From sangita.dandekar at GMAIL.COM  Fri Oct  1 18:00:41 2010
From: sangita.dandekar at GMAIL.COM (Sangita Dandekar)
Date: Fri, 1 Oct 2010 12:00:41 -0400
Subject: baseline, combine_planar, and freqanalysis
Message-ID: <FRI.1.OCT.2010.120041.0400.FIELDTRIP@NIC.SURFNET.NL>

Hi,

I'm wondering about the optimal order in which to apply combine_planar and
baselining (relative to a pretrial time window)  to time-frequency power
spectra data.

Does it make more sense to do:

A:
1. meg_planar
2. freqanalysis
3. combine_planar
4. freqbaseline (on a trial by trial basis?  see below)

or B:
1. meg_planar
2. freqanalysis
3. freqbaseline(on a trial by trial basis? see below)
4. combine_planar


Also, are there any opinions on whether baselining on a trial by trial basis
is preferable o  if it might be better to instead baseline with respect to
the average of all pretrial baseline power spectra?

Thanks in advance,
Sangi

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From e.maris at DONDERS.RU.NL  Fri Oct  1 21:10:09 2010
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Fri, 1 Oct 2010 21:10:09 +0200
Subject: coherence and inter-trial coherence questions
In-Reply-To: <AANLkTikDZ-p1qm+H0RUAZOskmfNuFQ9dHt79hu9t2WnX@mail.gmail.com>
Message-ID: <FRI.1.OCT.2010.211009.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Matteo,





I have two questions regarding statistical tests: first one regarding
coherence differences, second one pertaining testing inter-trial coherence.

We are analysing MEG data from an auditory experiment with 5 subjects. We
considered the deviant stimulus as the only stimulus in the recordings,
while the standard one was considered as baseline activity.

We analysed the TFR data in both designs: within-trial and within-subject
using respectively "actvsblT" and "depsamplesT" statistics. In both cases we
compared a time interval extracted from the baseline versus a time interval
from the deviant stimulus response.

We wish to assess coherence differences using "indepsampleZcoh" statistic in
both single-subject and multiple-subject cases. In a previous post
<https://listserv.surfnet.nl/scripts/wa.cgi?A2=ind1004&L=FIELDTRIP&D=0&P=108
12>  Dr. Maris replied that this statistic only works in a between-trial
design (for single-subject case) and suggested to compare the different
conditions as they were un-paired.
We exploited this idea for the single-subject case and we would like to know
if it is legitimate to extend the same idea for the multiple-subject
situation?



In the multiple-subject situation, you should first calculate the two
coherences (one for the deviant stimulus and one for the baseline condition)
for every subject. These coherences should be compared using depsamplesT
(and not using indepsamplesZcoh, which only works for a single-subject
study). I'm fairly sure that the testing of coherence in a multiple subject
study has already been addressed in the Fieldtrip discussion list. I think
it was Jan-Matthijs Schoffelen who gave a extensive description on how to do
it.




Furthermore we would like to know if there is a way to test inter-trial
coherence differences in Fieldtrip?
In a previous
<https://listserv.surfnet.nl/scripts/wa.cgi?A2=ind0803&L=FIELDTRIP&D=0&P=180
> post Stephan suggested how to deal with the problem; is it already
implemented?

If it has been implemented, I'm not aware of it. However, if you are a
little bit proficient in Matlab programming, you can write you own statfun
and have Fieldtrip apply it to your data. By debugging a statistical
analysis that uses a built-in statfun, you can learn how the algorithm
works.





Good luck,



Eric Maris













Thanks in advance for your time

Matteo


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

The aim of this list 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/neuroimaging/fieldtrip.
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From hubert.preissl at UNI-TUEBINGEN.DE  Mon Oct  4 09:49:21 2010
From: hubert.preissl at UNI-TUEBINGEN.DE (Hubert Preissl)
Date: Mon, 4 Oct 2010 09:49:21 +0200
Subject: Conference and Autumn School at the M EG Center in
 T=?ISO-8859-1?Q?=FCbingen,?= November 2010
In-Reply-To: <00ca01cb619c$44074270$cc15c750$@maris@donders.ru.nl>
Message-ID: <MON.4.OCT.2010.094921.0200.FIELDTRIP@NIC.SURFNET.NL>



*Lifelong Imaging Conference: 25^th -27^th November 2010*

*Autumn School "Analyze the brain": 24^th -25^th November 2010 *


Hello,
we are pleased to announce the upcoming "Autumn school" followed by the
"Lifelong Imaging conference" in Tübingen organized by the MEG Center.

For application and further information on invited speakers and
scientific program
please visit our website:

http://www.mp.uni-tuebingen.de/lli-konferenz/


We look forward to meet you in Tübingen!

Best regards ,

Hubert Preissl

ps: we encountered over the last week several problems with our web-server and

hope that it is running smoothly now. If you encounter any problems please contact:

  meg at med.uni-tuebingen.de  <mailto:meg at med.uni-tuebingen.de>.



--
Dr. Hubert Preissl
MEG-Center                   	phone: ++49-(0)7071-2987704
Otfried Mueller Str 47       	fax: ++49-(0)7071-295706
72076 Tübingen, Germany      	email: hubert.preissl at uni-tuebingen.de



----------------------------------
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From sangita.dandekar at GMAIL.COM  Tue Oct  5 13:56:32 2010
From: sangita.dandekar at GMAIL.COM (Sangita Dandekar)
Date: Tue, 5 Oct 2010 07:56:32 -0400
Subject: baseline, combine_planar, and freqanalysis
In-Reply-To: <AANLkTikmWUXPGLEY+=LGiE8TH0=ZSXPTK7n+ukv=e5C3@mail.gmail.com>
Message-ID: <TUE.5.OCT.2010.075632.0400.FIELDTRIP@NIC.SURFNET.NL>

Thought I'd try reposting once, since I happened to send this on a weekend
and didn't receive any reply. Sorry for the repost.
Thanks,
Sangi

---------- Forwarded message ----------
From: Sangita Dandekar <sangita.dandekar at gmail.com>
Date: Fri, Oct 1, 2010 at 12:00 PM
Subject: baseline, combine_planar, and freqanalysis
To: FieldTrip discussion list <FIELDTRIP at nic.surfnet.nl>


Hi,

I'm wondering about the optimal order in which to apply combine_planar and
baselining (relative to a pretrial time window)  to time-frequency power
spectra data.

Does it make more sense to do:

A:
1. meg_planar
2. freqanalysis
3. combine_planar
4. freqbaseline (on a trial by trial basis?  see below)

or B:
1. meg_planar
2. freqanalysis
3. freqbaseline(on a trial by trial basis? see below)
4. combine_planar


Also, are there any opinions on whether baselining on a trial by trial basis
is preferable or  if it might be better to instead baseline with respect to
the average of all pretrial baseline power spectra?

Thanks in advance,
Sangi

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between  users of the FieldTrip  toolbox, to share experiences
and to discuss  new ideas for MEG and EEG analysis.
See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
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From r.oostenveld at DONDERS.RU.NL  Wed Oct  6 09:13:23 2010
From: r.oostenveld at DONDERS.RU.NL (Robert Oostenveld)
Date: Wed, 6 Oct 2010 09:13:23 +0200
Subject: MEG scientist position in St Louis
Message-ID: <WED.6.OCT.2010.091323.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear FieldTrip colleagues,

Please find a job advertisement attached. Feel free to distribute this
to potentially interested candidates.

best regards,
Robert

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From coppolar at MAIL.NIH.GOV  Wed Oct  6 23:47:39 2010
From: coppolar at MAIL.NIH.GOV (Coppola, Richard (NIH/NIMH) [E])
Date: Wed, 6 Oct 2010 17:47:39 -0400
Subject: MEG Positions TBI Research
Message-ID: <WED.6.OCT.2010.174739.0400.FIELDTRIP@NIC.SURFNET.NL>

MEG Positions TBI Research:  We expect several positions to be available in support of the new MEG Laboratory (Elekta Neuromag 306 Channel Vectorview) being set up in the National Intrepid Center of Excellence (NICoE) located at the Natlonal Naval Medical Center in Bethesda MD.
 http://www.dcoe.health.mil/ComponentCenters/NICoE.aspx <http://www.dcoe.health.mil/ComponentCenters/NICoE.aspx>
The Center addresses interdisciplinary evaluation and treatment planning for Warriors with mild traumatic brain injury (TBI) and psychological health (PH) issues resulting from battle-related exposure. It is planned that the MEG Lab will operate cooperatively with the National Institute of Mental Health, NIH.
The positions will include personnel at several levels of background as needed to staff the facility including Lab Manager/Technologist, MEG engineer/physicist/neuroscientist, MEG research scientist, clinical researcher and post-doctoral researcher.  The Technologist should have background in Clinical Neurophysiology, familiarity with patient populations, good computer skills, and will be responsible for scheduling and running subjects, and general laboratory management.  The MEG engineer/physicist/neuroscientist will provide expertise and support for the MEG system and for other scientists involved in MEG studies. Background will include a  PhD or other qualifying degree in Neuroinformatics, Neuroscience, Physics or a related area and expertise in principles of experimental design, data handling and analysis and statistical methods.  Good computing skills including task programming, MEG processing software and statistical software are also necessary, as are good interpersonal skills.  The MEG Scientist and /or Clinical Researcher should have a strong background in cognitive neuroscience, neuropsychology, or neurorehabilitation, with expertise in neuroimaging along with requisite methodological skills.  Salaries will be competitive and commensurate with background and anticipated to be awarded as renewable contract positions.
To indicate your interest please email to Dr. Richard Coppola at coppolar at mail.nih.gov<mailto:coppolar at mail.nih.gov> with a cover letter and CV and contact details for three professional references.  Please specify NICOE in the subject line.


