also have a
>> matlab file from Don Rojas for the 148 channel layout and a file which
>> he created for the 146 channel layout. Please give some time today, as
>> I run those programs on a different machine.
>> regards
>> gopa
>>
>>
>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>
>>> Dear Gopa and Almu,
>>>
>>>   do I understand the procedure correctly: we should export data from
>>> 4D in FIF format (currently we export in native e,... (binary), and
>>> the text files for the header and the surface points), and then use a
>>> modified xyz file containing the layout of 148 sensors. I would be
>>> grateful for one sample xyz file to see whether we can read data this
>>> way. Naturally, the best would be to incorporate it into the reading
>>> procedures of FieldTrip.
>>>
>>> Best wishes
>>> Andrej
>>>
>>>
>>> Prof. Andrej Stancak, PhD.
>>> The University of Liverpool
>>> School of Psychology
>>> The Eleanor Rathbone Building
>>> Bedford Street South, Room 209
>>> Liverpool
>>> L69 7ZA
>>>
>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>            stancak at centrum.cz (secondary)
>>> Phone: 0151 7946951
>>> Office hours: Monday 10-12, Wednesday 10-12
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>>> Sent: Mon 06/10/2008 14:12
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>>
>>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>>
>>> the other users. There was also a discussion about whether the
>>> systems
>>> were using third order gradiometers and/or magnetometers as the
>>> reference. There are mail postings in that thread.
>>> Everyone: I apologize for the typos in my hastily composed response
>>> earlier.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>>
>>>> Dear Gopa,
>>>>
>>>> I have got a template for the 4D - 148 channels system. I could
>>> give
>>>> it to
>>>> the Fieldtrip developers if this is helpful for other users of
>>> this
>>>> system.
>>>>
>>>> Best,
>>>> Almu
>>>>
>>>> -----Original Message-----
>>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>>> On
>>>> Behalf
>>>> Of Gopakumar Venugopalan
>>>> Sent: 06 October 2008 13:22
>>>> To: FIELDTRIP at NIC.SURFNET.NL
>>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>>
>>>> Hello everyone, I have been wrestling with these problems for a
>>> while
>>>>
>>>> too.
>>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>>> (.avg,
>>>> and .eeg), and will read raw data (e,..)from 4D.
>>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>>> 148-
>>>> Channel system co-ordinates. Christian and Don Rojas created one
>>> for
>>>> me
>>>> in early April this year.
>>>> A FIF export from the 4D system may also solve this problem.
>>> Stephen
>>>>
>>>> Moratti helped me with this a while a ago. It puts out three
>>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>>> which
>>>> has coordinates for 148 channels does not match with the template,
>>>> then
>>>> the data will not load. I think for one may have to load a create
>>> a
>>>> 148
>>>> channel template for this purpose. This is my experience with
>>> EEGLAB,
>>>>
>>>> and I think that they underlying engine is the same for both
>>> EEGLAB
>>>> and
>>>> Fieldtrip
>>>> Then again, I may be completely wrong about everything except the
>>>> templates that were created for me.
>>>> regards
>>>> gopa
>>>>
>>>>
>>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>>
>>>>> Dear all,
>>>>>
>>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>>> sensors). For now, we export original 4D data into BESA format,
>>>> and
>>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>>> gradient
>>>>> coils information is not transferred into FieldTrip. We would be
>>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>>> directly into FieldTrip.
>>>>>
>>>>>   Best wishes
>>>>>   Andrej Stancak
>>>>>
>>>>>
>>>>> Prof. Andrej Stancak, PhD.
>>>>> The University of Liverpool
>>>>> School of Psychology
>>>>> The Eleanor Rathbone Building
>>>>> Bedford Street South, Room 209
>>>>> Liverpool
>>>>> L69 7ZA
>>>>>
>>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>>            stancak at centrum.cz (secondary)
>>>>> Phone: 0151 7946951
>>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>>
>>>>>
>>>>> ----------------------------------
>>>>> The aim of this list is to facilitate the discussion between
>>> users
>>>> of
>>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>>> ideas
>>>>> for MEG and EEG analysis. See also
>>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between users
>>> of
>>>> the
>>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for
>>>> MEG
>>>> and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of
>>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of
>>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
>> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users   
> of the FieldTrip  toolbox, to share experiences and to discuss new   
> ideas for MEG and EEG analysis. See also   
> http://listserv.surfnet.nl/archives/fieldtrip.html and   
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users   
> of the FieldTrip  toolbox, to share experiences and to discuss new   
> ideas for MEG and EEG analysis. See also   
> http://listserv.surfnet.nl/archives/fieldtrip.html and   
> http://www.ru.nl/fcdonders/fieldtrip.
>



------------------------------------------------------------------
The University of Glasgow, Department of Psychology WebMail system
------------------------------------------------------------------

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From A.Stancak at LIVERPOOL.AC.UK  Wed Oct  8 15:07:40 2008
From: A.Stancak at LIVERPOOL.AC.UK (Stancak, Andrej)
Date: Wed, 8 Oct 2008 14:07:40 +0100
Subject: 4D data reading
Message-ID: <WED.8.OCT.2008.140740.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs,

  thanks for your e-mail and further information. It turned out that the archive data I used for testing the data reading did not have a config file, and neither it is displayed in the MSI window in the list of posted/non-posted files so I was not sure where to find it. Today I have exported data using the MSI disk/tape utilities, and the config file was there as it should be.  

I have now tested reading the 4D files with a correct config file on board and it worked well. I still have to do "dbcont" but this is a small cosmetic issue compared to the way we handled data before. Again many thanks for your advice and information.

 With best wishes
 Andrej

   


  

Prof. Andrej Stancak, PhD. 
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA

E:mail: a.stancak at liverpool.ac.uk  (primary)
           stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12



-----Original Message-----
From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
Sent: Tue 07/10/2008 18:58
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
 
Dear Andrej,

I am glad it works now. The keyboard statement in the code (leading to  
K>>) was just to debug some code. I forgot to clear it when I was  
done. I fixed it yesterday, and it should be correct in the latest  
version of fieldtrip (20081007). The idea is certainly not to read the  
events/header/data only once, store it, and refer to it for later use.  
However, depending on what you want, it could be useful (I often save  
my trial definitions after artifact rejection because this is a time  
consuming step). Hopefully you can run batch with the keyboard  
statement removed.
As far as I understood from the formatting of the data coming from our  
248-channel system, each recording is automatically saved with a  
config-file, which is a copy of the system config-file, and which is  
adjusted with run-specific parameters (most importantly weight tables  
for the denoising, and filter setting (I am not entirely sure about  
the filter settings). Anyway, as it is programmed at the moment, the  
code assumes the run-specific config file to be present in the  
run-directory, and it assumes the file to be named 'config'. This of  
course can be made a bit more flexible (for example one could provide  
an explicit path/filename to the system's config file).
Do I understand correctly, that the data you record does not generally  
contain a config-file in the data-directories themselves?

Yours,

Jan-Mathijs


Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:

> Dear Jan-Mathijs,
>
>   I have followed your path (in parallel to the one suggested by   
> Gopakumar) and it worked. It took me a while to dig out the   
> configuration file in the MSI server and to realise it needs to be   
> renamed and put into the data directory, but it works now.
>
>   As you write, the procedures change the prompt to K:> and continue  
>  after typing dbcont. I do not mind this if it is for once, but what  
>  about running batch files? Or is the idea to read data, the header,  
>  and the events and then save all for further processing in some   
> different format (e.g. Matlab?). I work with the FieldTrip_20051006   
> version that I downloaded today, and I do not know whether it has   
> been fixed or whether this feature (K:> dbcont) will stay.
>
> Thank you for your advice. Thanks to you and Gopakumar and few other  
>  colleagues we are now close to smooth reading our MEG data into   
> FieldTrip.
>
>  Best wishes
>  Andrej
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk  (primary)
>            stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of jan-mathijs schoffelen
> Sent: Mon 06/10/2008 15:54
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Dear Andrej, dear Gopa,
>
> Sorry to bother you again, but I tried to make a point in my last
> mail that it is not necessary to intermediately convert your raw
> epoched or continuous 4D-data into another format, prior to be able
> to read it into Fieldtrip. Of course you are free to do so, but the
> most natural way to me would seem to work on the raw datafiles
> directly. Fieldtrip should support this and it has reading routines
> for the raw data-file (beginning with e, or c,), the config-file, and
> the file containing the digitized head-surface positions.
> You should be able to obtain the header information directly by
> calling: hdr = read_header('e,thenameofyourrawdatafile') (give or
> take an accidental 'keyboard'-statement in the low-level function
> read_4d_hdr, this will be fixed in tonight's release version: if it
> occurs now, just type dbcont on the command line when it prompts:
> K>>) As far as I know hdr contains a structure grad, which specifies
> the sensor-positions. At least it works on our Glaswegian 248-sensor
> system.
>
> Yours,
>
> Jan-Mathijs
>
>
> On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:
>
>> Sure will send you those files. Please remember in my files there are
>> only 146 channel locations as we turned off two channels.I also have a
>> matlab file from Don Rojas for the 148 channel layout and a file which
>> he created for the 146 channel layout. Please give some time today, as
>> I run those programs on a different machine.
>> regards
>> gopa
>>
>>
>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>
>>> Dear Gopa and Almu,
>>>
>>>   do I understand the procedure correctly: we should export data from
>>> 4D in FIF format (currently we export in native e,... (binary), and
>>> the text files for the header and the surface points), and then use a
>>> modified xyz file containing the layout of 148 sensors. I would be
>>> grateful for one sample xyz file to see whether we can read data this
>>> way. Naturally, the best would be to incorporate it into the reading
>>> procedures of FieldTrip.
>>>
>>> Best wishes
>>> Andrej
>>>
>>>
>>> Prof. Andrej Stancak, PhD.
>>> The University of Liverpool
>>> School of Psychology
>>> The Eleanor Rathbone Building
>>> Bedford Street South, Room 209
>>> Liverpool
>>> L69 7ZA
>>>
>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>            stancak at centrum.cz (secondary)
>>> Phone: 0151 7946951
>>> Office hours: Monday 10-12, Wednesday 10-12
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
>>> Sent: Mon 06/10/2008 14:12
>>> To: FIELDTRIP at NIC.SURFNET.NL
>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>
>>> Dear Almu (that is a nice name!) thank you  Rob Oostenveld, Christian
>>>
>>> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>>>
>>> the other users. There was also a discussion about whether the
>>> systems
>>> were using third order gradiometers and/or magnetometers as the
>>> reference. There are mail postings in that thread.
>>> Everyone: I apologize for the typos in my hastily composed response
>>> earlier.
>>> regards
>>> gopa
>>>
>>>
>>> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>>>
>>>> Dear Gopa,
>>>>
>>>> I have got a template for the 4D - 148 channels system. I could
>>> give
>>>> it to
>>>> the Fieldtrip developers if this is helpful for other users of
>>> this
>>>> system.
>>>>
>>>> Best,
>>>> Almu
>>>>
>>>> -----Original Message-----
>>>> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
>>> On
>>>> Behalf
>>>> Of Gopakumar Venugopalan
>>>> Sent: 06 October 2008 13:22
>>>> To: FIELDTRIP at NIC.SURFNET.NL
>>>> Subject: Re: [FIELDTRIP] 4D data reading
>>>>
>>>> Hello everyone, I have been wrestling with these problems for a
>>> while
>>>>
>>>> too.
>>>> Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
>>>> (.avg,
>>>> and .eeg), and will read raw data (e,..)from 4D.
>>>> I believe that EEGLAB/Fieldtrip may not have a template for the
>>> 148-
>>>> Channel system co-ordinates. Christian and Don Rojas created one
>>> for
>>>> me
>>>> in early April this year.
>>>> A FIF export from the 4D system may also solve this problem.
>>> Stephen
>>>>
>>>> Moratti helped me with this a while a ago. It puts out three
>>>> files .xyz, .4D and the original e,.. file. But, if the .xyz file
>>>> which
>>>> has coordinates for 148 channels does not match with the template,
>>>> then
>>>> the data will not load. I think for one may have to load a create
>>> a
>>>> 148
>>>> channel template for this purpose. This is my experience with
>>> EEGLAB,
>>>>
>>>> and I think that they underlying engine is the same for both
>>> EEGLAB
>>>> and
>>>> Fieldtrip
>>>> Then again, I may be completely wrong about everything except the
>>>> templates that were created for me.
>>>> regards
>>>> gopa
>>>>
>>>>
>>>> Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
>>>>
>>>>> Dear all,
>>>>>
>>>>>   we have some problems reading 4D Neuroimaging MEG data (148
>>>>> sensors). For now, we export original 4D data into BESA format,
>>>> and
>>>>> then read those into FieldTrip. This is not optimal, as e.g.
>>>> gradient
>>>>> coils information is not transferred into FieldTrip. We would be
>>>>> grateful for a plugin or a hint enabling us to read the 4D data
>>>>> directly into FieldTrip.
>>>>>
>>>>>   Best wishes
>>>>>   Andrej Stancak
>>>>>
>>>>>
>>>>> Prof. Andrej Stancak, PhD.
>>>>> The University of Liverpool
>>>>> School of Psychology
>>>>> The Eleanor Rathbone Building
>>>>> Bedford Street South, Room 209
>>>>> Liverpool
>>>>> L69 7ZA
>>>>>
>>>>> E:mail: a.stancak at liverpool.ac.uk  (primary)
>>>>>            stancak at centrum.cz (secondary)
>>>>> Phone: 0151 7946951
>>>>> Office hours: Monday 10-12, Wednesday 10-12
>>>>>
>>>>>
>>>>> ----------------------------------
>>>>> The aim of this list is to facilitate the discussion between
>>> users
>>>> of
>>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>>> ideas
>>>>> for MEG and EEG analysis. See also
>>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>>
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between users
>>> of
>>>> the
>>>> FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for
>>>> MEG
>>>> and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between users
>>> of
>>>> the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas
>>>> for MEG and EEG analysis. See also
>>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of
>>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of
>>> the FieldTrip  toolbox, to share experiences and to discuss new ideas
>>> for MEG and EEG analysis. See also
>>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
>> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users   
> of the FieldTrip  toolbox, to share experiences and to discuss new   
> ideas for MEG and EEG analysis. See also   
> http://listserv.surfnet.nl/archives/fieldtrip.html and   
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users   
> of the FieldTrip  toolbox, to share experiences and to discuss new   
> ideas for MEG and EEG analysis. See also   
> http://listserv.surfnet.nl/archives/fieldtrip.html and   
> http://www.ru.nl/fcdonders/fieldtrip.
>



------------------------------------------------------------------
The University of Glasgow, Department of Psychology WebMail system
------------------------------------------------------------------

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.



----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From julian.keil at GMAIL.COM  Wed Oct  8 17:22:14 2008
From: julian.keil at GMAIL.COM (Julian Keil)
Date: Wed, 8 Oct 2008 17:22:14 +0200
Subject: 4D data reading -> 148 channel system
Message-ID: <WED.8.OCT.2008.172214.0200.FIELDTRIP@NIC.SURFNET.NL>

Hello everyone,

i just tried to read 4D raw data as was suggested in the recent
discussion.
Unfortunately, I encountered 2 Problems:

First, Matlab still enters the debug-mode, although I'm using the
latest version of Fieldtrip
Second, though I can read the raw datal, the labels for the MEG
channels are missing. The data.hdr.label contains the 165 recorded
channels but the labels are not the Names but - as I think - the
locations.
(e.g. A3+03).
Could it be, that the definition for the 148-channel 4d-system is
missing?
Does anyone have a hint hw to solve this?

Thanks a lot

Julian Keil


Dipl. Psych. Julian Keil

OBOB-Lab
University of Konstanz
Department of Psychology
P.O. Box D23
78457 Konstanz
Germany

Tel: ++49 - (0)7531 - 88 45 84
Email: julian.keil at uni-konstanz.de
Homepage: http://www.uni-konstanz.de/obob





----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From j.schoffelen at PSY.GLA.AC.UK  Wed Oct  8 17:53:58 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Wed, 8 Oct 2008 16:53:58 +0100
Subject: 4D data reading -> 148 channel system
In-Reply-To: <BD4DCA44-4C7F-4076-9BFA-2531597267A7@GMAIL.COM>
Message-ID: <WED.8.OCT.2008.165358.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Julian,

As of the debugging thingy: sorry about that, I thought I adjusted it
but apparently something went wrong. You can easily fix this yourself
by going to the appropriate function. It's read_4d_hdr and you just
have to remove the keyboard-statement somewhere in the code. I don't
know where the function is located in the release version of
fieldtrip, but it should be somewhere like fieldtrip/private, or
fieldtrip/fileio/private. I hope that as of tomorrow the trailing
keyboard statement is removed from the release version.
Regarding your second point: I tried it out with a 148-channel
dataset I have lying around, and you're absolutely right.
Interestingly, for the 248-system it works just fine. Give me some
time to look into this. I hope to get it working robustly for both
systems. Could you for the time being check whether the field
data.hdr.orig.Channel looks meaningful for your data? A solution for
now would be to replace data.hdr.label (and data.label) with
hdr.orig.Channel.


Yours,

Jan-Mathijs



On Oct 8, 2008, at 4:22 PM, Julian Keil wrote:

> Hello everyone,
>
> i just tried to read 4D raw data as was suggested in the recent
> discussion.
> Unfortunately, I encountered 2 Problems:
>
> First, Matlab still enters the debug-mode, although I'm using the
> latest version of Fieldtrip
> Second, though I can read the raw datal, the labels for the MEG
> channels are missing. The data.hdr.label contains the 165 recorded
> channels but the labels are not the Names but - as I think - the
> locations.
> (e.g. A3+03).
> Could it be, that the definition for the 148-channel 4d-system is
> missing?
> Does anyone have a hint hw to solve this?
>
> Thanks a lot
>
> Julian Keil
>
>
> Dipl. Psych. Julian Keil
>
> OBOB-Lab
> University of Konstanz
> Department of Psychology
> P.O. Box D23
> 78457 Konstanz
> Germany
>
> Tel: ++49 - (0)7531 - 88 45 84
> Email: julian.keil at uni-konstanz.de
> Homepage: http://www.uni-konstanz.de/obob
>
>
>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From julian.keil at GMAIL.COM  Thu Oct  9 12:01:38 2008
From: julian.keil at GMAIL.COM (Julian Keil)
Date: Thu, 9 Oct 2008 12:01:38 +0200
Subject: 4D data reading -> 148 channel system
In-Reply-To: <AAD7D620-D190-4A0E-8649-4F2706ECC5DB@psy.gla.ac.uk>
Message-ID: <THU.9.OCT.2008.120138.0200.FIELDTRIP@NIC.SURFNET.NL>

Hello Jan-Mathijs,

thanks for the fast fix of problem 1.
As for problem 2: the data.hdr.orig.channel indeed looks meaningful
and replacing the files as you mentioned works fine.

Thanks a lot.

Julian

Am 08.10.2008 um 17:53 schrieb jan-mathijs schoffelen:

> Dear Julian,
>
> As of the debugging thingy: sorry about that, I thought I adjusted
> it but apparently something went wrong. You can easily fix this
> yourself by going to the appropriate function. It's read_4d_hdr and
> you just have to remove the keyboard-statement somewhere in the
> code. I don't know where the function is located in the release
> version of fieldtrip, but it should be somewhere like fieldtrip/
> private, or fieldtrip/fileio/private. I hope that as of tomorrow the
> trailing keyboard statement is removed from the release version.
> Regarding your second point: I tried it out with a 148-channel
> dataset I have lying around, and you're absolutely right.
> Interestingly, for the 248-system it works just fine. Give me some
> time to look into this. I hope to get it working robustly for both
> systems. Could you for the time being check whether the field
> data.hdr.orig.Channel looks meaningful for your data? A solution for
> now would be to replace data.hdr.label (and data.label) with
> hdr.orig.Channel.
>
>
> Yours,
>
> Jan-Mathijs
>
>
>
> On Oct 8, 2008, at 4:22 PM, Julian Keil wrote:
>
>> Hello everyone,
>>
>> i just tried to read 4D raw data as was suggested in the recent
>> discussion.
>> Unfortunately, I encountered 2 Problems:
>>
>> First, Matlab still enters the debug-mode, although I'm using the
>> latest version of Fieldtrip
>> Second, though I can read the raw datal, the labels for the MEG
>> channels are missing. The data.hdr.label contains the 165 recorded
>> channels but the labels are not the Names but - as I think - the
>> locations.
>> (e.g. A3+03).
>> Could it be, that the definition for the 148-channel 4d-system is
>> missing?
>> Does anyone have a hint hw to solve this?
>>
>> Thanks a lot
>>
>> Julian Keil
>>
>>
>> Dipl. Psych. Julian Keil
>>
>> OBOB-Lab
>> University of Konstanz
>> Department of Psychology
>> P.O. Box D23
>> 78457 Konstanz
>> Germany
>>
>> Tel: ++49 - (0)7531 - 88 45 84
>> Email: julian.keil at uni-konstanz.de
>> Homepage: http://www.uni-konstanz.de/obob
>>
>>
>>
>>
>> ----------------------------------
>>
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis.
>>
>> http://listserv.surfnet.nl/archives/fieldtrip.html
>>
>> http://www.ru.nl/fcdonders/fieldtrip/
>>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From j.schoffelen at PSY.GLA.AC.UK  Thu Oct  9 12:28:34 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Thu, 9 Oct 2008 11:28:34 +0100
Subject: 4D data reading -> 148 channel system
In-Reply-To: <3423F7AA-91CB-4B9A-81AD-2411538B516C@gmail.com>
Message-ID: <THU.9.OCT.2008.112834.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Julian,

You can easily make this change yourself in the appropriate place of
read_4d_hdr for the time being.
I made the change as well (it seems to look ok for both the 148 and
248 channel systems) and put it in the fieldtrip release.

Yours,

Jan-Mathijs

On Oct 9, 2008, at 11:01 AM, Julian Keil wrote:

> Hello Jan-Mathijs,
>
> thanks for the fast fix of problem 1.
> As for problem 2: the data.hdr.orig.channel indeed looks meaningful
> and replacing the files as you mentioned works fine.
>
> Thanks a lot.
>
> Julian
>
> Am 08.10.2008 um 17:53 schrieb jan-mathijs schoffelen:
>
>> Dear Julian,
>>
>> As of the debugging thingy: sorry about that, I thought I adjusted
>> it but apparently something went wrong. You can easily fix this
>> yourself by going to the appropriate function. It's read_4d_hdr
>> and you just have to remove the keyboard-statement somewhere in
>> the code. I don't know where the function is located in the
>> release version of fieldtrip, but it should be somewhere like
>> fieldtrip/private, or fieldtrip/fileio/private. I hope that as of
>> tomorrow the trailing keyboard statement is removed from the
>> release version.
>> Regarding your second point: I tried it out with a 148-channel
>> dataset I have lying around, and you're absolutely right.
>> Interestingly, for the 248-system it works just fine. Give me some
>> time to look into this. I hope to get it working robustly for both
>> systems. Could you for the time being check whether the field
>> data.hdr.orig.Channel looks meaningful for your data? A solution
>> for now would be to replace data.hdr.label (and data.label) with
>> hdr.orig.Channel.
>>
>>
>> Yours,
>>
>> Jan-Mathijs
>>
>>
>>
>> On Oct 8, 2008, at 4:22 PM, Julian Keil wrote:
>>
>>> Hello everyone,
>>>
>>> i just tried to read 4D raw data as was suggested in the recent
>>> discussion.
>>> Unfortunately, I encountered 2 Problems:
>>>
>>> First, Matlab still enters the debug-mode, although I'm using the
>>> latest version of Fieldtrip
>>> Second, though I can read the raw datal, the labels for the MEG
>>> channels are missing. The data.hdr.label contains the 165
>>> recorded channels but the labels are not the Names but - as I
>>> think - the locations.
>>> (e.g. A3+03).
>>> Could it be, that the definition for the 148-channel 4d-system is
>>> missing?
>>> Does anyone have a hint hw to solve this?
>>>
>>> Thanks a lot
>>>
>>> Julian Keil
>>>
>>>
>>> Dipl. Psych. Julian Keil
>>>
>>> OBOB-Lab
>>> University of Konstanz
>>> Department of Psychology
>>> P.O. Box D23
>>> 78457 Konstanz
>>> Germany
>>>
>>> Tel: ++49 - (0)7531 - 88 45 84
>>> Email: julian.keil at uni-konstanz.de
>>> Homepage: http://www.uni-konstanz.de/obob
>>>
>>>
>>>
>>>
>>> ----------------------------------
>>>
>>> The aim of this list is to facilitate the discussion between
>>> users of the FieldTrip toolbox, to share experiences and to
>>> discuss new ideas for MEG and EEG analysis.
>>>
>>> http://listserv.surfnet.nl/archives/fieldtrip.html
>>>
>>> http://www.ru.nl/fcdonders/fieldtrip/
>>>
>>
>> ----------------------------------
>>
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis.
>>
>> http://listserv.surfnet.nl/archives/fieldtrip.html
>>
>> http://www.ru.nl/fcdonders/fieldtrip/
>>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From michelic72 at GMAIL.COM  Fri Oct 10 09:27:28 2008
From: michelic72 at GMAIL.COM (Cristiano Micheli)
Date: Fri, 10 Oct 2008 09:27:28 +0200
Subject: sourceplot - 'surface'
Message-ID: <FRI.10.OCT.2008.092728.0200.FIELDTRIP@NIC.SURFNET.NL>

I am trying to visualize coherence on a 3D surface, after DICS processing,
with a template given in Fieldtrip :

    cfg              = [];
    cfg.parameter    = 'coh'; 
    cfg.downsample = 1;
    cfg.sourceunits  = 'cm';
    cfg.mriunits       = 'mm';
    interp                = sourceinterpolate(cfg, source, mri); 

    cfg                   = [];
    cfg.coordinates = 'ctf';
    cfg.template     = '/home/common/matlab/spm2/templates/T1.mnc'; 
    sourceN  = volumenormalise(cfg, interp);

    sourceN = rmfield(sourceN,'inside'); 
    cfg = [];
    cfg.method = 'surface';
    cfg.funparameter = 'coh';
    cfg.funcolorlim = [0.0 0.5e-3];
    cfg.funcolormap = 'jet';
    cfg.opacitylim = [0.0 0.1]; 
    cfg.opacitymap = 'rampup';  
    cfg.projmethod = 'nearest'; 
    cfg.surffile = 'surface_l4_both.mat';
    cfg.surfdownsample = 10; 
    figure, sourceplot(cfg,sourceN); view ([90 0])

I get stuck at the normalisation when I get this error:

??? Error using ==> spm_create_vol>create_vol at 32
"dim" field is the wrong size (1  4).

Error in ==> spm_create_vol at 16
        v = create_vol(V(i));

Error in ==> fieldtrip-20080729/private/volumewrite_spm at 61
Va         = spm_create_vol(Va);

Error in ==> volumenormalise at 178
VF = volumewrite_spm([cfg.intermediatename,'_anatomy.img'], interp.anatomy,
interp.transform);


I thank you in advance for any suggestion
Cristiano

M.Sc. Ing. Cristiano Micheli
Institute of Medical Psychology and Behavioral Neurobiology MEG-Center
Otfried-Müller-Strasse 47 72076 Tübingen
Phone: +49-7071-29-87689
Fax:   +49-7071-29-5706
Privat: +49-176-26326149
Email: cristiano.micheli at med.uni-tuebingen.de 

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From jlucan at NKI.RFMH.ORG  Tue Oct 14 20:15:33 2008
From: jlucan at NKI.RFMH.ORG (Joshua Lucan)
Date: Tue, 14 Oct 2008 20:15:33 +0200
Subject: within subjects partitioning
Message-ID: <TUE.14.OCT.2008.201533.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi,
  I'm using timelockstatistics to perform a within subjects cluster based non-
parametric test.  I have two conditions and ten subjects.  The data from each 
subject consists of a spatial array of 160 electrodes at one time point.
  My question is how are the data randomly partitioned. Are all samples across 
subjects and conditions put into one group and 20 random drawings (10 
subjects, 2 conditions) of 160 electrodes performed?  Or is data within each 
subject preserved so that there are 10 groups of 320 electrodes from each of 
which two partitions are made?
  Thanks so much,
  Josh

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From e.maris at DONDERS.RU.NL  Tue Oct 14 21:21:08 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Tue, 14 Oct 2008 21:21:08 +0200
Subject: within subjects partitioning
In-Reply-To: <LISTSERV%200810142015333110.139F@NIC.SURFNET.NL>
Message-ID: <TUE.14.OCT.2008.212108.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Josh,


>   I'm using timelockstatistics to perform a within subjects cluster based
non-
> parametric test.  I have two conditions and ten subjects.  The data from
each
> subject consists of a spatial array of 160 electrodes at one time point.
>   My question is how are the data randomly partitioned. Are all samples
across
> subjects and conditions put into one group and 20 random drawings (10
> subjects, 2 conditions) of 160 electrodes performed?  Or is data within
each
> subject preserved so that there are 10 groups of 320 electrodes from each
of
> which two partitions are made?


In a within-subjects design with two conditions, the permutation is
performed as follows: the two spatio-spectral-temporal (possibly with empty
spectral and temporal dimensions) data matrices (one for every condition)
per subject are randomly permuted WITHIN every subject. This is also
described in Maris & Oostenveld (JNM, 2007).