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From michael.wibral at WEB.DE  Thu Oct  7 15:32:27 2010
From: michael.wibral at WEB.DE (Michael Wibral)
Date: Thu, 7 Oct 2010 15:32:27 +0200
Subject: 2 Post Doc Positions in MEG/Brain Imaging,
 Max Planck Institute for Brain Research, Frankfurt
Message-ID: <THU.7.OCT.2010.153227.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Filedtrip users,

please find attached below a job posting by Peter Uhlhaas:


Postdoctoral
Position in Brain Imaging

2 postdoctoral positions in brain imaging are available at the Max Planck Institute
for Brain Research, Department of Neurophysiology
(Director: Professor W. Singer) in the groups of Dr. Peter J. Uhlhaas
and Dr. Lucia Melloni.
The successful applicant will work on projects examining neural
oscillations in psychiatric disorders (schizophrenia and synesthesia)
with magnetoencephalography (MEG) and advanced signal-processing
analyses (Beamforming, Transfer Entropy). The position is in
collaboration with Dr. Michael Wibral (MEG-Unit, Brain Imaging
Center Frankfurt).

The ideal candidate should have a PhD in neuroimaging
and expertise with a neuroimaging technique (EEG, MEG, fMRI/MRI).
Prior experience with MEG is not a prerequisite. Excellent research
opportunities are available at the nearby Brain Imaging Center.
Applications from a physics or engineering background are welcome as
well. Expertise in Matlab programming is required. The position will
run initially for two years. The position will start on the 1st
of January 2010.

Informal inquiries can be directed to Peter Uhlhaas
([uhlhaas at mpih-frankfurt.mpg.de])
or to Lucia Melloni (melloni at mpih-frankfurt.mpg.de).


To apply, please send curriculum
vitae, letter of interest, names and contact information of two
references to:

Peter Uhlhaas
Max Planck Institute for Brain Research
Department of Neurophysiology
Deutschordenstr. 46
60528 Frankfurt am Main
GERMANY

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From michael.wibral at WEB.DE  Thu Oct  7 21:34:30 2010
From: michael.wibral at WEB.DE (Michael Wibral)
Date: Thu, 7 Oct 2010 21:34:30 +0200
Subject: baseline, combine_planar, and freqanalysis
In-Reply-To: <AANLkTi=mnEDzKAZD0c+f7QaWEX0xQnmOz-c2-dyLhEMU@mail.gmail.com>
Message-ID: <THU.7.OCT.2010.213430.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Sangita,

the problem you raised is actually a tough one, that does not have a fully satifactory solution. The fundamental reason is the loss of spatial direction information in combineplanar that either affects interpretability of the resulting quantity or implies certain assumptions. Below I try to give you a quick explanation - the mathematical details are a bit lengthy.

Baseline correcting before combineplanar would either amount to the same as subtracting the baseline timecourse from the task time course directly - if done on the 4D (!!) object composed of the two complex fourier coeffients in the x,y gradient vector. Else, if you subtract amplitudes or power values per spatial direction separately a relatively uninterpretable quantity (because spatial angles between task and baseline would play a major role) results after combineplanar. This is because of the effect of different gradient field angles between task and baseline. So the only viable way seems to be to correct after combineplanar. The implicit assumptions then is however, that source configuration (orientation) does not change between task and baseline, this should be justified/discussed for the case at hand. This problem does not occur for axial quantities as there is no loss of spatial information there.

Hope this helps, please also let me know if you (or anyone else) disagrees!
Michael

PS: If anyone knows how to quantify spectral power of *arbitrary time varying vector fields* (not linearly or circularily polarized ones) uniquely and without assumptions on correlations between vector components please post it to the list.


---------------------
Von: "Sangita Dandekar" <sangita.dandekar at GMAIL.COM>
Gesendet: Oct 5, 2010 1:56:32 PM
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: [FIELDTRIP] baseline, combine_planar, and freqanalysis

Thought I'd try reposting once, since I happened to send this on a weekend and didn't receive any reply. Sorry for the repost.
Thanks,
Sangi


---------- Forwarded message ----------
 From: Sangita Dandekar <[sangita.dandekar at gmail.com]>
Date: Fri, Oct 1, 2010 at 12:00 PM
Subject: baseline, combine_planar, and freqanalysis
 To: FieldTrip discussion list <[FIELDTRIP at nic.surfnet.nl]>


Hi,

I'm wondering about the optimal order in which to apply combine_planar and baselining (relative to a pretrial time window)  to time-frequency power spectra data.

Does it make more sense to do:

 A:
1. meg_planar
2. freqanalysis
3. combine_planar
4. freqbaseline (on a trial by trial basis?  see below)

or B:
1. meg_planar
 2. freqanalysis
 3. freqbaseline(on a trial by trial basis? see below)
 4. combine_planar


Also, are there any opinions on whether baselining on a trial by trial basis is preferable or  if it might be better to instead baseline with respect to the average of all pretrial baseline power spectra?

Thanks in advance,
Sangi






--------------------------------------------------------------------------- You are receiving this message because you are subscribed to
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 between  users of the FieldTrip  toolbox, to share experiences
 and to discuss  new ideas for MEG and EEG analysis.
 See also http://listserv.surfnet.nl/archives/fieldtrip.html
 and http://www.ru.nl/neuroimaging/fieldtrip.
 ---------------------------------------------------------------------------

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You are receiving this message because you are subscribed to
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and to discuss  new ideas for MEG and EEG analysis.
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and http://www.ru.nl/neuroimaging/fieldtrip.
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From e.vandenbroeke at ANES.UMCN.NL  Fri Oct  8 11:51:15 2010
From: e.vandenbroeke at ANES.UMCN.NL (Emanuel van den Broeke)
Date: Fri, 8 Oct 2010 11:51:15 +0200
Subject: one sided or two sided testing
Message-ID: <FRI.8.OCT.2010.115115.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Eric and/or others,

If you have prior knowledge that the ERP is to be expected to be lower in one 
group as compared to the other group of subjects is it then allowed to only 
test the positive T-sum clusters (alpha 0.05) and neglect the negative 
clusters?

Thank you in advance,
Best, Emanuel

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From e.vandenbroeke at ANES.UMCN.NL  Fri Oct  8 14:59:28 2010
From: e.vandenbroeke at ANES.UMCN.NL (Emanuel van den Broeke)
Date: Fri, 8 Oct 2010 14:59:28 +0200
Subject: What if there are no negative clusters?
Message-ID: <FRI.8.OCT.2010.145928.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear people
Who can answer my question?

So I understand that is always the best to test two-sided with the non-
parametric permutation test, because one is interested in both directions of 
the effect; so both the positive and negative clusters. but what if your 
observed dat shows no negative clusters? There is no negative cluster 
detected above the threshold. Do you still have to use an alpha of 0.025 then?

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and to discuss  new ideas for MEG and EEG analysis.
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and http://www.ru.nl/neuroimaging/fieldtrip.
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From michael.wibral at WEB.DE  Fri Oct  8 15:21:49 2010
From: michael.wibral at WEB.DE (Michael Wibral)
Date: Fri, 8 Oct 2010 15:21:49 +0200
Subject: What if there are no negative clusters?
In-Reply-To: <LISTSERV%201010081459284770.9D55@NIC.SURFNET.NL>
Message-ID: <FRI.8.OCT.2010.152149.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Emanuel,

of course you have to use an alpha of 0.025 if you want to test both effect directions independently (as I assume). This is because you only know post hoc that there are no negative clusters. There is no way around it.

Michael

-----Ursprüngliche Nachricht-----
Von: "<Emanuel van den Broeke>" <e.vandenbroeke at ANES.UMCN.NL>
Gesendet: Oct 8, 2010 2:59:28 PM
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: [FIELDTRIP] What if there are no negative clusters?

>Dear people
>Who can answer my question?
>
>So I understand that is always the best to test two-sided with the non-
>parametric permutation test, because one is interested in both directions of 
>the effect; so both the positive and negative clusters. but what if your 
>observed dat shows no negative clusters? There is no negative cluster 
>detected above the threshold. Do you still have to use an alpha of 0.025 then?
>
>---------------------------------------------------------------------------
>You are receiving this message because you are subscribed to
>the  FieldTrip list. The aim of this list is to facilitate the discussion
>between  users of the FieldTrip  toolbox, to share experiences
>and to discuss  new ideas for MEG and EEG analysis.
>See also http://listserv.surfnet.nl/archives/fieldtrip.html
>and http://www.ru.nl/neuroimaging/fieldtrip.
>---------------------------------------------------------------------------

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From e.maris at DONDERS.RU.NL  Fri Oct  8 16:14:43 2010
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Fri, 8 Oct 2010 16:14:43 +0200
Subject: one sided or two sided testing
In-Reply-To: <LISTSERV%201010081151158780.9B04@NIC.SURFNET.NL>
Message-ID: <FRI.8.OCT.2010.161443.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Emanuel,


> If you have prior knowledge that the ERP is to be expected to be lower
> in one
> group as compared to the other group of subjects is it then allowed to
> only
> test the positive T-sum clusters (alpha 0.05) and neglect the negative
> clusters?