Good luck,

Eric Maris




>   Thanks so much,
>   Josh
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip
> toolbox, to share experiences and to discuss new ideas for MEG and EEG
analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From jlucan at NKI.RFMH.ORG  Tue Oct 14 21:33:09 2008
From: jlucan at NKI.RFMH.ORG (Joshua Lucan)
Date: Tue, 14 Oct 2008 21:33:09 +0200
Subject: within subjects partitioning
Message-ID: <TUE.14.OCT.2008.213309.0200.FIELDTRIP@NIC.SURFNET.NL>

Excellent! Thank you!

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From v.litvak at ION.UCL.AC.UK  Thu Oct 16 09:05:08 2008
From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak)
Date: Thu, 16 Oct 2008 08:05:08 +0100
Subject: Postdoctoral position in neuroimaging
Message-ID: <THU.16.OCT.2008.080508.0100.FIELDTRIP@NIC.SURFNET.NL>

Please contact Prof. Huber directly about this ad.


Title of the advert
Postdoctoral position in neuroimaging

Description
A one year postdoctoral position is available for a first year
post-doc at the University Children's Hospital Zurich, Switzerland.

The group of Prof. Reto Huber is seeking a postdoctoral fellow to
develop and apply advanced MRI techniques, including diffusion tensor
imaging (DTI), in combination with high-density
electroencephalographic recordings in children and adolescents.

The topic of research will be the study of the relationship between
anatomical and electrophysiological markers of brain maturation. Both
MRI and EEG data of healthy children between 8 and 18 years of age are
available.

Education
We are looking for a qualified candidate with research experience in
computational and statistical methods for MRI imaging (e.g. SPM,
MatLab, DTI and gray matter density analysis). Strong image
processing, data analysis and computing skills are essential.
Applicants should have a PhD, preferably in neuroscience. The position
is fully funded for 1 year and is offered to a first year post-doc.

Start
Available now.

Link
http://www.kispi.uzh.ch/sleep


Please send your CV with scientific record, letter of motivation and 2
referees (including e-mail addresses) as a single PDF file by e-mail
to: reto.huber at kispi.uzh.ch

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From h.leuthold at PSY.GLA.AC.UK  Thu Oct 16 18:44:40 2008
From: h.leuthold at PSY.GLA.AC.UK (Hartmut Leuthold)
Date: Thu, 16 Oct 2008 17:44:40 +0100
Subject: 1-year postdoctoral position
Message-ID: <THU.16.OCT.2008.174440.0100.FIELDTRIP@NIC.SURFNET.NL>

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From florisdelange at GMAIL.COM  Fri Oct 17 16:44:39 2008
From: florisdelange at GMAIL.COM (Floris de Lange)
Date: Fri, 17 Oct 2008 16:44:39 +0200
Subject: cluster statistic on one sample
Message-ID: <FRI.17.OCT.2008.164439.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrippers,

I have a question about statistical analysis on the sensor level.
I would like to make use of the cluster size thresholding of the
clusterrand routine in Fieldtrip. Unfortunately, in the current
wrapper, it seems there is no option for a one-sample T-test? There is
an activation-baseline test, and a (in)dependent samples test between
two conditions, but what I want to do is simply test whether a 14
(subjects) x 275 (channels) matrix is different from zero, taking into
account the spatial relations between adjacent sensors. (The data
points are regression weights from a multiple-regression analysis, so
there's no easy way to split it into two parts.)
I assume this should be easy to tweak, but I couldn't come up with any
smart ideas how to do it.
Anyone any ideas?

Thanks in advance!

Floris

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From ali.mazaheri at FCDONDERS.RU.NL  Fri Oct 17 16:57:09 2008
From: ali.mazaheri at FCDONDERS.RU.NL (Ali Mazaheri)
Date: Fri, 17 Oct 2008 16:57:09 +0200
Subject: cluster statistic on one sample
Message-ID: <FRI.17.OCT.2008.165709.0200.FIELDTRIP@NIC.SURFNET.NL>

Dearest Floris,

Why not just create a zero matrices with a 14 x 275 dimension
 and do a dependent samples test between
your regresion weights and the zero matrices ?



Hope this helps !


best

Ali



----- Original Message -----
From: Floris de Lange <florisdelange at GMAIL.COM>
Date: Friday, October 17, 2008 4:44 pm
Subject: [FIELDTRIP] cluster statistic on one sample

> Dear Fieldtrippers,
>
> I have a question about statistical analysis on the sensor level.
> I would like to make use of the cluster size thresholding of the
> clusterrand routine in Fieldtrip. Unfortunately, in the current
> wrapper, it seems there is no option for a one-sample T-test? There is
> an activation-baseline test, and a (in)dependent samples test between
> two conditions, but what I want to do is simply test whether a 14
> (subjects) x 275 (channels) matrix is different from zero, taking into
> account the spatial relations between adjacent sensors. (The data
> points are regression weights from a multiple-regression analysis, so
> there's no easy way to split it into two parts.)
> I assume this should be easy to tweak, but I couldn't come up with any
> smart ideas how to do it.
> Anyone any ideas?
>
> Thanks in advance!
>
> Floris
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From zanasilva at GMAIL.COM  Fri Oct 17 18:04:14 2008
From: zanasilva at GMAIL.COM (Susana Silva)
Date: Fri, 17 Oct 2008 18:04:14 +0200
Subject: clusterrandanalysis vs timelockstatistics
Message-ID: <FRI.17.OCT.2008.180414.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi all

I have run both clusterrandanalysis and timelockstatistics (with
cfg.correctm=cluster) over the same data.
The t values in clusrand (clusterrandanalysis) are equal to the t values in
stat (timelockstatistics).

However, in timelockstatistics, the number of clusters is much higher and
the prob is much lower than in the clusterrandanalysis procedure.

1-Should I expect it?
2-where can I get some more information on clusrandanalysis function (the
tutorial does not seem to have)?

Thank you
Susana Silva

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From spike377 at KOREA.COM  Sat Oct 18 22:05:36 2008
From: spike377 at KOREA.COM (=?EUC-KR?B?udrH/LW/?=)
Date: Sun, 19 Oct 2008 05:05:36 +0900
Subject: time-frequency representation of PLV
Message-ID: <SUN.19.OCT.2008.050536.0900.FIELDTRIP@NIC.SURFNET.NL>

An HTML attachment was scrubbed...
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From e.maris at DONDERS.RU.NL  Mon Oct 20 11:17:19 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Mon, 20 Oct 2008 11:17:19 +0200
Subject: cluster statistic on one sample
In-Reply-To: <9fb563140810170744m400d703dkf66c6e6a22145e24@mail.gmail.com>
Message-ID: <MON.20.OCT.2008.111719.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Floris,



> I have a question about statistical analysis on the sensor level.
> I would like to make use of the cluster size thresholding of the
> clusterrand routine in Fieldtrip. Unfortunately, in the current
> wrapper, it seems there is no option for a one-sample T-test? There is
> an activation-baseline test, and a (in)dependent samples test between
> two conditions, but what I want to do is simply test whether a 14
> (subjects) x 275 (channels) matrix is different from zero, taking into
> account the spatial relations between adjacent sensors. (The data
> points are regression weights from a multiple-regression analysis, so
> there's no easy way to split it into two parts.)
> I assume this should be easy to tweak, but I couldn't come up with any
> smart ideas how to do it.
> Anyone any ideas?

I'm afraid that I have to disappoint you, Floris. Your null hypothesis is a
typical parametric null hypothesis; the expected value of some
(matrix-valued) variable being equal to zero. The null hypothesis that is
tested by a nonparametric permutation test is equality across experimental
conditions of the probability distribution from which the
(condition-specific) data are drawn. Since you have single condition only, I
see no way of applying the theory behind nonparametric permutation testing
(of the type described by Maris & Oostenveld, 2007) to your data.

To solve your problem we need a brilliant theoretical insight.


Greetings,

Eric






>
> Thanks in advance!
>
> Floris
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip
> toolbox, to share experiences and to discuss new ideas for MEG and EEG
analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From v.litvak at ION.UCL.AC.UK  Mon Oct 20 12:05:30 2008
From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak)
Date: Mon, 20 Oct 2008 11:05:30 +0100
Subject: cluster statistic on one sample
In-Reply-To: <e1e7c57c0810200304v45bd0061j18c2afce55a16ce@mail.gmail.com>
Message-ID: <MON.20.OCT.2008.110530.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Floris and Eric,

Parametric tests at scalp level taking into account spatial
relationship between sensors can be done in SPM (with RFT correction).
That'll require using some low-level functions to convert
coefficients to images but in principle shouldn't be that difficult.

Best,

Vladimir
>
> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris <e.maris at donders.ru.nl> wrote:
>> Dear Floris,
>>
>>
>>
>>> I have a question about statistical analysis on the sensor level.
>>> I would like to make use of the cluster size thresholding of the
>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
>>> wrapper, it seems there is no option for a one-sample T-test? There is
>>> an activation-baseline test, and a (in)dependent samples test between
>>> two conditions, but what I want to do is simply test whether a 14
>>> (subjects) x 275 (channels) matrix is different from zero, taking into
>>> account the spatial relations between adjacent sensors. (The data
>>> points are regression weights from a multiple-regression analysis, so
>>> there's no easy way to split it into two parts.)
>>> I assume this should be easy to tweak, but I couldn't come up with any
>>> smart ideas how to do it.
>>> Anyone any ideas?
>>
>> I'm afraid that I have to disappoint you, Floris. Your null hypothesis is a
>> typical parametric null hypothesis; the expected value of some
>> (matrix-valued) variable being equal to zero. The null hypothesis that is
>> tested by a nonparametric permutation test is equality across experimental
>> conditions of the probability distribution from which the
>> (condition-specific) data are drawn. Since you have single condition only, I
>> see no way of applying the theory behind nonparametric permutation testing
>> (of the type described by Maris & Oostenveld, 2007) to your data.
>>
>> To solve your problem we need a brilliant theoretical insight.
>>
>>
>> Greetings,
>>
>> Eric
>>
>>
>>
>>
>>
>>
>>>
>>> Thanks in advance!
>>>
>>> Floris
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users of the
>> FieldTrip
>>> toolbox, to share experiences and to discuss new ideas for MEG and EEG
>> analysis.
>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>>> http://www.ru.nl/fcdonders/fieldtrip.
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>>
>>
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From marco.buiatti at UNITN.IT  Mon Oct 20 14:00:30 2008
From: marco.buiatti at UNITN.IT (Marco Buiatti)
Date: Mon, 20 Oct 2008 14:00:30 +0200
Subject: data format for 'between trials' cluster randomization analysis
Message-ID: <MON.20.OCT.2008.140030.0200.>

Dear Fieldtrippers,

I have data from a single subject with two conditions, and I am trying
to perform the cluster randomization analysis on the statistical
difference between the conditions - therefore a 'between trials'
analysis.

However, my data are not in the fieldtrip format, and I have problems
in converting them in the correct format. Could anyone provide me an
example of such format?

Also, the eeglab2fieldtrip function (which I tried without success) is
not included in the last Fieldtrip release: is it because there are
some problems with that function?

Thank you in advance,

Marco Buiatti

-- 
Marco Buiatti, PhD
Postdoctoral Researcher
Functional NeuroImaging Laboratory
Center for Mind Brain Sciences
Trento University
Via delle Regole, 101
38060, Mattarello (TN) - ITALY
email: marco.buiatti at unitn.it
http://www.cimec.unitn.it
Telephone: +39-0461-88 3077
Fax: +39-0461-88 3066

***********************************************
In occasione del 70° anniversario della promulgazione delle leggi
razziali, LEGGI FIRMA E DIFFONDI IL MANIFESTO ANTIRAZZISTA!
http://www.regione.toscana.it/regione/opencms/RT/sito-RT/MenuUtility/SanRossore-Firma-Manifesto-Antirazzismo
***********************************************

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From j.schoffelen at PSY.GLA.AC.UK  Mon Oct 20 14:13:11 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Mon, 20 Oct 2008 13:13:11 +0100
Subject: cluster statistic on one sample
In-Reply-To: <e1e7c57c0810200305w7ea38eddt767591636ff2b926@mail.gmail.com>
Message-ID: <MON.20.OCT.2008.131311.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Floris, Eric, Vladimir and all other people reading this message,

What about performing a nonparametric test, based on the bootstrap
distribution of the beta weights under the null-hypothesis?
This problem sounds similar to one I came across recently (and which
I still have to write something about on fieldtrip's wiki-page (sorry
Eric)), which has to do with the testing of the significance of the F-
value for interaction in a 2x2 repeated measure anova. Also in this
case, one also wants to test a parametric null-hypothesis, as Eric
phrased it in his last e-mail. One way to test this (I don't have the
reference at hand), is to test the observed F-statistic against a
null-distribution, obtained from bootstrapping your data, which you
preconditioned as to impose the null-hypothesis (in the case of an
anova it would be to remove from each of the observations the mean of
the cell to which the observation belongs). I don't know yet how to
impose the null-hypothesis in the regression case, but would this
line of thought be a possibility?
As to a potential implementation: Robert and I are pretty close to
have the bootstrapping implemented.

Yours,

Jan-Mathijs


On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:

> Dear Floris and Eric,
>
> Parametric tests at scalp level taking into account spatial
> relationship between sensors can be done in SPM (with RFT correction).
> That'll require using some low-level functions to convert
> coefficients to images but in principle shouldn't be that difficult.
>
> Best,
>
> Vladimir
>>
>> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris
>> <e.maris at donders.ru.nl> wrote:
>>> Dear Floris,
>>>
>>>
>>>
>>>> I have a question about statistical analysis on the sensor level.
>>>> I would like to make use of the cluster size thresholding of the
>>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
>>>> wrapper, it seems there is no option for a one-sample T-test?
>>>> There is
>>>> an activation-baseline test, and a (in)dependent samples test
>>>> between
>>>> two conditions, but what I want to do is simply test whether a 14
>>>> (subjects) x 275 (channels) matrix is different from zero,
>>>> taking into
>>>> account the spatial relations between adjacent sensors. (The data
>>>> points are regression weights from a multiple-regression
>>>> analysis, so
>>>> there's no easy way to split it into two parts.)
>>>> I assume this should be easy to tweak, but I couldn't come up
>>>> with any
>>>> smart ideas how to do it.
>>>> Anyone any ideas?
>>>
>>> I'm afraid that I have to disappoint you, Floris. Your null
>>> hypothesis is a
>>> typical parametric null hypothesis; the expected value of some
>>> (matrix-valued) variable being equal to zero. The null hypothesis
>>> that is
>>> tested by a nonparametric permutation test is equality across
>>> experimental
>>> conditions of the probability distribution from which the
>>> (condition-specific) data are drawn. Since you have single
>>> condition only, I
>>> see no way of applying the theory behind nonparametric
>>> permutation testing
>>> (of the type described by Maris & Oostenveld, 2007) to your data.
>>>
>>> To solve your problem we need a brilliant theoretical insight.
>>>
>>>
>>> Greetings,
>>>
>>> Eric
>>>
>>>
>>>
>>>
>>>
>>>
>>>>
>>>> Thanks in advance!
>>>>
>>>> Floris
>>>>
>>>> ----------------------------------
>>>> The aim of this list is to facilitate the discussion between
>>>> users of the
>>> FieldTrip
>>>> toolbox, to share experiences and to discuss new ideas for MEG
>>>> and EEG
>>> analysis.
>>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between
>>> users of the FieldTrip  toolbox, to share experiences and to
>>> discuss new ideas for MEG and EEG analysis. See also http://
>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/
>>> fcdonders/fieldtrip.
>>>
>>>
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From venug001 at BAMA.UA.EDU  Mon Oct 20 14:27:31 2008
From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan)
Date: Mon, 20 Oct 2008 07:27:31 -0500
Subject: cluster statistic on one sample
In-Reply-To: <66D7BE2A-86F7-48BA-A94C-0561DF0A568E@psy.gla.ac.uk>
Message-ID: <MON.20.OCT.2008.072731.0500.FIELDTRIP@NIC.SURFNET.NL>

Hello everyone, I just finished testing the null across two conditions
using EEGLAB which puts out t-values at various points on the waveform,
and then by exporting values to excel converting them to RMS and
averaging them over left vs right and post vs ant. I have the SPSS
multivariate code, I have been wondering about this for months now how
to integrate something like this into all the packages. Off course
since MATLAB is very powerful I suspect that adding the required MANOVA
code into those routines will solve the problem.After that is done, the
mathematical formula for generating the F distribution, and the root of
which is the t distribution can be placed in a separate sheet for a
parametric test, even though the data is non-parametric. We can make
parametric assumptions of our data even though it is non-parametric by
nature. I hand did this using a combination of excel, spss, eeglab, and
scan 4.3 which--runs on a matlab engine and is a commercial product.
A paper by Pascual-Marqui (2002) talks about how the F values in the
dipole fit and Current Density Reconstruction is a pseudo-statistic.
That paper also provides a correction so that they can be used as
parametric values. I wonder if such a correction can be applied to the
non-parametric values here, so that they can be treated and interpreted
as parametric values.
 I can see this in my mind by can tweak the c code in MATLAB with some
guidance. Am not a programmer by any strech of imagination.
regards
gopa


Quoting jan-mathijs schoffelen <j.schoffelen at PSY.GLA.AC.UK>:

> Dear Floris, Eric, Vladimir and all other people reading this
> message,
>
> What about performing a nonparametric test, based on the bootstrap
> distribution of the beta weights under the null-hypothesis?
> This problem sounds similar to one I came across recently (and which
>
> I still have to write something about on fieldtrip's wiki-page (sorry
>
> Eric)), which has to do with the testing of the significance of the
> F-
> value for interaction in a 2x2 repeated measure anova. Also in this
>
> case, one also wants to test a parametric null-hypothesis, as Eric
> phrased it in his last e-mail. One way to test this (I don't have the
>
> reference at hand), is to test the observed F-statistic against a
> null-distribution, obtained from bootstrapping your data, which you
>
> preconditioned as to impose the null-hypothesis (in the case of an
> anova it would be to remove from each of the observations the mean of
>
> the cell to which the observation belongs). I don't know yet how to
>
> impose the null-hypothesis in the regression case, but would this
> line of thought be a possibility?
> As to a potential implementation: Robert and I are pretty close to
> have the bootstrapping implemented.
>
> Yours,
>
> Jan-Mathijs
>
>
> On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:
>
> > Dear Floris and Eric,
> >
> > Parametric tests at scalp level taking into account spatial
> > relationship between sensors can be done in SPM (with RFT
> correction).
> > That'll require using some low-level functions to convert
> > coefficients to images but in principle shouldn't be that
> difficult.
> >
> > Best,
> >
> > Vladimir
> >>
> >> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris
> >> <e.maris at donders.ru.nl> wrote:
> >>> Dear Floris,
> >>>
> >>>
> >>>
> >>>> I have a question about statistical analysis on the sensor
> level.
> >>>> I would like to make use of the cluster size thresholding of
> the
> >>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
> >>>> wrapper, it seems there is no option for a one-sample T-test?
> >>>> There is
> >>>> an activation-baseline test, and a (in)dependent samples test
> >>>> between
> >>>> two conditions, but what I want to do is simply test whether a
> 14
> >>>> (subjects) x 275 (channels) matrix is different from zero,
> >>>> taking into
> >>>> account the spatial relations between adjacent sensors. (The
> data
> >>>> points are regression weights from a multiple-regression
> >>>> analysis, so
> >>>> there's no easy way to split it into two parts.)
> >>>> I assume this should be easy to tweak, but I couldn't come up
> >>>> with any
> >>>> smart ideas how to do it.
> >>>> Anyone any ideas?
> >>>
> >>> I'm afraid that I have to disappoint you, Floris. Your null
> >>> hypothesis is a
> >>> typical parametric null hypothesis; the expected value of some
> >>> (matrix-valued) variable being equal to zero. The null hypothesis
>
> >>> that is
> >>> tested by a nonparametric permutation test is equality across
> >>> experimental
> >>> conditions of the probability distribution from which the
> >>> (condition-specific) data are drawn. Since you have single
> >>> condition only, I
> >>> see no way of applying the theory behind nonparametric
> >>> permutation testing
> >>> (of the type described by Maris & Oostenveld, 2007) to your
> data.
> >>>
> >>> To solve your problem we need a brilliant theoretical insight.
> >>>
> >>>
> >>> Greetings,
> >>>
> >>> Eric
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>
> >>>> Thanks in advance!
> >>>>
> >>>> Floris
> >>>>
> >>>> ----------------------------------
> >>>> The aim of this list is to facilitate the discussion between
> >>>> users of the
> >>> FieldTrip
> >>>> toolbox, to share experiences and to discuss new ideas for MEG
>
> >>>> and EEG
> >>> analysis.
> >>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> >>>> http://www.ru.nl/fcdonders/fieldtrip.
> >>>
> >>> ----------------------------------
> >>> The aim of this list is to facilitate the discussion between
> >>> users of the FieldTrip  toolbox, to share experiences and to
> >>> discuss new ideas for MEG and EEG analysis. See also http://
> >>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/
>
> >>> fcdonders/fieldtrip.
> >>>
> >>>
> >>
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
>
> > of the FieldTrip  toolbox, to share experiences and to discuss new
>
> > ideas for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/
> > archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From e.maris at DONDERS.RU.NL  Mon Oct 20 16:02:39 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Mon, 20 Oct 2008 16:02:39 +0200
Subject: cluster statistic on one sample
In-Reply-To: <66D7BE2A-86F7-48BA-A94C-0561DF0A568E@psy.gla.ac.uk>
Message-ID: <MON.20.OCT.2008.160239.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrip-list-readers,


> What about performing a nonparametric test, based on the bootstrap
> distribution of the beta weights under the null-hypothesis?
> This problem sounds similar to one I came across recently (and which
> I still have to write something about on fieldtrip's wiki-page (sorry
> Eric)), which has to do with the testing of the significance of the F-
> value for interaction in a 2x2 repeated measure anova. Also in this
> case, one also wants to test a parametric null-hypothesis, as Eric
> phrased it in his last e-mail. One way to test this (I don't have the
> reference at hand), is to test the observed F-statistic against a
> null-distribution, obtained from bootstrapping your data, which you
> preconditioned as to impose the null-hypothesis (in the case of an
> anova it would be to remove from each of the observations the mean of
> the cell to which the observation belongs). I don't know yet how to
> impose the null-hypothesis in the regression case, but would this
> line of thought be a possibility?
> As to a potential implementation: Robert and I are pretty close to
> have the bootstrapping implemented.

Again, I can only try to clarify some points here. I will not be able to
offer a solution for your problems.

1. Contrary to the permutation test, there is no useful statistical theory
for statistical tests based on the bootstrap distribution. By "useful", I
mean a theory that allows one to specify a scientifically interesting null
hypothesis (such as, "An expected value equal to 0") under which the false
alarm rate of a boostrap-p-value-based test can be controlled.

2. The bootstrap distribution has a nice intuitive appeal, because the
procedure to generate it (sampling with replacement) mimicks the sampling
process behind the sampling distribution (which is the ultimate "thing to
get" if you want to quantify the reliability of some quantity). But that is
not a proof of false alarm rate control!

3. I think the bootstrap distribution can be useful in situations where
parametric statistical tests do not exists, but I know of no rigourous
statistical argument to substantiate this claim.


Greetings,

Eric Maris


>
> Yours,
>
> Jan-Mathijs
>
>
> On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:
>
> > Dear Floris and Eric,
> >
> > Parametric tests at scalp level taking into account spatial
> > relationship between sensors can be done in SPM (with RFT correction).
> > That'll require using some low-level functions to convert
> > coefficients to images but in principle shouldn't be that difficult.
> >
> > Best,
> >
> > Vladimir
> >>
> >> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris
> >> <e.maris at donders.ru.nl> wrote:
> >>> Dear Floris,
> >>>
> >>>
> >>>
> >>>> I have a question about statistical analysis on the sensor level.
> >>>> I would like to make use of the cluster size thresholding of the
> >>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
> >>>> wrapper, it seems there is no option for a one-sample T-test?
> >>>> There is
> >>>> an activation-baseline test, and a (in)dependent samples test
> >>>> between
> >>>> two conditions, but what I want to do is simply test whether a 14
> >>>> (subjects) x 275 (channels) matrix is different from zero,
> >>>> taking into
> >>>> account the spatial relations between adjacent sensors. (The data
> >>>> points are regression weights from a multiple-regression
> >>>> analysis, so
> >>>> there's no easy way to split it into two parts.)
> >>>> I assume this should be easy to tweak, but I couldn't come up
> >>>> with any
> >>>> smart ideas how to do it.
> >>>> Anyone any ideas?
> >>>
> >>> I'm afraid that I have to disappoint you, Floris. Your null
> >>> hypothesis is a
> >>> typical parametric null hypothesis; the expected value of some
> >>> (matrix-valued) variable being equal to zero. The null hypothesis
> >>> that is
> >>> tested by a nonparametric permutation test is equality across
> >>> experimental
> >>> conditions of the probability distribution from which the
> >>> (condition-specific) data are drawn. Since you have single
> >>> condition only, I
> >>> see no way of applying the theory behind nonparametric
> >>> permutation testing
> >>> (of the type described by Maris & Oostenveld, 2007) to your data.
> >>>
> >>> To solve your problem we need a brilliant theoretical insight.
> >>>
> >>>
> >>> Greetings,
> >>>
> >>> Eric
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>
> >>>> Thanks in advance!
> >>>>
> >>>> Floris
> >>>>
> >>>> ----------------------------------
> >>>> The aim of this list is to facilitate the discussion between
> >>>> users of the
> >>> FieldTrip
> >>>> toolbox, to share experiences and to discuss new ideas for MEG
> >>>> and EEG
> >>> analysis.
> >>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> >>>> http://www.ru.nl/fcdonders/fieldtrip.
> >>>
> >>> ----------------------------------
> >>> The aim of this list is to facilitate the discussion between
> >>> users of the FieldTrip  toolbox, to share experiences and to
> >>> discuss new ideas for MEG and EEG analysis. See also http://
> >>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/
> >>> fcdonders/fieldtrip.
> >>>
> >>>
> >>
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> > of the FieldTrip  toolbox, to share experiences and to discuss new
> > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> > archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip
> toolbox, to share experiences and to discuss new ideas for MEG and EEG
analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From g.rousselet at PSY.GLA.AC.UK  Mon Oct 20 18:00:47 2008
From: g.rousselet at PSY.GLA.AC.UK (Guillaume Rousselet)
Date: Mon, 20 Oct 2008 17:00:47 +0100
Subject: cluster statistic on one sample
In-Reply-To: <20081020140232.D0CA2AA0B6@smtp.ru.nl>
Message-ID: <MON.20.OCT.2008.170047.0100.FIELDTRIP@NIC.SURFNET.NL>

Hey Eric,

I am not sure I understand your point against the bootstrap. My main
source of information about robust statistics is Wilcox, R. R. (2005).
Introduction to Robust Estimation and Hypothesis Testing (2nd Ed.
ed.): Academic Press.
In this book, Wilcox makes an extensive use of the bootstrap
technique. The validation of the technique, when it has been
performed, relies on Monte-Carlo simulations. Also, over almost 600
pages, Wilcox spends only one page on permutations, basically saying
that it is a special case of the bootstrap and that there is no
particular reason to use it.
Do you have references showing validation tests with a direct
comparison of bootstrap and permutation? My understanding is that such
comparisons do not exist for EEG/MEG data.
Also, one must keep in mind that bootstrap is particularly efficient
when applied to robust measures of central tendency, like trimmed
means and M-estimators, see my recent EEG paper for instance (http://www.journalofvision.org/8/12/3/
).
Finally, Wilcox provides a large number of recipes to test
significance of linear regression results, that could be applied to
the problem outlined earlier about the hypothesis test against zero.