Yes, this is allowed. Such a procedure controls the false alarm rate at
0.05.


Best,

Eric Maris



>
> Thank you in advance,
> Best, Emanuel
>
> -----------------------------------------------------------------------
> ----
> You are receiving this message because you are subscribed to
> the  FieldTrip list. The aim of this list is to facilitate the
> discussion
> between  users of the FieldTrip  toolbox, to share experiences
> and to discuss  new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> -----------------------------------------------------------------------
> ----

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From akiko at NYU.EDU  Mon Oct 11 00:54:28 2010
From: akiko at NYU.EDU (Akiko Ikkai)
Date: Sun, 10 Oct 2010 18:54:28 -0400
Subject: plotting plv
In-Reply-To: <1704750977.1475589.1286480070322.JavaMail.fmail@mwmweb056>
Message-ID: <SUN.10.OCT.2010.185428.0400.FIELDTRIP@NIC.SURFNET.NL>

Hi,

I'm trying to plot plv between channel pairs that I get from ft_connectivityanalysis.

when I run
cfg                  = [];
cfg.xparam           = 'time';
cfg.yparam           = 'freq';
cfg.zparam           = 'cohsprctm';  % need to run stat.cohsprctm = stat.plvspctrm;
                                                  % fixed in the latest version?
cfg.cohrefchannel    = '1';
cfg.layout = 'ordered';
cfg.showlabels       = 'yes';
cfg.colorbar         = 'yes';
figure; ft_multiplotTFR(cfg, stat)

I get this error:
ft_multiplotTFR(cfg, stat)
??? Index exceeds matrix dimensions.

Error in ==> ft_multiplotTFR at 242
datavector = data.(cfg.zparam)(seldat,yidc,xidc);


... I'm guessing the error is something like wrong channel combination or refchannel selection, but not able to locate where the error is coming from (have tried different channel combination). stat.dimord is "chan_chan_freq_time", which might not be formatted appropriately for ft_multiplotTFR...?  Below, I'm attaching the code used to get "stat" (plv).

Any suggestions? Thanks in advance! Akiko


%%%%% code for connectivityanalysis %%%%%%
cfg = [];
cfg.output ='fourier'; % instead of 'powandcsd'... fixed in the latest version?
cfg.method          = 'mtmconvol';
cfg.channel = {'1', '7', '120'}; % contra & unrelated channels to test
cfg.channelcmb = {'1' '7'; '1' '120'; '7', '120'};
cfg.keeptrials = 'yes';
cfg.keeptapers = 'no';
cfg.toi             = [-.8:.1:2]
cfg.foi             = [1:0.5:30];
cfg.taper           = 'hanning';
cfg.t_ftimwin       = zeros(1,length(cfg.foi));
cfg.t_ftimwin(:)    = 5./cfg.foi;
TFR = ft_freqanalysis(cfg, ft_data);

cfg=[];
cfg.method  = 'plv';
[stat] = ft_connectivityanalysis(cfg,  TFR);

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and to discuss  new ideas for MEG and EEG analysis.
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From jan.schoffelen at DONDERS.RU.NL  Mon Oct 11 09:17:29 2010
From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen)
Date: Mon, 11 Oct 2010 09:17:29 +0200
Subject: plotting plv
In-Reply-To: <5a40df8d99c3d.4cb20be4@mail.nyu.edu>
Message-ID: <MON.11.OCT.2010.091729.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Akiko,

A small comment first: there's a type in the naming of your zparam
'cohsprctm' should probably read 'cohspctrm', but I don't think that
this is the show stopper. Next, I guess that given your configuration
for ft_freqanalysis, the eventual output of ft_connectivityanalysis is
a 3x3xNfreqxNtime - matrix containing plv-values. Is that correct?
I do not understand why the visualization fails, but it seems that the
correct part of the code is not reached.
Could you save the variable 'stat' to a file and upload it to our ftp-
server, so that we can reproduce your bug. Recently we spent quite
some time in streamlining the visualisation for this type of data and
I am pretty sure that in your case it just should work. Please have a
look at http://fieldtrip.fcdonders.nl/faq/how_should_i_send_example_data_to_the_developers
  to upload your data.

Best,

Jan-Mathijs

On Oct 11, 2010, at 12:54 AM, Akiko Ikkai wrote:

> Hi,
>
> I'm trying to plot plv between channel pairs that I get from
> ft_connectivityanalysis.
>
> when I run
> cfg                  = [];
> cfg.xparam           = 'time';
> cfg.yparam           = 'freq';
> cfg.zparam           = 'cohsprctm';  % need to run stat.cohsprctm =
> stat.plvspctrm;
>                                                  % fixed in the
> latest version?
> cfg.cohrefchannel    = '1';
> cfg.layout = 'ordered';
> cfg.showlabels       = 'yes';
> cfg.colorbar         = 'yes';
> figure; ft_multiplotTFR(cfg, stat)
>
> I get this error:
> ft_multiplotTFR(cfg, stat)
> ??? Index exceeds matrix dimensions.
>
> Error in ==> ft_multiplotTFR at 242
> datavector = data.(cfg.zparam)(seldat,yidc,xidc);
>
>
> ... I'm guessing the error is something like wrong channel
> combination or refchannel selection, but not able to locate where
> the error is coming from (have tried different channel combination).
> stat.dimord is "chan_chan_freq_time", which might not be formatted
> appropriately for ft_multiplotTFR...?  Below, I'm attaching the code
> used to get "stat" (plv).
>
> Any suggestions? Thanks in advance! Akiko
>
>
> %%%%% code for connectivityanalysis %%%%%%
> cfg = [];
> cfg.output ='fourier'; % instead of 'powandcsd'... fixed in the
> latest version?
> cfg.method          = 'mtmconvol';
> cfg.channel = {'1', '7', '120'}; % contra & unrelated channels to test
> cfg.channelcmb = {'1' '7'; '1' '120'; '7', '120'};
> cfg.keeptrials = 'yes';
> cfg.keeptapers = 'no';
> cfg.toi             = [-.8:.1:2]
> cfg.foi             = [1:0.5:30];
> cfg.taper           = 'hanning';
> cfg.t_ftimwin       = zeros(1,length(cfg.foi));
> cfg.t_ftimwin(:)    = 5./cfg.foi;
> TFR = ft_freqanalysis(cfg, ft_data);
>
> cfg=[];
> cfg.method  = 'plv';
> [stat] = ft_connectivityanalysis(cfg,  TFR);
>
> ---------------------------------------------------------------------------
> You are receiving this message because you are subscribed to
> the  FieldTrip list. The aim of this list is to facilitate the
> discussion
> between  users of the FieldTrip  toolbox, to share experiences
> and to discuss  new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------
>

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

---------------------------------------------------------------------------
You are receiving this message because you are subscribed to
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between  users of the FieldTrip  toolbox, to share experiences
and to discuss  new ideas for MEG and EEG analysis.
See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
---------------------------------------------------------------------------


From michael.wibral at WEB.DE  Mon Oct 11 12:16:33 2010
From: michael.wibral at WEB.DE (Michael Wibral)
Date: Mon, 11 Oct 2010 12:16:33 +0200
Subject: one sided or two sided testing
In-Reply-To: <015801cb66f3$2a6ec660$7f4c5320$@maris@donders.ru.nl>
Message-ID: <MON.11.OCT.2010.121633.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Emanual,

just a comment on the posts below. 'Prior' knowledge should come from independent data - e.g. collected in a different experiment or from another finding in the literature. It's best if you find some prior knowledge that you can *CITE* - otherwise it'll typically get pretty difficult to publish your one-sided test. I guess you knew this already (so please do not feel insulted by this post), just wanted to save you the trouble with reviewers in the very unlikely event that you didn't. 

Good luck for your study,
Michael

-----Ursprüngliche Nachricht-----
Von: "Eric Maris" <e.maris at DONDERS.RU.NL>
Gesendet: Oct 8, 2010 4:14:43 PM
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: Re: [FIELDTRIP] one sided or two sided testing

>Dear Emanuel,
>
>
>> If you have prior knowledge that the ERP is to be expected to be lower
>> in one
>> group as compared to the other group of subjects is it then allowed to
>> only
>> test the positive T-sum clusters (alpha 0.05) and neglect the negative
>> clusters?
>
>Yes, this is allowed. Such a procedure controls the false alarm rate at
>0.05.
>
>
>Best,
>
>Eric Maris
>
>
>
>> 
>> Thank you in advance,
>> Best, Emanuel
>> 
>> -----------------------------------------------------------------------
>> ----
>> You are receiving this message because you are subscribed to
>> the  FieldTrip list. The aim of this list is to facilitate the
>> discussion
>> between  users of the FieldTrip  toolbox, to share experiences
>> and to discuss  new ideas for MEG and EEG analysis.
>> See also http://listserv.surfnet.nl/archives/fieldtrip.html
>> and http://www.ru.nl/neuroimaging/fieldtrip.
>> -----------------------------------------------------------------------
>> ----
>
>---------------------------------------------------------------------------
>You are receiving this message because you are subscribed to
>the  FieldTrip list. The aim of this list is to facilitate the discussion
>between  users of the FieldTrip  toolbox, to share experiences
>and to discuss  new ideas for MEG and EEG analysis.
>See also http://listserv.surfnet.nl/archives/fieldtrip.html
>and http://www.ru.nl/neuroimaging/fieldtrip.
>---------------------------------------------------------------------------