Best,

GAR




On 20 Oct 2008, at 15:02, Eric Maris wrote:

> Dear Fieldtrip-list-readers,
>
>
>> What about performing a nonparametric test, based on the bootstrap
>> distribution of the beta weights under the null-hypothesis?
>> This problem sounds similar to one I came across recently (and which
>> I still have to write something about on fieldtrip's wiki-page (sorry
>> Eric)), which has to do with the testing of the significance of the
>> F-
>> value for interaction in a 2x2 repeated measure anova. Also in this
>> case, one also wants to test a parametric null-hypothesis, as Eric
>> phrased it in his last e-mail. One way to test this (I don't have the
>> reference at hand), is to test the observed F-statistic against a
>> null-distribution, obtained from bootstrapping your data, which you
>> preconditioned as to impose the null-hypothesis (in the case of an
>> anova it would be to remove from each of the observations the mean of
>> the cell to which the observation belongs). I don't know yet how to
>> impose the null-hypothesis in the regression case, but would this
>> line of thought be a possibility?
>> As to a potential implementation: Robert and I are pretty close to
>> have the bootstrapping implemented.
>
> Again, I can only try to clarify some points here. I will not be
> able to
> offer a solution for your problems.
>
> 1. Contrary to the permutation test, there is no useful statistical
> theory
> for statistical tests based on the bootstrap distribution. By
> "useful", I
> mean a theory that allows one to specify a scientifically
> interesting null
> hypothesis (such as, "An expected value equal to 0") under which the
> false
> alarm rate of a boostrap-p-value-based test can be controlled.
>
> 2. The bootstrap distribution has a nice intuitive appeal, because the
> procedure to generate it (sampling with replacement) mimicks the
> sampling
> process behind the sampling distribution (which is the ultimate
> "thing to
> get" if you want to quantify the reliability of some quantity). But
> that is
> not a proof of false alarm rate control!
>
> 3. I think the bootstrap distribution can be useful in situations
> where
> parametric statistical tests do not exists, but I know of no rigourous
> statistical argument to substantiate this claim.
>
>
> Greetings,
>
> Eric Maris
>
>
>>
>> Yours,
>>
>> Jan-Mathijs
>>
>>
>> On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:
>>
>>> Dear Floris and Eric,
>>>
>>> Parametric tests at scalp level taking into account spatial
>>> relationship between sensors can be done in SPM (with RFT
>>> correction).
>>> That'll require using some low-level functions to convert
>>> coefficients to images but in principle shouldn't be that difficult.
>>>
>>> Best,
>>>
>>> Vladimir
>>>>
>>>> On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris
>>>> <e.maris at donders.ru.nl> wrote:
>>>>> Dear Floris,
>>>>>
>>>>>
>>>>>
>>>>>> I have a question about statistical analysis on the sensor level.
>>>>>> I would like to make use of the cluster size thresholding of the
>>>>>> clusterrand routine in Fieldtrip. Unfortunately, in the current
>>>>>> wrapper, it seems there is no option for a one-sample T-test?
>>>>>> There is
>>>>>> an activation-baseline test, and a (in)dependent samples test
>>>>>> between
>>>>>> two conditions, but what I want to do is simply test whether a 14
>>>>>> (subjects) x 275 (channels) matrix is different from zero,
>>>>>> taking into
>>>>>> account the spatial relations between adjacent sensors. (The data
>>>>>> points are regression weights from a multiple-regression
>>>>>> analysis, so
>>>>>> there's no easy way to split it into two parts.)
>>>>>> I assume this should be easy to tweak, but I couldn't come up
>>>>>> with any
>>>>>> smart ideas how to do it.
>>>>>> Anyone any ideas?
>>>>>
>>>>> I'm afraid that I have to disappoint you, Floris. Your null
>>>>> hypothesis is a
>>>>> typical parametric null hypothesis; the expected value of some
>>>>> (matrix-valued) variable being equal to zero. The null hypothesis
>>>>> that is
>>>>> tested by a nonparametric permutation test is equality across
>>>>> experimental
>>>>> conditions of the probability distribution from which the
>>>>> (condition-specific) data are drawn. Since you have single
>>>>> condition only, I
>>>>> see no way of applying the theory behind nonparametric
>>>>> permutation testing
>>>>> (of the type described by Maris & Oostenveld, 2007) to your data.
>>>>>
>>>>> To solve your problem we need a brilliant theoretical insight.
>>>>>
>>>>>
>>>>> Greetings,
>>>>>
>>>>> Eric
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>> Thanks in advance!
>>>>>>
>>>>>> Floris
>>>>>>
>>>>>> ----------------------------------
>>>>>> The aim of this list is to facilitate the discussion between
>>>>>> users of the
>>>>> FieldTrip
>>>>>> toolbox, to share experiences and to discuss new ideas for MEG
>>>>>> and EEG
>>>>> analysis.
>>>>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>>>> http://www.ru.nl/fcdonders/fieldtrip.
>>>>>
>>>>> ----------------------------------
>>>>> The aim of this list is to facilitate the discussion between
>>>>> users of the FieldTrip  toolbox, to share experiences and to
>>>>> discuss new ideas for MEG and EEG analysis. See also http://
>>>>> listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/
>>>>> fcdonders/fieldtrip.
>>>>>
>>>>>
>>>>
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between users
>>> of the FieldTrip  toolbox, to share experiences and to discuss new
>>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
>>> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the
> FieldTrip
>> toolbox, to share experiences and to discuss new ideas for MEG and
>> EEG
> analysis.
>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/fcdonders/fieldtrip.






************************************************************************************
Guillaume A. Rousselet, Ph.D.

Lecturer

Centre for Cognitive Neuroimaging (CCNi)
Department of Psychology
Faculty of Information & Mathematical Sciences (FIMS)
University of Glasgow
58 Hillhead Street
Glasgow, UK
G12 8QB

The University of Glasgow, charity number SC004401

http://web.me.com/rousseg/GARs_website/

Email: g.rousselet at psy.gla.ac.uk
Fax. +44 (0)141 330 4606
Tel. +44 (0)141 330 6652
Cell +44 (0)791 779 7833


"no test based upon a theory of probability can by itself
provide any valuable evidence of the truth or falsehood
of a hypothesis.

But we may look at the purpose of tests from another
viewpoint. Without hoping to know whether each separate
hypothesis is true or false, we may search for
rules to govern our behaviour with regard to them, in
following which we insure that, in the long run of
experience, we shall not often be wrong."

	Neyman J & Pearson E, 1933
************************************************************************************







----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
-------------- next part --------------
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From e.maris at DONDERS.RU.NL  Mon Oct 20 21:15:30 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Mon, 20 Oct 2008 21:15:30 +0200
Subject: cluster statistic on one sample
In-Reply-To: <287D1AC6-92F5-466A-BD05-535711CA5AD0@psy.gla.ac.uk>
Message-ID: <MON.20.OCT.2008.211530.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Guillaume,





I am not sure I understand your point against the bootstrap. My main source
of information about robust statistics is Wilcox, R. R. (2005). Introduction
to Robust Estimation and Hypothesis Testing (2nd Ed. ed.): Academic Press.

In this book, Wilcox makes an extensive use of the bootstrap technique. The
validation of the technique, when it has been performed, relies on
Monte-Carlo simulations. Also, over almost 600 pages, Wilcox spends only one
page on permutations, basically saying that it is a special case of the
bootstrap and that there is no particular reason to use it.

Do you have references showing validation tests with a direct comparison of
bootstrap and permutation? My understanding is that such comparisons do not
exist for EEG/MEG data.

Also, one must keep in mind that bootstrap is particularly efficient when
applied to robust measures of central tendency, like trimmed means and
M-estimators, see my recent EEG paper for instance
(http://www.journalofvision.org/8/12/3/).

Finally, Wilcox provides a large number of recipes to test significance of
linear regression results, that could be applied to the problem outlined
earlier about the hypothesis test against zero.





Please do not misunderstand me. I would love to see rigorous mathematical
proofs substantiating the use of the bootstrap distribution for false alarm
rate control under some scientifically interesting null hypothesis. Also, I
am not married to permutation tests (fortunately!). However, I cannot ignore
the fact that a very nice proof exists (which is even very intuitive)
showing that permutation tests control the false alarm rate of any test
statistic and for any correlation pattern in data of arbitrary
dimensionality. Moreover, it does so under a null hypothesis that is
scientifically interesting (data from multiple  experimental conditions
governed by the same probability distribution).



Please forgive for being explicit, but I do not think it is scientifically
appropriate to ask me for "references showing validation tests with a direct
comparison of bootstrap and permutation". The burden of the proof is
completely on the side of the side of the advocates of the bootstrap. They
have to show that a statistical test based on a bootstrap p-value controls
the false alarm rate under a scientifically interesting null hypothesis.
With such a proof on the table, I will become a vigourous defender of the
bootstrap, but until that I will only present it as procedure with an
intuitively appealing rationale.



After showing false alarm rate control by the bootstrap (i.e., under some
null hypothesis), there is the issue of comparing it with permutation tests
with respect to statistical sensitivity (i.e., under the alternative
hypothesis). I have no idea about the relative performance of bootstrap and
permutation tests in this respect, but intuitively I do not expect a big
difference. However, what will make a big difference is the type of test
statistic that is evaluated in under either the permutation or the bootstrap
distribution.







Greetings,



Eric Maris











Best,



GAR









On 20 Oct 2008, at 15:02, Eric Maris wrote:





Dear Fieldtrip-list-readers,





What about performing a nonparametric test, based on the bootstrap

distribution of the beta weights under the null-hypothesis?

This problem sounds similar to one I came across recently (and which

I still have to write something about on fieldtrip's wiki-page (sorry

Eric)), which has to do with the testing of the significance of the F-

value for interaction in a 2x2 repeated measure anova. Also in this

case, one also wants to test a parametric null-hypothesis, as Eric

phrased it in his last e-mail. One way to test this (I don't have the

reference at hand), is to test the observed F-statistic against a

null-distribution, obtained from bootstrapping your data, which you

preconditioned as to impose the null-hypothesis (in the case of an

anova it would be to remove from each of the observations the mean of

the cell to which the observation belongs). I don't know yet how to

impose the null-hypothesis in the regression case, but would this

line of thought be a possibility?

As to a potential implementation: Robert and I are pretty close to

have the bootstrapping implemented.


Again, I can only try to clarify some points here. I will not be able to
offer a solution for your problems.

1. Contrary to the permutation test, there is no useful statistical theory
for statistical tests based on the bootstrap distribution. By "useful", I
mean a theory that allows one to specify a scientifically interesting null
hypothesis (such as, "An expected value equal to 0") under which the false
alarm rate of a boostrap-p-value-based test can be controlled.

2. The bootstrap distribution has a nice intuitive appeal, because the
procedure to generate it (sampling with replacement) mimicks the sampling
process behind the sampling distribution (which is the ultimate "thing to
get" if you want to quantify the reliability of some quantity). But that is
not a proof of false alarm rate control!

3. I think the bootstrap distribution can be useful in situations where
parametric statistical tests do not exists, but I know of no rigourous
statistical argument to substantiate this claim.


Greetings,

Eric Maris







Yours,



Jan-Mathijs





On Oct 20, 2008, at 11:05 AM, Vladimir Litvak wrote:



Dear Floris and Eric,



Parametric tests at scalp level taking into account spatial

relationship between sensors can be done in SPM (with RFT correction).

That'll require using some low-level functions to convert

coefficients to images but in principle shouldn't be that difficult.



Best,



Vladimir



On Mon, Oct 20, 2008 at 10:17 AM, Eric Maris

<e.maris at donders.ru.nl> wrote:

Dear Floris,







I have a question about statistical analysis on the sensor level.

I would like to make use of the cluster size thresholding of the

clusterrand routine in Fieldtrip. Unfortunately, in the current

wrapper, it seems there is no option for a one-sample T-test?

There is

an activation-baseline test, and a (in)dependent samples test

between

two conditions, but what I want to do is simply test whether a 14

(subjects) x 275 (channels) matrix is different from zero,

taking into

account the spatial relations between adjacent sensors. (The data

points are regression weights from a multiple-regression

analysis, so

there's no easy way to split it into two parts.)

I assume this should be easy to tweak, but I couldn't come up

with any

smart ideas how to do it.

Anyone any ideas?



I'm afraid that I have to disappoint you, Floris. Your null

hypothesis is a

typical parametric null hypothesis; the expected value of some

(matrix-valued) variable being equal to zero. The null hypothesis

that is

tested by a nonparametric permutation test is equality across

experimental

conditions of the probability distribution from which the

(condition-specific) data are drawn. Since you have single

condition only, I

see no way of applying the theory behind nonparametric

permutation testing

(of the type described by Maris & Oostenveld, 2007) to your data.



To solve your problem we need a brilliant theoretical insight.





Greetings,



Eric















Thanks in advance!



Floris



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

The aim of this list is to facilitate the discussion between

users of the

FieldTrip

toolbox, to share experiences and to discuss new ideas for MEG

and EEG

analysis.

See also http://listserv.surfnet.nl/archives/fieldtrip.html and

http://www.ru.nl/fcdonders/fieldtrip.



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

The aim of this list is to facilitate the discussion between

users of the FieldTrip  toolbox, to share experiences and to

discuss new ideas for MEG and EEG analysis. See also http://

listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/

fcdonders/fieldtrip.









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

The aim of this list is to facilitate the discussion between users

of the FieldTrip  toolbox, to share experiences and to discuss new

ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/

archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.



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

The aim of this list is to facilitate the discussion between users of the

FieldTrip



toolbox, to share experiences and to discuss new ideas for MEG and EEG

analysis.



See also http://listserv.surfnet.nl/archives/fieldtrip.html and

http://www.ru.nl/fcdonders/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the
FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
and EEG analysis. See also
http://listserv.surfnet.nl/archives/fieldtrip.html and
http://www.ru.nl/fcdonders/fieldtrip.











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

Guillaume A. Rousselet, Ph.D.



Lecturer



Centre for Cognitive Neuroimaging (CCNi)

Department of Psychology

Faculty of Information & Mathematical Sciences (FIMS)

University of Glasgow

58 Hillhead Street

Glasgow, UK

G12 8QB



The University of Glasgow, charity number SC004401



http://web.me.com/rousseg/GARs_website/



Email: g.rousselet at psy.gla.ac.uk

Fax. +44 (0)141 330 4606

Tel. +44 (0)141 330 6652

Cell +44 (0)791 779 7833





"no test based upon a theory of probability can by itself

provide any valuable evidence of the truth or falsehood

of a hypothesis.



But we may look at the purpose of tests from another

viewpoint. Without hoping to know whether each separate

hypothesis is true or false, we may search for

rules to govern our behaviour with regard to them, in

following which we insure that, in the long run of

experience, we shall not often be wrong."



             Neyman J & Pearson E, 1933

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













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

The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/fieldtrip/


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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From florisdelange at GMAIL.COM  Tue Oct 21 00:33:45 2008
From: florisdelange at GMAIL.COM (Floris de Lange)
Date: Tue, 21 Oct 2008 00:33:45 +0200
Subject: cluster statistic on one sample
Message-ID: <TUE.21.OCT.2008.003345.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Eric and other fieldtrippers,

I am a bit puzzled about your comment that:
"Your null hypothesis is a typical parametric null hypothesis; the
expected value of some
(matrix-valued) variable being equal to zero.The null hypothesis that is
tested by a nonparametric permutation test is equality across experimental
conditions of the probability distribution from which the
(condition-specific) data are drawn."

If I understand what SnPM (for fMRI) does well, it uses a permutation
test on one sample, creating a probability distribution by randomly
changing the sign of the observations. I quote (taken from
http://www.sph.umich.edu/ni-stat/SnPM/)

"Under the null hypothesis we can permute the labels of the effects of
interest. One way of implementing this with contrast images is to
randomly change the sign of each subject's contrast. This
sign-flipping approach can be justified by a symmetric distribution
for each voxel's data under the null hypothesis. While symmetry may
sound like a strong assumption, it is weaker than Normality, and can
be justified by a subtraction of two sample means with the same
(arbitrary) distribution.

Hence the null hypothesis here is:
    H0: The symmetric distribution of (the voxel values of the)
subjects' contrast images have zero mean.

And some more detail on the assumptions:

(..) to analyze a group of subjects for population inference, we need
to only assume exchangeability of subjects. The conventional
assumption of independent subjects implies exchangeability, and hence
a single exchangeability block (EB) consisting of all subjects.

(On a technical note, the assumption of exchangeability can actually
be relaxed for the one-sample case considered here. A sufficient
assumption for the contrast data to have a symmetric distribution, is
for each subject's contrast data to have a symmetric but possibly
different distribution. Such differences between subjects violates
exchangeability of all the data; however, since the null distribution
of the statistic of interest is invariant with respect to
sign-flipping, the test is valid.)

I don't see why this approach wouldn't be applicable for MEG data?
As a side note, comparing my regression weights with a condition of
all zeros with a dependent sample T-test works well, and is
mathematically equivalent to a one-sample T-test as far as I can see,
at least in the parametric domain?


Best wishes,
Floris

--
--
Floris de Lange
http://www.florisdelange.com

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From e.maris at DONDERS.RU.NL  Tue Oct 21 11:03:50 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Tue, 21 Oct 2008 11:03:50 +0200
Subject: cluster statistic on one sample
In-Reply-To: <9fb563140810201533i7e045770n8b88936106ed34b4@mail.gmail.com>
Message-ID: <TUE.21.OCT.2008.110350.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Floris and others,



> If I understand what SnPM (for fMRI) does well, it uses a permutation
> test on one sample, creating a probability distribution by randomly
> changing the sign of the observations. I quote (taken from
> http://www.sph.umich.edu/ni-stat/SnPM/)
>
> "Under the null hypothesis we can permute the labels of the effects of
> interest. One way of implementing this with contrast images is to
> randomly change the sign of each subject's contrast. This
> sign-flipping approach can be justified by a symmetric distribution
> for each voxel's data under the null hypothesis. While symmetry may
> sound like a strong assumption, it is weaker than Normality, and can
> be justified by a subtraction of two sample means with the same
> (arbitrary) distribution.

This quote is about a study involving TWO experimental conditions that are
manipulated within every subject. This is also called a paired-samples
design. So, it is NOT a one-sample study. The confusion probably arises from
the fact that a paired-samples (dependent-samples) T-test is identical to a
one-sample T-test on the difference scores. For a paired-samples T-test it
makes sense to construct a reference distribution by randomly switching the
signs of the difference scores. For a one-sample T-test on the data of a
single condition (e.g., the IQ-scores of a group of students), however, it
does not make sense to think about such an operation. (This is a brief,
intuitive explanation, which could be made more precise, but only at the
expense of more text.)

In your quote, also the concepts "symmetry of the distribution" and
"exchangeability" are mentioned. To keep things clear in our minds, it is
good to know that

1. Some statisticians (e.g., Tom Nichols, the author of your quote) motivate
permutation tests from considerations involving the shape of the probability
distribution (such as symmetry). Other statisticians (like Fortunato
Pesarin, and I) motivate permutation tests from considerations about
exchangeability between experimental conditions.

2. "Exchangeability" is a very general concept that can be used in very
different contexts. Some statisticians (e.g., Tom Nichols) use the term
"exchangeability" to denote a property of the probability distribution from
which the subjects are drawn, not mentioning the fact that these subjects
were observed in two experimental conditions. Other statisticians (like I)
use "exchangeability" with explicit reference to the data observed in the
two experimental conditions. For me, exchangeability involves that the
probability distribution of paired observations is invariant under random
permutations of the members of these pairs. This assumption of
exchangeability implies that the data in the two experimental conditions
have the same marginal probability distribution.


(If you like this explanation, Floris, you could join Jan-Mathijs in his
effort to make a Wiki-tutorial about the statistical rationale of
permutation tests.)




Don't start cursing the statisticians now!


Eric Maris

>
> Hence the null hypothesis here is:
>     H0: The symmetric distribution of (the voxel values of the)
> subjects' contrast images have zero mean.
>
> And some more detail on the assumptions:
>
> (..) to analyze a group of subjects for population inference, we need
> to only assume exchangeability of subjects. The conventional
> assumption of independent subjects implies exchangeability, and hence
> a single exchangeability block (EB) consisting of all subjects.
>
> (On a technical note, the assumption of exchangeability can actually
> be relaxed for the one-sample case considered here. A sufficient
> assumption for the contrast data to have a symmetric distribution, is
> for each subject's contrast data to have a symmetric but possibly
> different distribution. Such differences between subjects violates
> exchangeability of all the data; however, since the null distribution
> of the statistic of interest is invariant with respect to
> sign-flipping, the test is valid.)
>
> I don't see why this approach wouldn't be applicable for MEG data?
> As a side note, comparing my regression weights with a condition of
> all zeros with a dependent sample T-test works well, and is
> mathematically equivalent to a one-sample T-test as far as I can see,
> at least in the parametric domain?
>
>
> Best wishes,
> Floris
>
> --
> --
> Floris de Lange
> http://www.florisdelange.com
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip
> toolbox, to share experiences and to discuss new ideas for MEG and EEG
analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From florisdelange at GMAIL.COM  Tue Oct 21 17:47:30 2008
From: florisdelange at GMAIL.COM (Floris de Lange)
Date: Tue, 21 Oct 2008 17:47:30 +0200
Subject: cluster statistic on one sample
Message-ID: <TUE.21.OCT.2008.174730.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Eric,

>This quote is about a study involving TWO experimental conditions that are
>manipulated within every subject. This is also called a paired-samples
>design. So, it is NOT a one-sample study. 

I agree. Note that in my original question I didn't ask about a one-sample
*study*, but a one-sample *T-test* (on regression weights, which reflect a
weighted difference between several conditions, so not a one-sample study).
Ali's suggestion of simply comparing the regression weights against a matrix
of zeros, using paired samples T-test is excellent I think, and amounts to
the same as sign-flipping in a one-sample T-test. 

Thanks at any rate for your clarification, and best wishes from Paris
Floris

>In your quote, also the concepts "symmetry of the distribution" and
>"exchangeability" are mentioned. To keep things clear in our minds, it is
>good to know that
>
>1. Some statisticians (e.g., Tom Nichols, the author of your quote) motivate
>permutation tests from considerations involving the shape of the probability
>distribution (such as symmetry). Other statisticians (like Fortunato
>Pesarin, and I) motivate permutation tests from considerations about
>exchangeability between experimental conditions.
>
>2. "Exchangeability" is a very general concept that can be used in very
>different contexts. Some statisticians (e.g., Tom Nichols) use the term
>"exchangeability" to denote a property of the probability distribution from
>which the subjects are drawn, not mentioning the fact that these subjects
>were observed in two experimental conditions. Other statisticians (like I)
>use "exchangeability" with explicit reference to the data observed in the
>two experimental conditions. For me, exchangeability involves that the
>probability distribution of paired observations is invariant under random
>permutations of the members of these pairs. This assumption of
>exchangeability implies that the data in the two experimental conditions
>have the same marginal probability distribution.
>
>
>(If you like this explanation, Floris, you could join Jan-Mathijs in his
>effort to make a Wiki-tutorial about the statistical rationale of
>permutation tests.)
>
>
>
>
>Don't start cursing the statisticians now!
>
>
>Eric Maris
>
>>
>> Hence the null hypothesis here is:
>>     H0: The symmetric distribution of (the voxel values of the)
>> subjects' contrast images have zero mean.
>>
>> And some more detail on the assumptions:
>>
>> (..) to analyze a group of subjects for population inference, we need
>> to only assume exchangeability of subjects. The conventional
>> assumption of independent subjects implies exchangeability, and hence
>> a single exchangeability block (EB) consisting of all subjects.
>>
>> (On a technical note, the assumption of exchangeability can actually
>> be relaxed for the one-sample case considered here. A sufficient
>> assumption for the contrast data to have a symmetric distribution, is
>> for each subject's contrast data to have a symmetric but possibly
>> different distribution. Such differences between subjects violates
>> exchangeability of all the data; however, since the null distribution
>> of the statistic of interest is invariant with respect to
>> sign-flipping, the test is valid.)
>>
>> I don't see why this approach wouldn't be applicable for MEG data?
>> As a side note, comparing my regression weights with a condition of
>> all zeros with a dependent sample T-test works well, and is
>> mathematically equivalent to a one-sample T-test as far as I can see,
>> at least in the parametric domain?
>>
>>
>> Best wishes,
>> Floris
>>
>> --
>> --
>> Floris de Lange
>> http://www.florisdelange.com
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of the
>FieldTrip
>> toolbox, to share experiences and to discuss new ideas for MEG and EEG
>analysis.
>> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/fcdonders/fieldtrip.
>
>----------------------------------
>The aim of this list is to facilitate the discussion between users of the
FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
and EEG analysis. See also
http://listserv.surfnet.nl/archives/fieldtrip.html and
http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From spike377 at KOREA.COM  Wed Oct 22 04:01:15 2008
From: spike377 at KOREA.COM (=?EUC-KR?B?aHlvdW5nZG9uZy5wYXJr?=)
Date: Wed, 22 Oct 2008 11:01:15 +0900
Subject: question about topoplot
Message-ID: <WED.22.OCT.2008.110115.0900.FIELDTRIP@NIC.SURFNET.NL>

An HTML attachment was scrubbed...
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From e.maris at DONDERS.RU.NL  Wed Oct 22 11:22:44 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Wed, 22 Oct 2008 11:22:44 +0200
Subject: cluster statistic on one sample
In-Reply-To: <LISTSERV%200810211747300670.67ED@NIC.SURFNET.NL>
Message-ID: <WED.22.OCT.2008.112244.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Floris,



> >This quote is about a study involving TWO experimental conditions that
are
> >manipulated within every subject. This is also called a paired-samples
> >design. So, it is NOT a one-sample study.
>
> I agree. Note that in my original question I didn't ask about a one-sample
> *study*, but a one-sample *T-test* (on regression weights, which reflect a
> weighted difference between several conditions, so not a one-sample
study).
> Ali's suggestion of simply comparing the regression weights against a
matrix
> of zeros, using paired samples T-test is excellent I think, and amounts to
> the same as sign-flipping in a one-sample T-test.


I do not agree. If your regression weights are calculated over multiple
conditions (each indexed by some number), then the appropriate permutation
is permutation across these multiple conditions. The appropriate "statfun"
(this is Fieldtrip terminology) is "indepsamplesregrT" for a between-units
design (typically, between-trials) and "depsamplesregrT" for a within-units
design (typically, within-subjects).


Good luck,

Eric






>
> Thanks at any rate for your clarification, and best wishes from Paris
> Floris
>
> >In your quote, also the concepts "symmetry of the distribution" and
> >"exchangeability" are mentioned. To keep things clear in our minds, it is
> >good to know that
> >
> >1. Some statisticians (e.g., Tom Nichols, the author of your quote)
motivate
> >permutation tests from considerations involving the shape of the
probability
> >distribution (such as symmetry). Other statisticians (like Fortunato
> >Pesarin, and I) motivate permutation tests from considerations about
> >exchangeability between experimental conditions.
> >
> >2. "Exchangeability" is a very general concept that can be used in very
> >different contexts. Some statisticians (e.g., Tom Nichols) use the term
> >"exchangeability" to denote a property of the probability distribution
from
> >which the subjects are drawn, not mentioning the fact that these subjects
> >were observed in two experimental conditions. Other statisticians (like
I)
> >use "exchangeability" with explicit reference to the data observed in the
> >two experimental conditions. For me, exchangeability involves that the
> >probability distribution of paired observations is invariant under random
> >permutations of the members of these pairs. This assumption of
> >exchangeability implies that the data in the two experimental conditions
> >have the same marginal probability distribution.
> >
> >
> >(If you like this explanation, Floris, you could join Jan-Mathijs in his
> >effort to make a Wiki-tutorial about the statistical rationale of
> >permutation tests.)
> >
> >
> >
> >
> >Don't start cursing the statisticians now!
> >
> >
> >Eric Maris
> >
> >>
> >> Hence the null hypothesis here is:
> >>     H0: The symmetric distribution of (the voxel values of the)
> >> subjects' contrast images have zero mean.
> >>
> >> And some more detail on the assumptions:
> >>
> >> (..) to analyze a group of subjects for population inference, we need
> >> to only assume exchangeability of subjects. The conventional
> >> assumption of independent subjects implies exchangeability, and hence
> >> a single exchangeability block (EB) consisting of all subjects.
> >>
> >> (On a technical note, the assumption of exchangeability can actually
> >> be relaxed for the one-sample case considered here. A sufficient
> >> assumption for the contrast data to have a symmetric distribution, is
> >> for each subject's contrast data to have a symmetric but possibly
> >> different distribution. Such differences between subjects violates
> >> exchangeability of all the data; however, since the null distribution
> >> of the statistic of interest is invariant with respect to
> >> sign-flipping, the test is valid.)
> >>
> >> I don't see why this approach wouldn't be applicable for MEG data?
> >> As a side note, comparing my regression weights with a condition of
> >> all zeros with a dependent sample T-test works well, and is
> >> mathematically equivalent to a one-sample T-test as far as I can see,
> >> at least in the parametric domain?
> >>
> >>
> >> Best wishes,
> >> Floris
> >>
> >> --
> >> --
> >> Floris de Lange
> >> http://www.florisdelange.com
> >>
> >> ----------------------------------
> >> The aim of this list is to facilitate the discussion between users of
the
> >FieldTrip
> >> toolbox, to share experiences and to discuss new ideas for MEG and EEG
> >analysis.
> >> See also http://listserv.surfnet.nl/archives/fieldtrip.html and
> >> http://www.ru.nl/fcdonders/fieldtrip.
> >
> >----------------------------------
> >The aim of this list is to facilitate the discussion between users of the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From olga at GRAPHICMIND.INFO  Wed Oct 22 13:10:01 2008
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Wed, 22 Oct 2008 12:10:01 +0100
Subject: Fwd: RE: clusterrandomization for 2 epochs separately
Message-ID: <WED.22.OCT.2008.121001.0100.>

> Dear Eric, 
> I would like to consult with you about some our ERP data and
> application of the clusterrandomization to it. 
> 
> I am writing now the article about ERP signs of visual change
> detection. 
> 
> We have ERP to the "deviant" and "standard" stimuli sampling rate
> 512 Hz, 64 channels (Biosemi), 12 subjects. 
> 
> If we use the paired-wise t-test to compare the ERPs' amplitudes in
> response to standard and deviant stimuli separately for each
> electrode and time point (and plot it see the picture at the end of
> the letter) we can see 2 (4) time regions of differences. But
> application of clusterrandomization analysis to these data (latency
> 0-500 ms) reveal only late cluster as significant, the early cluster
> is marginally significant (p=0.1). But I really believe in this early
> effect (120-160 ms), it is very important for our paper. When I run
> the clusterrandomization analysis on the narrowed epoch (0-300 ms) I
> got the early cluster significant. But the problem than that I loose
> the late effect, which is also worth mentioning in the paper. 
> 
> Therefore, I would like you opinion about the possibility to use the
> clusterrandomization analysis separately on the 2 epochs of interest,
> let say first 250 ms post-stimulus (0-250 ms) and next (250-500 ms). 
> 
> In this case there would be two significant clusters...  
> Best Regards, 
> 
> Olga Sysoeva 
> P.S. 
> 
> I also used different parameters for clusterrandomization (ndis,
> nchannels) but this does not change the results much.  
> P.P.S. 
> 
> Additional material 
> The paired-wise t-test was used to compare the ERPs' amplitudes in
> response to standard and deviant stimuli separately for each
> electrode and time point. 
> 
> The standard and deviant ERPs comparison reveals 2(4) intervals of
> significant differences:  
> 
> Fig.1. At this weird J picture we see the boxes of significant
> differences between standard and deviant ERPs for each time point (x
> axis) and electrode (y axis). 
> Olga Sysoeva, PhD
> Institute of Higher Nervous 
> Activity and Neurophysiology
> Russian Academy of Sciences
> 5a Butlerova str.
> Moscow 117485
> RUSSIA
> tel.: (7-095)-3347011, 
> fax:(7-095)-338-85-00.    
> 
> Links:
> ------
> [2] http://www.ru.nl/master/cns/
> 
> 

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From enteka at HOTMAIL.COM  Wed Oct 22 15:24:15 2008
From: enteka at HOTMAIL.COM (Nicolas Robitaille)
Date: Wed, 22 Oct 2008 13:24:15 +0000
Subject: Fwd: RE: clusterrandomization for 2 epochs separately
In-Reply-To: <49214.1224673801@graphicmind.info>
Message-ID: <WED.22.OCT.2008.132415.0000.FIELDTRIP@NIC.SURFNET.NL>


Dear Olga,

I have a quick answer for you, and would be please to heard people's comment on it. If you had a priori reason to belive something would happen for these electrodes and time-window, you don't need cluster analysis at all. All the solutions to the multiple-comparison problem are to be used in exploratory situation, when you don't know what to expect. If you had specific hypothesis, don't be shy: test them directy with a T-Test on the average voltage for a pre-determined time-window. 