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You are receiving this message because you are subscribed to
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From Jens.Schwarzbach at UNITN.IT  Tue Oct 12 10:31:07 2010
From: Jens.Schwarzbach at UNITN.IT (Schwarzbach, Jens Volkmar)
Date: Tue, 12 Oct 2010 10:31:07 +0200
Subject: Assistant or Associate Research Professors,
 Center for Mind/Brain Sciences, Trento
In-Reply-To: <828827820.2751349.1286792193574.JavaMail.fmail@mwmweb053>
Message-ID: <TUE.12.OCT.2010.103107.0200.FIELDTRIP@NIC.SURFNET.NL>

Assistant or Associate Research Professors, Center for Mind/Brain Sciences, Trento 


The Center for Mind/Brain Sciences (CIMeC) at the University of Trento is seeking to fill a number of research positions in cognitive neuroscience at the Assistant or Associate Research Professor level. The Center offers an international and vibrant research setting in which to investigate the functioning of the brain through the analysis of its functional, structural and physiological characteristics, in both normal and pathological states. Researchers at the Center make use of state-of-the-art neuroimaging methodologies, including a research-only MRI scanner, MEG, EEG and TMS, as well as behavioral, eye tracking and motion tracking laboratories. The Center also includes a neuropsychology and neuro-rehabilitation clinic (CERiN). The Center strongly encourages collaborative and innovative research, and provides the opportunity for all researchers to access laboratory resources and to be part of the Doctoral School in Cognitive and Brain Sciences. CIMeC also has close collaborations with local research centers, including FBK (Fondazione Bruno Kessler) and IIT (Italian Institute of Technology), through joint projects and through the doctoral school. Further information about the Center can be found at: http://www.cimec.unitn.it.

The ideal researchers (from all areas of cognitive neuroscience, including computational neuroscience and neuroimaging methods) must hold the Ph.D. or M.D. degree, and should have a record documenting research creativity, independence, and productivity. We are looking for researchers able to build and maintain a high quality research program and to contribute to the maintenance of a collegial and collaborative academic environment.

The Center offers excellent experimental facilities and a competitive European-level salary in the context of a rapidly growing and dynamic environment. Funding is available for 6 years. The initial contract would be for 3 years. There is no associated university teaching load, although researchers will be expected to participate in the research culture of the Center through seminars, supervision of students and other activities. 

The University of Trento is ranked first among research universities in Italy, and the Trentino region is consistently at the top for quality of life and for the most efficient services in Italy. English is the official language of the CIMeC, where a large proportion of the faculty, post-docs and students come from a wide range of countries outside of Italy. CIMeC’s labs and the PhD School are in Rovereto (about thirty kilometres south of Trento) and Mattarello (eight kilometers south of Trento).

If you wish to receive further information please contact the Director of the CIMeC, Prof. Alfonso Caramazza (alfonso.caramazza at unitn.it) or Vice-Director Prof. Giorgio Vallortigara (giorgio.vallortigara at unitn.it) by November 15, 2010.

------------------------
Prof. Jens Schwarzbach
Functional NeuroImaging Laboratories, MR Lab Co-Director
Center for Mind Brain Sciences, University of Trento, 
Via delle Regole, 101, 38100 Mattarello (TN), Italy
Telephone: +39-0461-28 3061
Fax: +39-0461-28-3066
http://www.cimec.unitn.it/


From nathanweisz at MAC.COM  Tue Oct 12 17:08:11 2010
From: nathanweisz at MAC.COM (Nathan Weisz)
Date: Tue, 12 Oct 2010 17:08:11 +0200
Subject: plotting plv
In-Reply-To: <5a40df8d99c3d.4cb20be4@mail.nyu.edu>
Message-ID: <TUE.12.OCT.2010.170811.0200.>

hi akiko,

just via coincidence i had the same issue today.

after calculating ft_connectivityanalysis (i used 'coh' as method), the label field was missing. additionally i had to throw out the reference electrode.

cohsniff.label=freqcsd.label;
cohsniff.label(1)=[];

then plotting worked fine.

good luck,
nathan


On 11.10.2010, at 00:54, Akiko Ikkai wrote:

> Hi,
>
> I'm trying to plot plv between channel pairs that I get from ft_connectivityanalysis.
>
> when I run
> cfg                  = [];
> cfg.xparam           = 'time';
> cfg.yparam           = 'freq';
> cfg.zparam           = 'cohsprctm';  % need to run stat.cohsprctm = stat.plvspctrm;
>                                                  % fixed in the latest version?
> cfg.cohrefchannel    = '1';
> cfg.layout = 'ordered';
> cfg.showlabels       = 'yes';
> cfg.colorbar         = 'yes';
> figure; ft_multiplotTFR(cfg, stat)
>
> I get this error:
> ft_multiplotTFR(cfg, stat)
> ??? Index exceeds matrix dimensions.
>
> Error in ==> ft_multiplotTFR at 242
> datavector = data.(cfg.zparam)(seldat,yidc,xidc);
>
>
> ... I'm guessing the error is something like wrong channel combination or refchannel selection, but not able to locate where the error is coming from (have tried different channel combination). stat.dimord is "chan_chan_freq_time", which might not be formatted appropriately for ft_multiplotTFR...?  Below, I'm attaching the code used to get "stat" (plv).
>
> Any suggestions? Thanks in advance! Akiko
>
>
> %%%%% code for connectivityanalysis %%%%%%
> cfg = [];
> cfg.output ='fourier'; % instead of 'powandcsd'... fixed in the latest version?
> cfg.method          = 'mtmconvol';
> cfg.channel = {'1', '7', '120'}; % contra & unrelated channels to test
> cfg.channelcmb = {'1' '7'; '1' '120'; '7', '120'};
> cfg.keeptrials = 'yes';
> cfg.keeptapers = 'no';
> cfg.toi             = [-.8:.1:2]
> cfg.foi             = [1:0.5:30];
> cfg.taper           = 'hanning';
> cfg.t_ftimwin       = zeros(1,length(cfg.foi));
> cfg.t_ftimwin(:)    = 5./cfg.foi;
> TFR = ft_freqanalysis(cfg, ft_data);
>
> cfg=[];
> cfg.method  = 'plv';
> [stat] = ft_connectivityanalysis(cfg,  TFR);
>
> ---------------------------------------------------------------------------
> You are receiving this message because you are subscribed to
> the  FieldTrip list. The aim of this list is to facilitate the discussion
> between  users of the FieldTrip  toolbox, to share experiences
> and to discuss  new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------

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


From thomas.hartmann at UNI-KONSTANZ.DE  Fri Oct 15 15:30:40 2010
From: thomas.hartmann at UNI-KONSTANZ.DE (Thomas Hartmann)
Date: Fri, 15 Oct 2010 15:30:40 +0200
Subject: specifying individual lateralization in sourcestatistic
Message-ID: <FRI.15.OCT.2010.153040.0200.FIELDTRIP@NIC.SURFNET.NL>

  hi,
i want to do a roi analysis on source data and average over the all the
voxels. the problem is that i am dealing with a lateralized effect that
i expect to show up either on the left or the right side of the same
structure. this lateralization is individual for each subject and known
a priori.
is there any possibility to individually define, which side to take into
account for the statistics?

thanks in advance,
thomas

--
Dipl. Psych. Thomas Hartmann

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

Tel.: +49 (0)7531 88 4612
Fax: +49 (0)7531-88 4601
Email: thomas.hartmann at uni-konstanz.de
Homepage: http://www.uni-konstanz.de/obob

"I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle)

---------------------------------------------------------------------------
You are receiving this message because you are subscribed to
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and to discuss  new ideas for MEG and EEG analysis.
See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
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From michael.wibral at WEB.DE  Fri Oct 15 16:08:09 2010
From: michael.wibral at WEB.DE (Michael Wibral)
Date: Fri, 15 Oct 2010 16:08:09 +0200
Subject: specifying individual lateralization in sourcestatistic
In-Reply-To: <4CB85780.3000805@uni-konstanz.de>
Message-ID: <FRI.15.OCT.2010.160809.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Thomas,

I suggest you simply extract the power values from the results of sourceanalysis (or t-values if you already did a fisrt level statistics) and average them by hand in MATLAB - as ROI is known for each subject this should be easy (you have to extract the values by the voxel indices contained in your ROI. These in turn you can find in interactive mode source plotting if everything else fails). This way you end up with a single value per subject and condition. Afterwards you do a simple permutation test by hand in MATLAB. 

((The test for two conditions for example can be done this way:
1. concatenate all data in a vector D first data in one condition, then in the other)
2. compute your test metric between first and second half of D.
3. shuffle the entries of D: DS=D(randperm(length(D)); % creates a new D with shuffled entries by shuffling the indexes of the old one
4. compute your test metric for DS and remember it
5. Do 3+4 N times (e.g. >1901 times for accurate testing at alpha<0.05)
6. check where your original test metric obtained from D is in the distribution of the mtrices obtained from the DS.))