Think about it, if you did expect these effects to be there, you could had create a montage with only one or two electrodes, and the multiple-comparison problem would not apply at all.

Hope this help,

Nic

************************************
Nicolas Robitaille, candidat Ph.D
Département de Psychologie
Université de Montréal
C.P. 6128, succursale Centre-ville
Montréal, Québec H3C 3J7
Tel.: 514-343-6111 x2631
Fax: 514-343-5787
************************************


> Date: Wed, 22 Oct 2008 12:10:01 +0100
> From: olga at GRAPHICMIND.INFO
> Subject: [FIELDTRIP] Fwd: RE: clusterrandomization for 2 epochs separately
> To: FIELDTRIP at NIC.SURFNET.NL
> 
> > Dear Eric, 
> > I would like to consult with you about some our ERP data and
> > application of the clusterrandomization to it. 
> > 
> > I am writing now the article about ERP signs of visual change
> > detection. 
> > 
> > We have ERP to the "deviant" and "standard" stimuli sampling rate
> > 512 Hz, 64 channels (Biosemi), 12 subjects. 
> > 
> > If we use the paired-wise t-test to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point (and plot it see the picture at the end of
> > the letter) we can see 2 (4) time regions of differences. But
> > application of clusterrandomization analysis to these data (latency
> > 0-500 ms) reveal only late cluster as significant, the early cluster
> > is marginally significant (p=0.1). But I really believe in this early
> > effect (120-160 ms), it is very important for our paper. When I run
> > the clusterrandomization analysis on the narrowed epoch (0-300 ms) I
> > got the early cluster significant. But the problem than that I loose
> > the late effect, which is also worth mentioning in the paper. 
> > 
> > Therefore, I would like you opinion about the possibility to use the
> > clusterrandomization analysis separately on the 2 epochs of interest,
> > let say first 250 ms post-stimulus (0-250 ms) and next (250-500 ms). 
> > 
> > In this case there would be two significant clusters...  
> > Best Regards, 
> > 
> > Olga Sysoeva 
> > P.S. 
> > 
> > I also used different parameters for clusterrandomization (ndis,
> > nchannels) but this does not change the results much.  
> > P.P.S. 
> > 
> > Additional material 
> > The paired-wise t-test was used to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point. 
> > 
> > The standard and deviant ERPs comparison reveals 2(4) intervals of
> > significant differences:  
> > 
> > Fig.1. At this weird J picture we see the boxes of significant
> > differences between standard and deviant ERPs for each time point (x
> > axis) and electrode (y axis). 
> > Olga Sysoeva, PhD
> > Institute of Higher Nervous 
> > Activity and Neurophysiology
> > Russian Academy of Sciences
> > 5a Butlerova str.
> > Moscow 117485
> > RUSSIA
> > tel.: (7-095)-3347011, 
> > fax:(7-095)-338-85-00.    
> > 
> > Links:
> > ------
> > [2] http://www.ru.nl/master/cns/
> > 
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

_________________________________________________________________


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
-------------- next part --------------
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From e.maris at DONDERS.RU.NL  Wed Oct 22 15:43:01 2008
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Wed, 22 Oct 2008 15:43:01 +0200
Subject: Fwd: RE: clusterrandomization for 2 epochs separately
In-Reply-To: <BAY136-W214848AC17B1ADB18F421EDF290@phx.gbl>
Message-ID: <WED.22.OCT.2008.154301.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Nic,

 

 

I have a quick answer for you, and would be please to heard people's comment
on it. If you had a priori reason to belive something would happen for these
electrodes and time-window, you don't need cluster analysis at all. All the
solutions to the multiple-comparison problem are to be used in exploratory
situation, when you don't know what to expect. If you had specific
hypothesis, don't be shy: test them directy with a T-Test on the average
voltage for a pre-determined time-window. 

Think about it, if you did expect these effects to be there, you could had
create a montage with only one or two electrodes, and the
multiple-comparison problem would not apply at all.



Your understanding makes me happy! I couldn’t have formulated it any better.

 

Eric Maris

 

 

 

 

 

 


Hope this help,

Nic

************************************
Nicolas Robitaille, candidat Ph.D
Département de Psychologie
Université de Montréal
C.P. 6128, succursale Centre-ville
Montréal, Québec H3C 3J7
Tel.: 514-343-6111 x2631
Fax: 514-343-5787
************************************


> Date: Wed, 22 Oct 2008 12:10:01 +0100
> From: olga at GRAPHICMIND.INFO
> Subject: [FIELDTRIP] Fwd: RE: clusterrandomization for 2 epochs separately
> To: FIELDTRIP at NIC.SURFNET.NL
> 
> > Dear Eric, 
> > I would like to consult with you about some our ERP data and
> > application of the clusterrandomization to it. 
> > 
> > I am writing now the article about ERP signs of visual change
> > detection. 
> > 
> > We have ERP to the "deviant" and "standard" stimuli sampling rate
> > 512 Hz, 64 channels (Biosemi), 12 subjects. 
> > 
> > If we use the paired-wise t-test to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point (and plot it see the picture at the end of
> > the letter) we can see 2 (4) time regions of differences. But
> > application of clusterrandomization analysis to these data (latency
> > 0-500 ms) reveal only late cluster as significant, the early cluster
> > is marginally significant (p=0.1). But I really believe in this early
> > effect (120-160 ms), it is very important for our paper. When I run
> > the clusterrandomization analysis on the narrowed epoch (0-300 ms) I
> > got the early cluster significant. But the problem than that I loose
> > the late effect, which is also worth mentioning in the paper. 
> > 
> > Therefore, I would like you opinion about the possibility to use the
> > clusterrandomization analysis separately on the 2 epochs of interest,
> > let say first 250 ms post-stimulus (0-250 ms) and next (250-500 ms). 
> > 
> > In this case there would be two significant clusters... 
> > Best Regards, 
> > 
> > Olga Sysoeva 
> > P.S. 
> > 
> > I also used different parameters for clusterrandomization (ndis,
> > nchannels) but this does not change the results much. 
> > P.P.S. 
> > 
> > Additional material 
> > The paired-wise t-test was used to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point. 
> > 
> > The standard and deviant ERPs comparison reveals 2(4) intervals of
> > significant differences: 
> > 
> > Fig.1. At this weird J picture we see the boxes of significant
> > differences between standard and deviant ERPs for each time point (x
> > axis) and electrode (y axis). 
> > Olga Sysoeva, PhD
> > Institute of Higher Nervous 
> > Activity and Neurophysiology
> > Russian Academy of Sciences
> > 5a Butlerova str.
> > Moscow 117485
> > RUSSIA
> > tel.: (7-095)-3347011, 
> > fax:(7-095)-338-85-00. 
> > 
> > Links:
> > ------
> > [2] http://www.ru.nl/master/cns/
> > 
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/fcdonders/fieldtrip.

  _____  

Obtenez votre dose d'information sur votre cellulaire. Avec MSN Mobile,
obtenez des mises à jour régulières sur l'actualité, les sports et les
finances Essayez-le aujourd'hui
<http://info.mobile.ca.msn.com/fr-ca/default.aspx>  !

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

The aim of this list is to facilitate the discussion between users of the
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http://listserv.surfnet.nl/archives/fieldtrip.html

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----------------------------------
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From olga at GRAPHICMIND.INFO  Wed Oct 22 17:12:27 2008
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Wed, 22 Oct 2008 19:12:27 +0400
Subject: Fwd: RE: clusterrandomization for 2 epochs separately
In-Reply-To: <20081022134258.CECC8A9FDE@smtp.ru.nl>
Message-ID: <WED.22.OCT.2008.191227.0400.FIELDTRIP@NIC.SURFNET.NL>

Thank you all for your answer. I perfectly understand what you wrote.

Unfortunately early effect I believe in is what only our group is found
therefore we could not use the former study and take the electrode and
latency from them.

I also know the way how I can represent our data using the conventional
t-test analysis.

I just want to use here the clusterrandomization analysis for more logical
and tense description of the results.

My question is does the usage of clusterrandomization on the 2 epochs
separately make sense here. If you think that the conventional t-test is
more suitable here, I’ll stand on it.

 

Best Regards,

Olga.

 

  _____  

From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Eric Maris
Sent: Wednesday, October 22, 2008 5:43 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] Fwd: RE: clusterrandomization for 2 epochs
separately

 

Dear Nic,

 

 

I have a quick answer for you, and would be please to heard people's comment
on it. If you had a priori reason to belive something would happen for these
electrodes and time-window, you don't need cluster analysis at all. All the
solutions to the multiple-comparison problem are to be used in exploratory
situation, when you don't know what to expect. If you had specific
hypothesis, don't be shy: test them directy with a T-Test on the average
voltage for a pre-determined time-window. 

Think about it, if you did expect these effects to be there, you could had
create a montage with only one or two electrodes, and the
multiple-comparison problem would not apply at all.

Your understanding makes me happy! I couldn’t have formulated it any better.

 

Eric Maris

 

 

 

 

 

 


Hope this help,

Nic

************************************
Nicolas Robitaille, candidat Ph.D
Département de Psychologie
Université de Montréal
C.P. 6128, succursale Centre-ville
Montréal, Québec H3C 3J7
Tel.: 514-343-6111 x2631
Fax: 514-343-5787
************************************


> Date: Wed, 22 Oct 2008 12:10:01 +0100
> From: olga at GRAPHICMIND.INFO
> Subject: [FIELDTRIP] Fwd: RE: clusterrandomization for 2 epochs separately
> To: FIELDTRIP at NIC.SURFNET.NL
> 
> > Dear Eric, 
> > I would like to consult with you about some our ERP data and
> > application of the clusterrandomization to it. 
> > 
> > I am writing now the article about ERP signs of visual change
> > detection. 
> > 
> > We have ERP to the "deviant" and "standard" stimuli sampling rate
> > 512 Hz, 64 channels (Biosemi), 12 subjects. 
> > 
> > If we use the paired-wise t-test to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point (and plot it see the picture at the end of
> > the letter) we can see 2 (4) time regions of differences. But
> > application of clusterrandomization analysis to these data (latency
> > 0-500 ms) reveal only late cluster as significant, the early cluster
> > is marginally significant (p=0.1). But I really believe in this early
> > effect (120-160 ms), it is very important for our paper. When I run
> > the clusterrandomization analysis on the narrowed epoch (0-300 ms) I
> > got the early cluster significant. But the problem than that I loose
> > the late effect, which is also worth mentioning in the paper. 
> > 
> > Therefore, I would like you opinion about the possibility to use the
> > clusterrandomization analysis separately on the 2 epochs of interest,
> > let say first 250 ms post-stimulus (0-250 ms) and next (250-500 ms). 
> > 
> > In this case there would be two significant clusters... 
> > Best Regards, 
> > 
> > Olga Sysoeva 
> > P.S. 
> > 
> > I also used different parameters for clusterrandomization (ndis,
> > nchannels) but this does not change the results much. 
> > P.P.S. 
> > 
> > Additional material 
> > The paired-wise t-test was used to compare the ERPs' amplitudes in
> > response to standard and deviant stimuli separately for each
> > electrode and time point. 
> > 
> > The standard and deviant ERPs comparison reveals 2(4) intervals of
> > significant differences: 
> > 
> > Fig.1. At this weird J picture we see the boxes of significant
> > differences between standard and deviant ERPs for each time point (x
> > axis) and electrode (y axis). 
> > Olga Sysoeva, PhD
> > Institute of Higher Nervous 
> > Activity and Neurophysiology
> > Russian Academy of Sciences
> > 5a Butlerova str.
> > Moscow 117485
> > RUSSIA
> > tel.: (7-095)-3347011, 
> > fax:(7-095)-338-85-00. 
> > 
> > Links:
> > ------
> > [2] http://www.ru.nl/master/cns/
> > 
> > 
> 
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/fcdonders/fieldtrip.

  _____  

Obtenez votre dose d'information sur votre cellulaire. Avec MSN Mobile,
obtenez des mises à jour régulières sur l'actualité, les sports et les
finances Essayez-le <http://info.mobile.ca.msn.com/fr-ca/default.aspx>
aujourd'hui !



__________ NOD32 3536 (20081019) Information __________

This message was checked by NOD32 antivirus system.
http://www.eset.com

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

The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis.

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http://www.ru.nl/fcdonders/fieldtrip/

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

The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and
EEG analysis.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/fieldtrip/


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From g.rousselet at PSY.GLA.AC.UK  Fri Oct 24 18:40:44 2008
From: g.rousselet at PSY.GLA.AC.UK (Guillaume Rousselet)
Date: Fri, 24 Oct 2008 17:40:44 +0100
Subject: Launch of CCNi and SI project
Message-ID: <FRI.24.OCT.2008.174044.0100.FIELDTRIP@NIC.SURFNET.NL>

The Department of Psychology at University of Glasgow is pleased to  
announce a Joint Event to launch the Centre for Cognitive Neuroimaging  
(CCNi) and  to officially launch our project: Social Interaction: a  
Cognitive Neurosciences Approach.
Date: Friday 28th November 2008; Venue: Kelvin Gallery, Gilbert Scott  
Building, University Avenue & the Department of Psychology / CCNi,  
University of Glasgow, UK.

The Event, starting at 10am, will include presentations by Professor  
Philippe Schyns (CCNi Director), Professor Nikos Logothetis (MPI  
Tübingen, Germany), Professor Riitta Hari (Low Temperature Laboratory,  
Helsinki, Finland), Professor Alvaro Pascual-Leone (Harvard Medical  
School, Boston, USA), Professor Paula Niedenthal (Université Blaise  
Pascal, Clermont-Ferrand, France), Professor Rainer Goebel (Univeridty  
of Maastricht, The Netherlands).

A drinks reception and a Tour of CCNi with poster presentation will be  
held from 5pm onwards in the Department of Psychology. Contact:  
Heather Robertson, CCNi Administrator, Department of Psychology (Room  
519) University of Glasgow, 58 Hillhead Street, Glasgow G12 8QB. tel:  
+44 (0)141 330 6173. Email: h.robertson at psy.gla.ac.uk. Web: www.ccni.gla.ac.uk 
,www.socialinteraction.gla.ac.uk




************************************************************************************
Guillaume A. Rousselet, Ph.D.

Lecturer

Centre for Cognitive Neuroimaging (CCNi)
Department of Psychology
Faculty of Information & Mathematical Sciences (FIMS)
University of Glasgow
58 Hillhead Street
Glasgow, UK
G12 8QB

The University of Glasgow, charity number SC004401

http://web.me.com/rousseg/GARs_website/

Email: g.rousselet at psy.gla.ac.uk
Fax. +44 (0)141 330 4606
Tel. +44 (0)141 330 6652
Cell +44 (0)791 779 7833


“Computers in the future may weigh no more than 1.5 tons.”
	
	Popular Mechanics, 1949
************************************************************************************




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From r.oostenveld at FCDONDERS.RU.NL  Mon Oct 27 10:03:39 2008
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Mon, 27 Oct 2008 10:03:39 +0100
Subject: time-frequency representation of PLV
In-Reply-To: <1224360344780798.0.outsmtp04@outsmtp04>
Message-ID: <MON.27.OCT.2008.100339.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi Hyoungdong

On 18 Oct 2008, at 22:05, 박형동 wrote:
> Is it possible to draw a time-frequency representation of PLV using  
> singleplotTFR ?
>
> It looks like that i can only draw TFR of power spectra with  
> singleplotTFR, even though multiplotTFR and topoplotTFR supports PLV.

You can specify xparam/yparam and zparam in the singleplotTFR  
configuration. Assuming that you have something like

freq = freqanalysis(...)

cfg.cohmethod = 'plv'
fd = freqdescriptives(cfg, freq)

then your fd structure contains
   fd.time
   fd.freq
   fd.plvspctrm
which are to be specified as x, y and z params for singleplotTFR.

best regards,
Robert

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From spil at OKWF.FUW.EDU.PL  Mon Oct 27 15:12:12 2008
From: spil at OKWF.FUW.EDU.PL (=?ISO-8859-2?Q?Szymon_Pi=B3at?=)
Date: Mon, 27 Oct 2008 15:12:12 +0100
Subject: Dipolefitting output coordinates
Message-ID: <MON.27.OCT.2008.151212.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi everyone!

For several days I have been trying to figure out the "dipolefitting"
script output.

I guess its output is in xyz coordinates. But is this in MNI space or
Talairach space?

BTW: How to visualise the dipole I found? I use "dipplot" from EEGLAB
but I am looking for other simple way to visualise a dipole.

Thank you in advance for your help.
Best regards,
Szymon Pilat
--
spil at okwf.fuw.edu.pl
Department of Biomedical Physics
University of Warsaw

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From a.maye at UKE.DE  Mon Oct 27 16:04:56 2008
From: a.maye at UKE.DE (Alexander Maye)
Date: Mon, 27 Oct 2008 16:04:56 +0100
Subject: Preproc - thresholding negative z-scores too?
Message-ID: <MON.27.OCT.2008.160456.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear List!

In my dataset I have a nice EOG signal, in which the respective artifact detection routines 
nonetheless do not detect artifacts,since its polarity is negative. Consequently the 
z-scores also deviate towards negative, and are always below (the positive) threshold 
value. So, shouldn't artifact_zvalue threshold the *absolute* z-value instead of the raw 
z-score? I know this has been asked last year, but couldn't find an answer. Any 
opinions/preferred solutions? Ah, and yes, I played with hilbert and rectify, but hilbert does 
not change the polarity (what does it anyway?), and rectify rectifies the data, not the 
z-scores.

Best,

                       ALEX.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From v.litvak at ION.UCL.AC.UK  Mon Oct 27 19:26:50 2008
From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak)
Date: Mon, 27 Oct 2008 18:26:50 +0000
Subject: Dipolefitting output coordinates
In-Reply-To: <8834c95d0810270712j6941eb08xf29d3ca5881fcb98@mail.gmail.com>
Message-ID: <MON.27.OCT.2008.182650.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Szymon,

Fieldtrip can work in any coordinate system so the coordinates of the
output are determined by coordinates of the input (i.e. the sensors
and the volume model that you provided). MNI space and Talairach space
are exactly the same. The only thing different is the template brain
i.e. anatomical interpretation of the coordinates.  But the
coordinates Fieldtrip outputs can be neither unless your sensor
locations are given in MNI coordinates.

You can use headmodelplot to plot your volume and sensors and then
plot3 to add the dipole locations to that plot.

Best,

Vladimir


On Mon, Oct 27, 2008 at 2:12 PM, Szymon Piłat <spil at okwf.fuw.edu.pl> wrote:
> Hi everyone!
>
> For several days I have been trying to figure out the "dipolefitting"
> script output.
>
> I guess its output is in xyz coordinates. But is this in MNI space or
> Talairach space?
>
> BTW: How to visualise the dipole I found? I use "dipplot" from EEGLAB
> but I am looking for other simple way to visualise a dipole.
>
> Thank you in advance for your help.
> Best regards,
> Szymon Pilat
> --
> spil at okwf.fuw.edu.pl
> Department of Biomedical Physics
> University of Warsaw
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
>

From j.schoffelen at PSY.GLA.AC.UK  Tue Oct 28 10:47:06 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Tue, 28 Oct 2008 09:47:06 +0000
Subject: Preproc - thresholding negative z-scores too?
In-Reply-To: <LISTSERV%200810271604560250.00C5@NIC.SURFNET.NL>
Message-ID: <TUE.28.OCT.2008.094706.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Alex,

As far as I remember, the default settings for artifact_eog (the
'higher' level function which calls artifact_zvalue later on) contain
the (absolute of the) hilbert transform.
The hilbert-transform of a bandpass filtered signal is an estimate of
the instantaneous amplitude. Since it is an absolute value, it is
always positive and should reverse
the polarity of the EOG, as would rectification.
I do not really understand your statement that the polarity is not
changed by either rectification of hilbert transformation. Could it
be that you specified your options in
cfg.artfctdef.eog, and then called artifact_zvalue? or
cfg.artfctdef.zvalue and called artifact_eog?

I guess specifying cfg.artfctdef.XXX. rectify/hilbert = 'yes', and
subsequently calling artifact_XXX (eog or zvalue) should do the
trick. Of course, specifying cfg.artfctdef.XXX.feedback = 'yes',
gives you an idea how the data look.

Good luck

Jan-Mathijs


On Oct 27, 2008, at 3:04 PM, Alexander Maye wrote:

> Dear List!
>
> In my dataset I have a nice EOG signal, in which the respective
> artifact detection routines
> nonetheless do not detect artifacts,since its polarity is negative.
> Consequently the
> z-scores also deviate towards negative, and are always below (the
> positive) threshold
> value. So, shouldn't artifact_zvalue threshold the *absolute* z-
> value instead of the raw
> z-score? I know this has been asked last year, but couldn't find an
> answer. Any
> opinions/preferred solutions? Ah, and yes, I played with hilbert
> and rectify, but hilbert does
> not change the polarity (what does it anyway?), and rectify
> rectifies the data, not the
> z-scores.
>
> Best,
>
>                        ALEX.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From a.maye at UKE.DE  Tue Oct 28 14:14:08 2008
From: a.maye at UKE.DE (Alexander Maye)
Date: Tue, 28 Oct 2008 14:14:08 +0100
Subject: Preproc - thresholding negative z-scores too?
Message-ID: <TUE.28.OCT.2008.141408.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs and All!

Thank you for the quick response. Hilbert indeed flips my eye blinks towards positive 
z-values - at the cost of reduced discriminability. That is to say that the amplitude of the 
z-score of the eye blink is twice as high without Hilbert (but in the "wrong" direction). Apart 
from that I still would like to know the rationale behind considering deviations of the z-value 
towards +Inf as artifacts, while those towards -Inf not. This is the same concern as in 
#Item001386 of this list exactly one year ago. Any opinions?

Best,

                         ALEX.

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From bps231 at NYU.EDU  Thu Oct 30 18:19:30 2008
From: bps231 at NYU.EDU (Bernhard Staresina)
Date: Thu, 30 Oct 2008 18:19:30 +0100
Subject: stats on single subject coherence
Message-ID: <THU.30.OCT.2008.181930.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear FieldTrip experts,

I was wondering if there is a way to test the significance of coherence
values between two channels across two different conditions within a single
subject (assuming, for simplicity, equal number of trials in both
conditions). As far as I know this is not implemented in the neat
randomization/cluster stats methods for now, but any advice would be greatly
appreciated.

Thanks,
Bernhard



----------------------------------
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From g.rousselet at PSY.GLA.AC.UK  Thu Oct 30 18:36:09 2008
From: g.rousselet at PSY.GLA.AC.UK (Guillaume Rousselet)
Date: Thu, 30 Oct 2008 17:36:09 +0000
Subject: stats on single subject coherence
In-Reply-To: <LISTSERV%200810301819306620.3CDB@NIC.SURFNET.NL>
Message-ID: <THU.30.OCT.2008.173609.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Bernhard,

what you want to do is the same as comparing 2 independent groups of
subjects. Thanks to the modular architecture of Filedtrip you can plug-
in a T-statistic for independent samples when you do the permutation +
clustering. The general procedure is described in Eric Maris' 2007 J.
Neurosci. Meth. paper.

Best,

GAR



On 30 Oct 2008, at 17:19, Bernhard Staresina wrote:

> Dear FieldTrip experts,
>
> I was wondering if there is a way to test the significance of
> coherence
> values between two channels across two different conditions within a
> single
> subject (assuming, for simplicity, equal number of trials in both
> conditions). As far as I know this is not implemented in the neat
> randomization/cluster stats methods for now, but any advice would be
> greatly
> appreciated.
>
> Thanks,
> Bernhard
>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/fcdonders/fieldtrip.



************************************************************************************
Guillaume A. Rousselet, Ph.D.

Lecturer

Centre for Cognitive Neuroimaging (CCNi)
Department of Psychology
Faculty of Information & Mathematical Sciences (FIMS)
University of Glasgow
58 Hillhead Street
Glasgow, UK
G12 8QB

The University of Glasgow, charity number SC004401

http://web.me.com/rousseg/GARs_website/

Email: g.rousselet at psy.gla.ac.uk
Fax. +44 (0)141 330 4606
Tel. +44 (0)141 330 6652
Cell +44 (0)791 779 7833


"There is, in short, a huge tacit conspiracy between the U.S.
government, its
agencies and its multinational corporations, on the one hand, and local
business and military cliques in the Third World, on the other, to
assume
complete control of these countries and "develop" them on a joint
venture
basis. The military leaders of the Third World were carefully nurtured
by the
U.S. security establishment to serve as the "enforcers" of this joint
venture
partnership, and they have been duly supplied with machine guns and the
latest data on methods of interrogation of subversives."

	Edward S. Herman - The Real terror network - 1982
************************************************************************************






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From j.schoffelen at PSY.GLA.AC.UK  Fri Oct 31 10:30:09 2008
From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen)
Date: Fri, 31 Oct 2008 09:30:09 +0000
Subject: Preproc - thresholding negative z-scores too?
In-Reply-To: <LISTSERV%200810281414088160.05C0@NIC.SURFNET.NL>
Message-ID: <FRI.31.OCT.2008.093009.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Alex,

The answer to you question would be in this case: it's a historical
thing. The Z-value thresholding was conceived to be done on filtered-
and-subsequently-rectified/hilberted data. No need to look for low
Zvalues in that case. In itself, there's no reason not to build in an
option to look for negative Z-values as well. I would gladly help to
build it into the release version for you. I would think of an
option: cfg.artfctdef.zvalue.tail, which will be 1 by default (that
is: only looking at high positive deviations), but could be -1 (for
the large negative ones), or 0 (for both sided). Could you propose an
adjusted version of artifact_zvalue to me, and I'll check it and
build it in.
As for the reduced discriminability: I still don't understand why
this is the case. I assume you have more than 1 EOG channel?
Probably, one of these guys is picking up most of the artifacts, but
if you use both channels in a single run of artifact_eog, the same
threshold is applied to both channels, which indeed would affect the
sensitivity. An alternative would be to call artifact_eog twice, with
the different EOG in cfg.artfctdef.eog.channel, so that you can use
channel-specific thresholds.

Yours,

Jan-Mathijs

On Oct 28, 2008, at 1:14 PM, Alexander Maye wrote:

> Dear Jan-Mathijs and All!
>
> Thank you for the quick response. Hilbert indeed flips my eye
> blinks towards positive
> z-values - at the cost of reduced discriminability. That is to say
> that the amplitude of the
> z-score of the eye blink is twice as high without Hilbert (but in
> the "wrong" direction). Apart
> from that I still would like to know the rationale behind
> considering deviations of the z-value
> towards +Inf as artifacts, while those towards -Inf not. This is
> the same concern as in
> #Item001386 of this list exactly one year ago. Any opinions?
>
> Best,
>
>                          ALEX.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.


From miguelconstante at GMAIL.COM  Fri Oct 31 18:23:09 2008
From: miguelconstante at GMAIL.COM (Miguel Constante)
Date: Fri, 31 Oct 2008 18:23:09 +0100
Subject: low frequency cut-off and filtfilt
Message-ID: <FRI.31.OCT.2008.182309.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi
I have been trying to high-pass filter my EEG data, 
cfg.hpfilter = 'yes';
cfg.hpfreq = 0.03;
data = preprocessing(cfg);

using cut offs under 1Hz (e.g. 0.03Hz) and systematically get this type of 
error:

Warning: Matrix is close to singular or badly scaled.
         Results may be inaccurate. RCOND = 2.221255e-017.

Can someone advise on how to overcome this?
Thanks
Miguel

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.