Hope this helps,
Michael

-----Ursprüngliche Nachricht-----
Von: "Thomas Hartmann" <thomas.hartmann at UNI-KONSTANZ.DE>
Gesendet: Oct 15, 2010 3:30:40 PM
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: [FIELDTRIP] specifying individual lateralization in sourcestatistic

>  hi,
>i want to do a roi analysis on source data and average over the all the 
>voxels. the problem is that i am dealing with a lateralized effect that 
>i expect to show up either on the left or the right side of the same 
>structure. this lateralization is individual for each subject and known 
>a priori.
>is there any possibility to individually define, which side to take into 
>account for the statistics?
>
>thanks in advance,
>thomas
>
>-- 
>Dipl. Psych. Thomas Hartmann
>
>OBOB-Lab
>University of Konstanz
>Department of Psychology
>P.O. Box D25
>78457 Konstanz
>Germany
>
>Tel.: +49 (0)7531 88 4612
>Fax: +49 (0)7531-88 4601
>Email: thomas.hartmann at uni-konstanz.de
>Homepage: http://www.uni-konstanz.de/obob
>
>"I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle)
>
>---------------------------------------------------------------------------
>You are receiving this message because you are subscribed to
>the  FieldTrip list. The aim of this list is to facilitate the discussion
>between  users of the FieldTrip  toolbox, to share experiences
>and to discuss  new ideas for MEG and EEG analysis.
>See also http://listserv.surfnet.nl/archives/fieldtrip.html
>and http://www.ru.nl/neuroimaging/fieldtrip.
>---------------------------------------------------------------------------

---------------------------------------------------------------------------
You are receiving this message because you are subscribed to
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and to discuss  new ideas for MEG and EEG analysis.
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From akiko at NYU.EDU  Mon Oct 18 18:27:16 2010
From: akiko at NYU.EDU (Akiko Ikkai)
Date: Mon, 18 Oct 2010 12:27:16 -0400
Subject: plot rotated in 20101011 version
In-Reply-To: <1DC3B8B1-9152-415B-B46B-9DB8488ABAAD@donders.ru.nl>
Message-ID: <MON.18.OCT.2010.122716.0400.FIELDTRIP@NIC.SURFNET.NL>

Hello,

I downloaded 20101011 version, and found that ft_clusterplot, ft_multiplotTFR plot images 90 degrees counter-clockwise (I only tried these commands, but it's possible that other plot fxns do the same). I ran the same codes with older versions and plots are fine. Could someone let me know if versions later than 20101011 behave the same (i.e. is this a new change that we should be aware of when plotting, or a bug in this version)?

Thanks in advance, Akiko

---------------------------------------------------------------------------
You are receiving this message because you are subscribed to
the  FieldTrip list. The aim of this list is to facilitate the discussion
between  users of the FieldTrip  toolbox, to share experiences
and to discuss  new ideas for MEG and EEG analysis.
See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
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From r.vandermeij at DONDERS.RU.NL  Tue Oct 19 09:49:04 2010
From: r.vandermeij at DONDERS.RU.NL (Roemer van der Meij)
Date: Tue, 19 Oct 2010 09:49:04 +0200
Subject: plot rotated in 20101011 version
In-Reply-To: <56f083dcec122.4cbc3d24@mail.nyu.edu>
Message-ID: <TUE.19.OCT.2010.094904.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Akiko,

Is everything rotated, i.e. the interpolated data, the channels and  
the head shape/contours or only one of these?

Best,
Roemer



Quoting Akiko Ikkai <akiko at NYU.EDU>:

> Hello,
>
> I downloaded 20101011 version, and found that ft_clusterplot,   
> ft_multiplotTFR plot images 90 degrees counter-clockwise (I only   
> tried these commands, but it's possible that other plot fxns do the   
> same). I ran the same codes with older versions and plots are fine.   
> Could someone let me know if versions later than 20101011 behave the  
>  same (i.e. is this a new change that we should be aware of when   
> plotting, or a bug in this version)?
>
> Thanks in advance, Akiko
>
> ---------------------------------------------------------------------------
> You are receiving this message because you are subscribed to
> the  FieldTrip list. The aim of this list is to facilitate the discussion
> between  users of the FieldTrip  toolbox, to share experiences
> and to discuss  new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------
>



-- 
Roemer van der Meij MSc
PhD student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognition
P.O. Box 9104
6500 HE Nijmegen
The Netherlands
Tel: +31(0)24 3655932
E-mail: r.vandermeij at donders.ru.nl

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See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
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From batrod at GMAIL.COM  Wed Oct 20 00:49:06 2010
From: batrod at GMAIL.COM (Rodolphe)
Date: Tue, 19 Oct 2010 17:49:06 -0500
Subject: Cluster change over time
Message-ID: <TUE.19.OCT.2010.174906.0500.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrip users,

I used the Monte-Carlo method with cluster correction to compare two
conditions within the same group of subjects.
I didnt average over time, thus the clusterplot showed several topographic
plot of the cluster that was found to be significant.
I can see that this cluster evolves over time (number and place of
significant electrodes highlighted). My question is, considering the
statistical method using for this analysis, can i say that this change over
time is significant or does it require further analysis like ANOVAS in
concerned electrodes?

Thanks a lot,

Rodolphe N., Ph.D.

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From batrod at GMAIL.COM  Wed Oct 20 00:54:23 2010
From: batrod at GMAIL.COM (Rodolphe Nenert)
Date: Wed, 20 Oct 2010 00:54:23 +0200
Subject: plot rotated in 20101011 version
Message-ID: <WED.20.OCT.2010.005423.0200.FIELDTRIP@NIC.SURFNET.NL>

Hello, 

actually i had the same problem with my layout. When i created it, i found out 
that it was 90 degrees rotated.
I solved this issue by adding a rotate option in the cfg as following: 

cfg=[];
cfg.rotate=90;
cfg.elec = mydata.elec;
lay = ft_prepare_layout(cfg);

Hope this helps, 

Rodolphe Nenert, Ph.D.

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From akiko at NYU.EDU  Wed Oct 20 01:55:08 2010
From: akiko at NYU.EDU (Akiko Ikkai)
Date: Tue, 19 Oct 2010 19:55:08 -0400
Subject: plot rotated in 20101011 version
In-Reply-To: <20101019094904.t3oo09c2sk4kwwc0@www.socsci.ru.nl>
Message-ID: <TUE.19.OCT.2010.195508.0400.FIELDTRIP@NIC.SURFNET.NL>

Hi Roemer,

It appears that interpolated data and contours in clusterplot/topoplot, and channel layout in multiplotTFR are rotated, but not the head outline. In my MEG data, data toward nose is displayed over the left ear on outline (90 degrees counter clockwise). If cfg.layout = 'ordered' is used, each channels are plotted accordingly, and within each channel, there is no rotation. singleplotTFR also plots normal.

As Dr. Nenert suggested, I could correct for it with ft_prepare_layout, but it'd be nice to have this problem solved.

Alternatively, I could download slightly older version of fieldtrip (assuming this rotation was introduced just recently), but I'd like to use the version that's spm8 compatible. Could you let me know how far back that would be (sometime in July 2010, I think)?

Thank you for your time! Akiko


----- Original Message -----
From: Roemer van der Meij <r.vandermeij at DONDERS.RU.NL>
Date: Tuesday, October 19, 2010 3:49 am
Subject: Re: [FIELDTRIP] plot rotated in 20101011 version
To: FIELDTRIP at NIC.SURFNET.NL

> Hi Akiko,
>
> Is everything rotated, i.e. the interpolated data, the channels and
> the head shape/contours or only one of these?
>
> Best,
> Roemer
>
>
>
> Quoting Akiko Ikkai <akiko at NYU.EDU>:
>
> > Hello,
> >
> > I downloaded 20101011 version, and found that ft_clusterplot,
> > ft_multiplotTFR plot images 90 degrees counter-clockwise (I only
> > tried these commands, but it's possible that other plot fxns do the
>
> > same). I ran the same codes with older versions and plots are fine.
>
> > Could someone let me know if versions later than 20101011 behave the
>
> >  same (i.e. is this a new change that we should be aware of when
> > plotting, or a bug in this version)?
> >
> > Thanks in advance, Akiko
> >
> > ---------------------------------------------------------------------------
> > You are receiving this message because you are subscribed to
> > the  FieldTrip list. The aim of this list is to facilitate the discussion
> > between  users of the FieldTrip  toolbox, to share experiences
> > and to discuss  new ideas for MEG and EEG analysis.
> > See also http://listserv.surfnet.nl/archives/fieldtrip.html
> > and http://www.ru.nl/neuroimaging/fieldtrip.
> > ---------------------------------------------------------------------------
> >
>
>
>
> --
> Roemer van der Meij MSc
> PhD student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognition
> P.O. Box 9104
> 6500 HE Nijmegen
> The Netherlands
> Tel: +31(0)24 3655932
> E-mail: r.vandermeij at donders.ru.nl
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
> ---------------------------------------------------------------------------
> You are receiving this message because you are subscribed to
> the  FieldTrip list. The aim of this list is to facilitate the discussion
> between  users of the FieldTrip  toolbox, to share experiences
> and to discuss  new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------

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From michael.wibral at WEB.DE  Thu Oct 21 19:32:41 2010
From: michael.wibral at WEB.DE (Michael Wibral)
Date: Thu, 21 Oct 2010 19:32:41 +0200
Subject: Cluster change over time
In-Reply-To: <AANLkTikAn_tfNykG3sGQc9fG80xyc2UEpg07Xk9nm69=@mail.gmail.com>
Message-ID: <THU.21.OCT.2010.193241.0200.FIELDTRIP@NIC.SURFNET.NL>

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From e.maris at DONDERS.RU.NL  Thu Oct 21 21:36:04 2010
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Thu, 21 Oct 2010 21:36:04 +0200
Subject: Cluster change over time
In-Reply-To: <979290850.1443255.1287682361965.JavaMail.fmail@mwmweb053>
Message-ID: <THU.21.OCT.2010.213604.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Rodolphe and Michael,

 

 

strictly speaking cluster analysis (as a construct to get a univariate test instead of a mass-univariate one) only tells you that there IS a significant cluster. The exact shape and temporal evolution of this cluster is not part of what's tested - as least as far as I understand this issue. That is a data point can surpass your cluster inclusion threshold by chance - a portion of alpha data points will actually do this. In addition, these point can be accidentally close to other clustermembers. Hence, it will be included in a cluster. So 'true' cluster membership of a certain electrode/timepoint/frequency is not statistically 'guaranteed'. Additional tests would be necessary.
Then one thing that this argument does not account for is that 'accidentally neighbouring a cluster' is not so likely because of the smoothness of MEEG data - but I do not know at the moment how you could exploit this.




This is well formulated. The null hypothesis that is tested by the cluster-based permutation tests involves that the spatiotemporal biological data in the experimental conditions that are being compared are drawn from the same probability distribution. They are NOT testing null hypotheses of the following type: there is no difference between the conditions at channel A and time point T whereas there may be differences at other (channel, time point)  pairs. In fact, such null hypotheses do not make much sense when dealing with electrophysiological data because (a) because of volume conduction, spatially localized effects are not plausible, and (2) because neurophysiological processes are not instantaneous, highly temporally localized effect are not plausible either.

 

Best,

 

Eric Maris

 

 

 

 

 

 

 

Michael

  _____  

Von: Rodolphe <batrod at GMAIL.COM>
Gesendet: Oct 20, 2010 12:49:06 AM
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: [FIELDTRIP] Cluster change over time

Dear Fieldtrip users,  

I used the Monte-Carlo method with cluster correction to compare two conditions within the same group of subjects.

I didnt average over time, thus the clusterplot showed several topographic plot of the cluster that was found to be significant.

I can see that this cluster evolves over time (number and place of significant electrodes highlighted). My question is, considering the statistical method using for this analysis, can i say that this change over time is significant or does it require further analysis like ANOVAS in concerned electrodes?

Thanks a lot, 

Rodolphe N., Ph.D.

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See also http://listserv.surfnet.nl/archives/fieldtrip.html 
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From daz at MIT.EDU  Thu Oct 21 21:49:21 2010
From: daz at MIT.EDU (David Ziegler)
Date: Thu, 21 Oct 2010 15:49:21 -0400
Subject: ft_channelrepair with neuromag data
Message-ID: <THU.21.OCT.2010.154921.0400.FIELDTRIP@NIC.SURFNET.NL>

  Hi Fieldtrippers,

I would like to use ft_channelrepair to interpolate data for some
missing/deleted channels with Neuromag 306 data.  I am just wondering
whether there are any potential problems with using the nearest neighbor
interpolation, given the triplet format of the Neuromag system (two
planar gradiometers and one magnetometer).

If this is problematic, are there other options to fixing bad/missing
channels (e.g., can ft_channelrepair be run on just a subset of the
channels, say the gradiometers after I run ft_combineplanar)?

Thanks!
David

--

David A. Ziegler

Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St, 46-5121
Cambridge, MA  02139

Tel: 617-258-0765

Fax: 617-253-1504

daz at mit.edu <mailto:daz at mit.edu>


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From batrod at GMAIL.COM  Fri Oct 22 01:47:43 2010
From: batrod at GMAIL.COM (Rodolphe)
Date: Thu, 21 Oct 2010 18:47:43 -0500
Subject: Coherence and dipole
Message-ID: <THU.21.OCT.2010.184743.0500.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrip users,

I recently run a coherence analysis on my data and i plotted a beautiful
Topographic plot showing a strong coherence between one electrode in left
parietal ( P5) and some right frontal electrodes.
The thing is, when i try with the right parietal equivalent ( P6 ) then i
find a coherence with left frontal. Ans so on with a couple of other
electrodes use as ref channels.
As this symmetry looks awkward to me, is any of you have an idea of a
posible artifact that can cause this, or a possible bias in the analysis? (
I tripled checked my code)

Best,

Rodolphe N., Ph.D.

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From jan.schoffelen at DONDERS.RU.NL  Fri Oct 22 09:02:11 2010
From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen)
Date: Fri, 22 Oct 2010 09:02:11 +0200
Subject: ft_channelrepair with neuromag data
In-Reply-To: <4CC09941.1060006@mit.edu>
Message-ID: <FRI.22.OCT.2010.090211.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear David,

This is a good point. As far as I can see from the code, no
distinction is made between gradiometers and magnetometers.
Naively, I would propose the following: first indeed split the data
into two subset: gradiometers only and magnetometers only, only then
apply the channel reparation routine. Yet, for the gradiometer subset
data, it is questionable whether as such the replacement of a bad
channel with its neighbours makes sense, because this would lead to
averaging gradients of the magnetic field with an orthogonal
orientation.

In other words, this is probably not the most sensible approach. I
don't think repairing after combining the planar gradients is
desired, because this leads to an unwanted amplification of the noise
(because the combination step results in taking an absolute value).
Alternatively, you could consider using ft_megrealign, which in
principle could be used to repair bad channels. The recipe would be to
only use the data with the clean channels in the input, and you would
want to interpolate the data back onto the original sensor-array. An
example for interpolating between two types of CTF-systems is shown
here http://fieldtrip.fcdonders.nl/example/megrealign.

Just out of curiosity: doesn't the maxfilter in the Neuromag software
allow for similar things?

Best wishes,

Jan-Mathijs

On Oct 21, 2010, at 9:49 PM, David Ziegler wrote:

> Hi Fieldtrippers,
>
> I would like to use ft_channelrepair to interpolate data for some
> missing/deleted channels with Neuromag 306 data.  I am just
> wondering whether there are any potential problems with using the
> nearest neighbor interpolation, given the triplet format of the
> Neuromag system (two planar gradiometers and one magnetometer).
>
> If this is problematic, are there other options to fixing bad/
> missing channels (e.g., can ft_channelrepair be run on just a subset
> of the channels, say the gradiometers after I run ft_combineplanar)?
>
> Thanks!
> David
>
> --
> David A. Ziegler
> Department of Brain and Cognitive Sciences
> Massachusetts Institute of Technology
> 43 Vassar St,  46-5121
> Cambridge, MA  02139
> Tel: 617-258-0765
> Fax: 617-253-1504
> daz at mit.edu
>
>
> --------------------------------------------------------------------------- You
>  are receiving this message because you are subscribed to
> the FieldTrip list. The aim of this list is to facilitate the
> discussion
> between users of the FieldTrip toolbox, to share experiences
> and to discuss new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------
>

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


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From jan.schoffelen at DONDERS.RU.NL  Fri Oct 22 09:04:00 2010
From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen)
Date: Fri, 22 Oct 2010 09:04:00 +0200
Subject: Coherence and dipole
In-Reply-To: <AANLkTikq0pD1MJf_4DjW0OTsFmTJ9tEq3XcHWjgKB-Y+@mail.gmail.com>
Message-ID: <FRI.22.OCT.2010.090400.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Rodolphe,

I guess you are analyzing EEG data? What reference electrode(s) did
you use?

Best,
JM



On Oct 22, 2010, at 1:47 AM, Rodolphe wrote:

> Dear Fieldtrip users,
>
> I recently run a coherence analysis on my data and i plotted a
> beautiful Topographic plot showing a strong coherence between one
> electrode in left parietal ( P5) and some right frontal electrodes.
> The thing is, when i try with the right parietal equivalent ( P6 )
> then i find a coherence with left frontal. Ans so on with a couple
> of other electrodes use as ref channels.
> As this symmetry looks awkward to me, is any of you have an idea of
> a posible artifact that can cause this, or a possible bias in the
> analysis? ( I tripled checked my code)
>
> Best,
>
> Rodolphe N., Ph.D.
> --------------------------------------------------------------------------- You
>  are receiving this message because you are subscribed to
> the FieldTrip list. The aim of this list is to facilitate the
> discussion
> between users of the FieldTrip toolbox, to share experiences
> and to discuss new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------
>

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

---------------------------------------------------------------------------
You are receiving this message because you are subscribed to
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From maess at CBS.MPG.DE  Fri Oct 22 09:25:01 2010
From: maess at CBS.MPG.DE (Burkhard Maess)
Date: Fri, 22 Oct 2010 09:25:01 +0200
Subject: ft_channelrepair with neuromag data
In-Reply-To: <0A9DF0C3-4149-4874-9E27-C095CC0654AA@donders.ru.nl>
Message-ID: <FRI.22.OCT.2010.092501.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear David,

I agree with Jan-Mathijs.

variant a: apply maxfilter - that will repair all broken channels. You
also can manually define certain channels as broken. Maxfilter may also
align data of different headpositions to a single position.

variant b: use megrealign - it includes a minimum norm localization and
from there MEG data is forward computed. In this way, you can repair
channels, align different head positions to the same and even convert
data between different systems.

all the best,
Burkhard


jan-mathijs schoffelen wrote:
> Dear David,
>
> This is a good point. As far as I can see from the code, no
> distinction is made between gradiometers and magnetometers.
> Naively, I would propose the following: first indeed split the data
> into two subset: gradiometers only and magnetometers only, only then
> apply the channel reparation routine. Yet, for the gradiometer subset
> data, it is questionable whether as such the replacement of a bad
> channel with its neighbours makes sense, because this would lead to
> averaging gradients of the magnetic field with an orthogonal orientation.
>
> In other words, this is probably not the most sensible approach. I
> don't think repairing after combining the planar gradients is
>  desired, because this leads to an unwanted amplification of the noise
> (because the combination step results in taking an absolute value).
> Alternatively, you could consider using ft_megrealign, which in
> principle could be used to repair bad channels. The recipe would be to
> only use the data with the clean channels in the input, and you would
> want to interpolate the data back onto the original sensor-array. An
> example for interpolating between two types of CTF-systems is shown
> here http://fieldtrip.fcdonders.nl/example/megrealign.
>
> Just out of curiosity: doesn't the maxfilter in the Neuromag software
> allow for similar things?
>
> Best wishes,
>
> Jan-Mathijs
>
> On Oct 21, 2010, at 9:49 PM, David Ziegler wrote:
>
>> Hi Fieldtrippers,
>>
>> I would like to use ft_channelrepair to interpolate data for some
>> missing/deleted channels with Neuromag 306 data.  I am just wondering
>> whether there are any potential problems with using the nearest
>> neighbor interpolation, given the triplet format of the Neuromag
>> system (two planar gradiometers and one magnetometer).
>>
>> If this is problematic, are there other options to fixing bad/missing
>> channels (e.g., can ft_channelrepair be run on just a subset of the
>> channels, say the gradiometers after I run ft_combineplanar)?
>>
>> Thanks!
>> David
>>
>> --
>> David A. Ziegler
>> Department of Brain and Cognitive Sciences
>> Massachusetts Institute of Technology
>> 43 Vassar St,  46-5121
>> Cambridge, MA  02139
>> Tel: 617-258-0765
>> Fax: 617-253-1504
>> daz at mit.edu <mailto:daz at mit.edu>
>>
>>
>>
>>
>>
>> ---------------------------------------------------------------------------
>> You are receiving this message because you are subscribed to
>> the FieldTrip list. The aim of this list is to facilitate the discussion
>> between users of the FieldTrip toolbox, to share experiences
>> and to discuss new ideas for MEG and EEG analysis.
>> See also http://listserv.surfnet.nl/archives/fieldtrip.html
>> and http://www.ru.nl/neuroimaging/fieldtrip.
>> ---------------------------------------------------------------------------
>>
>
> Dr. J.M. (Jan-Mathijs) Schoffelen
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
> Telephone: 0031-24-3614793
>
> ---------------------------------------------------------------------------
> You are receiving this message because you are subscribed to
> the FieldTrip list. The aim of this list is to facilitate the discussion
> between users of the FieldTrip toolbox, to share experiences
> and to discuss new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------
>

--
------------------------------------------------------------
Dr. Burkhard Maess
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig
Aussenstelle Bennewitz, phone/fax: +49(3425)887525-26/-11
mail: maess 'at' cbs.mpg.de,           http://www.cbs.mpg.de
------------------------------------------------------------
Please do not attach files which may contain executable code,
e.g. .rtf is preferred over .doc(x)

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and http://www.ru.nl/neuroimaging/fieldtrip.
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From batrod at GMAIL.COM  Sat Oct 23 00:12:31 2010
From: batrod at GMAIL.COM (Rodolphe Nenert)
Date: Sat, 23 Oct 2010 00:12:31 +0200
Subject: Coherence and dipole
Message-ID: <SAT.23.OCT.2010.001231.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan, 

yes i do analyze EEG data. The data was recorded using vertex  (CZ) as 
reference, but i modified to an average reference before doing any time-freq 
analysis.

Rodolphe.

On Fri, 22 Oct 2010 09:04:00 +0200, jan-mathijs schoffelen 
<jan.schoffelen at DONDERS.RU.NL> wrote:

>Dear Rodolphe,
>
>I guess you are analyzing EEG data? What reference electrode(s) did
>you use?
>
>Best,
>JM
>
>
>
>On Oct 22, 2010, at 1:47 AM, Rodolphe wrote:
>
>> Dear Fieldtrip users,
>>
>> I recently run a coherence analysis on my data and i plotted a
>> beautiful Topographic plot showing a strong coherence between one
>> electrode in left parietal ( P5) and some right frontal electrodes.
>> The thing is, when i try with the right parietal equivalent ( P6 )
>> then i find a coherence with left frontal. Ans so on with a couple
>> of other electrodes use as ref channels.
>> As this symmetry looks awkward to me, is any of you have an idea of
>> a posible artifact that can cause this, or a possible bias in the
>> analysis? ( I tripled checked my code)
>>
>> Best,
>>
>> Rodolphe N., Ph.D.
>> --------------------------------------------------------------------------- You
>>  are receiving this message because you are subscribed to
>> the FieldTrip list. The aim of this list is to facilitate the
>> discussion
>> between users of the FieldTrip toolbox, to share experiences
>> and to discuss new ideas for MEG and EEG analysis.
>> See also http://listserv.surfnet.nl/archives/fieldtrip.html
>> and http://www.ru.nl/neuroimaging/fieldtrip.
>> ---------------------------------------------------------------------------
>>
>
>Dr. J.M. (Jan-Mathijs) Schoffelen
>Donders Institute for Brain, Cognition and Behaviour,
>Centre for Cognitive Neuroimaging,
>Radboud University Nijmegen, The Netherlands
>J.Schoffelen at donders.ru.nl
>Telephone: 0031-24-3614793
>
>---------------------------------------------------------------------------
>You are receiving this message because you are subscribed to
>the  FieldTrip list. The aim of this list is to facilitate the discussion
>between  users of the FieldTrip  toolbox, to share experiences
>and to discuss  new ideas for MEG and EEG analysis.
>See also http://listserv.surfnet.nl/archives/fieldtrip.html
>and http://www.ru.nl/neuroimaging/fieldtrip.
>---------------------------------------------------------------------------

---------------------------------------------------------------------------
You are receiving this message because you are subscribed to
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and to discuss  new ideas for MEG and EEG analysis.
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and http://www.ru.nl/neuroimaging/fieldtrip.
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From jan.schoffelen at DONDERS.RU.NL  Mon Oct 25 12:25:32 2010
From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen)
Date: Mon, 25 Oct 2010 12:25:32 +0200
Subject: Coherence and dipole
In-Reply-To: <LISTSERV%201010230012312850.2915@NIC.SURFNET.NL>
Message-ID: <MON.25.OCT.2010.122532.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Rodolphe,

The problem with coherence analysis on channel level (EEG) data that
widely separated electrodes can 'see' the same neuronal sources. Also,
they see the same noise (as 'injected' by the choice of reference
electrode, which can be a single channel, or the average across all
channels). So, every channel contains an unknown mix of interesting
brain signal, uninteresting brain signal, and uninteresting noise.
Depending on the spatial structure of these 3 components and the way
they are mixed per channel determines the observations.
Troublesome sources which may cause the effect you are observing, may
be quite distant 'dipoles' accounting for the cardiac activity picked
up by the EEG electrode array. Although in general I believe that EEG-
channel-level coherence analysis is very problematic due to
interpretational difficulties, you could see whether your reported
spatial patterns change when constructing a Laplacian derivation for
each of your electrodes (if the number of electrodes allows for this).

Good luck,

Jan-Mathijs


On Oct 23, 2010, at 12:12 AM, Rodolphe Nenert wrote:

> Dear Jan,
>
> yes i do analyze EEG data. The data was recorded using vertex  (CZ) as
> reference, but i modified to an average reference before doing any
> time-freq
> analysis.
>
> Rodolphe.
>
> On Fri, 22 Oct 2010 09:04:00 +0200, jan-mathijs schoffelen
> <jan.schoffelen at DONDERS.RU.NL> wrote:
>
>> Dear Rodolphe,
>>
>> I guess you are analyzing EEG data? What reference electrode(s) did
>> you use?
>>
>> Best,
>> JM
>>
>>
>>
>> On Oct 22, 2010, at 1:47 AM, Rodolphe wrote:
>>
>>> Dear Fieldtrip users,
>>>
>>> I recently run a coherence analysis on my data and i plotted a
>>> beautiful Topographic plot showing a strong coherence between one
>>> electrode in left parietal ( P5) and some right frontal electrodes.
>>> The thing is, when i try with the right parietal equivalent ( P6 )
>>> then i find a coherence with left frontal. Ans so on with a couple
>>> of other electrodes use as ref channels.
>>> As this symmetry looks awkward to me, is any of you have an idea of
>>> a posible artifact that can cause this, or a possible bias in the
>>> analysis? ( I tripled checked my code)
>>>
>>> Best,
>>>
>>> Rodolphe N., Ph.D.
>>> --------------------------------------------------------------------------- You
>>> are receiving this message because you are subscribed to
>>> the FieldTrip list. The aim of this list is to facilitate the
>>> discussion
>>> between users of the FieldTrip toolbox, to share experiences
>>> and to discuss new ideas for MEG and EEG analysis.
>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html
>>> and http://www.ru.nl/neuroimaging/fieldtrip.
>>> ---------------------------------------------------------------------------
>>>
>>
>> Dr. J.M. (Jan-Mathijs) Schoffelen
>> Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>> J.Schoffelen at donders.ru.nl
>> Telephone: 0031-24-3614793
>>
>> ---------------------------------------------------------------------------
>> You are receiving this message because you are subscribed to
>> the  FieldTrip list. The aim of this list is to facilitate the
>> discussion
>> between  users of the FieldTrip  toolbox, to share experiences
>> and to discuss  new ideas for MEG and EEG analysis.
>> See also http://listserv.surfnet.nl/archives/fieldtrip.html
>> and http://www.ru.nl/neuroimaging/fieldtrip.
>> ---------------------------------------------------------------------------
>
> ---------------------------------------------------------------------------
> You are receiving this message because you are subscribed to
> the  FieldTrip list. The aim of this list is to facilitate the
> discussion
> between  users of the FieldTrip  toolbox, to share experiences
> and to discuss  new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------
>

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

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and to discuss  new ideas for MEG and EEG analysis.
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and http://www.ru.nl/neuroimaging/fieldtrip.
---------------------------------------------------------------------------


From paul_c at GMX.DE  Mon Oct 25 13:40:48 2010
From: paul_c at GMX.DE (Paul Czienskowski)
Date: Mon, 25 Oct 2010 13:40:48 +0200
Subject: Forward model conductivities
Message-ID: <MON.25.OCT.2010.134048.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear all,

Alexandre Gramford pointed out to me that there was some discussion
ongoing on which conductivities to use for EEG-Forward-Modeling and I'd
like to move this discussion more to public for it could be interesting
for many of us.
I was recently overflying some papers concerned with that very issues
and I made some interesting and discoveries, especially in

    Conductivity of living intracranial tissues. by Latikka J, Kuurne T,
    Eskola H.
    The electrical conductivity of human cerebrospinal fluid at body
    temperature by Baumann et al.

The first one measured the conductivities (or resistivities) of living
brain tissue and came to values of 3.51 Ohms*m and 3.91 Ohms*m for grey
respectively white matter and 0.80 Ohms*m for the CSF (which are about
0.28, 0.256 and 1.25 S/m). In contrary the second one found a value for
1.79 S/m for CSF at body temperature where it was about 1.4 S/m at room
temperature. The Skull-To-Brain conductivity ratio was measured for
example in

    Estimation of /in vivo/ brain-to-skull conductivity ratio in humans
    by Yingchun Zhang, Wim van Drongelen, and Bin He

where they found a ratio of about 1/18.7 which is way larger than the
commonly assumed value.

I would appreciate very much if many of you could contribute to this
discussion by telling us which values you use for the conductivities and
on which publications the are based.

Best,
Paul

--
Paul Czienskowski
Max Planck institute for human development
Lentzeallee 94
14195 Berlin

Björnsonstr. 25
12163 Berlin

Tel.: (+49)(0)30/221609359
Handy: (+49)(0)1788378772


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From carsten.wolters at UNI-MUENSTER.DE  Mon Oct 25 15:41:24 2010
From: carsten.wolters at UNI-MUENSTER.DE (Dr. Carsten Wolters)
Date: Mon, 25 Oct 2010 15:41:24 +0200
Subject: Forward model conductivities
In-Reply-To: <4CC56CC0.5070307@gmx.de>
Message-ID: <MON.25.OCT.2010.154124.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Paul,

head tissue conductivities seem to have a larger inter- and
intra-subject variability.
I attachted a 4-page-proceedings paper with regard to those issues that
we recently presented :
@InProceedings{CHW:Wol2010,
  author =       "C. H. Wolters and S.Lew and R. S. MacLeod and M. S.
H{\"a}m{\"a}l{\"a}inen",
  title =        "Combined {EEG/MEG} source analysis using calibrated
finite element head models",
  booktitle =    "Proc. of the 44th Annual Meeting, DGBMT",
  address =      "Rostock-Warnem{\"u}nde, Germany, Oct.5-8, 2010",
  year =         "2010",
  note =         "http://conference.vde.com/bmt-2010",
}

Best regards
   Carsten

Paul Czienskowski wrote:
> Dear all,
>
> Alexandre Gramford pointed out to me that there was some discussion
> ongoing on which conductivities to use for EEG-Forward-Modeling and
> I'd like to move this discussion more to public for it could be
> interesting for many of us.
> I was recently overflying some papers concerned with that very issues
> and I made some interesting and discoveries, especially in
>
>     Conductivity of living intracranial tissues. by Latikka J, Kuurne
>     T, Eskola H.
>     The electrical conductivity of human cerebrospinal fluid at body
>     temperature by Baumann et al.
>
> The first one measured the conductivities (or resistivities) of living
> brain tissue and came to values of 3.51 Ohms*m and 3.91 Ohms*m for
> grey respectively white matter and 0.80 Ohms*m for the CSF (which are
> about 0.28, 0.256 and 1.25 S/m). In contrary the second one found a
> value for 1.79 S/m for CSF at body temperature where it was about 1.4
> S/m at room temperature. The Skull-To-Brain conductivity ratio was
> measured for example in
>
>     Estimation of /in vivo/ brain-to-skull conductivity ratio in
>     humans by Yingchun Zhang, Wim van Drongelen, and Bin He
>
> where they found a ratio of about 1/18.7 which is way larger than the
> commonly assumed value.
>
> I would appreciate very much if many of you could contribute to this
> discussion by telling us which values you use for the conductivities
> and on which publications the are based.
>
> Best,
> Paul
> --
> Paul Czienskowski
> Max Planck institute for human development
> Lentzeallee 94
> 14195 Berlin
>
> Björnsonstr. 25
> 12163 Berlin
>
> Tel.: (+49)(0)30/221609359
> Handy: (+49)(0)1788378772
>
> ---------------------------------------------------------------------------
> You are receiving this message because you are subscribed to
> the FieldTrip list. The aim of this list is to facilitate the discussion
> between users of the FieldTrip toolbox, to share experiences
> and to discuss new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------
>


--
PD.Dr.rer.nat. Carsten Wolters
Institute for Biomagnetism and Biosignalanalysis
University of Muenster, 48149 Muenster, Germany
Tel.: +49/(0)251-83-56904
Fax:  +49/(0)251-83-56874
http://biomag.uni-muenster.de


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and to discuss  new ideas for MEG and EEG analysis.
See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
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From sklein at BERKELEY.EDU  Mon Oct 25 19:10:42 2010
From: sklein at BERKELEY.EDU (Stanley Klein)
Date: Mon, 25 Oct 2010 10:10:42 -0700
Subject: Forward model conductivities
In-Reply-To: <4CC56CC0.5070307@gmx.de>
Message-ID: <MON.25.OCT.2010.101042.0700.>

Dear Paul and Carsten,
The conductivity ratio of 1/20 that you mention is indeed on the low side of
many present estimates. It is way lower than the Rush  &  Driscoll  1/80
ratio that we used in our 30 year old "Ary Correction" paper that examined
the effect of skull and scalp thickness. My big worry however is
not simply to find the ratio (taking individual differences into account).
but
also to get estimates of the differences in conductivity across the skull.
I'm pretty confident that such inhomogeneities are present and that they
will
have significant effects on the BEM forward models. The inhomogeneities
will not only affect the effective depth of sources but also can laterally
shift
their locations to places on cortex with very different surface normals.

An important aspect of our EEG/MEG source localization work is to learn
how to calibrate each individual's conductivity partly based on differences
in EEG vs MEG localizations.

best,
Stan



On Mon, Oct 25, 2010 at 4:40 AM, Paul Czienskowski <paul_c at gmx.de> wrote:

> Dear all,
>
> Alexandre Gramford pointed out to me that there was some discussion ongoing
> on which conductivities to use for EEG-Forward-Modeling and I'd like to move
> this discussion more to public for it could be interesting for many of us.
> I was recently overflying some papers concerned with that very issues and I
> made some interesting and discoveries, especially in
>
> Conductivity of living intracranial tissues. by Latikka J, Kuurne T, Eskola
> H.
> The electrical conductivity of human cerebrospinal fluid at body
> temperature by Baumann et al.
>
> The first one measured the conductivities (or resistivities) of living
> brain tissue and came to values of 3.51 Ohms*m and 3.91 Ohms*m for grey
> respectively white matter and 0.80 Ohms*m for the CSF (which are about 0.28,
> 0.256 and 1.25 S/m). In contrary the second one found a value for 1.79 S/m
> for CSF at body temperature where it was about 1.4 S/m at room temperature.
> The Skull-To-Brain conductivity ratio was measured for example in
>
> Estimation of *in vivo* brain-to-skull conductivity ratio in humans by
> Yingchun Zhang, Wim van Drongelen, and Bin He
>
> where they found a ratio of about 1/18.7 which is way larger than the
> commonly assumed value.
>
> I would appreciate very much if many of you could contribute to this
> discussion by telling us which values you use for the conductivities and on
> which publications the are based.
>
> Best,
> Paul
>
>
> --
> Paul Czienskowski
> Max Planck institute for human development
> Lentzeallee 94
> 14195 Berlin
>
> Björnsonstr. 25
> 12163 Berlin
>
> Tel.: (+49)(0)30/221609359
> Handy: (+49)(0)1788378772
>
> ---------------------------------------------------------------------------
> You are receiving this message because you are subscribed to
> the FieldTrip list. The aim of this list is to facilitate the discussion
> between users of the FieldTrip toolbox, to share experiences
> and to discuss new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------
>

---------------------------------------------------------------------------
You are receiving this message because you are subscribed to
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and to discuss  new ideas for MEG and EEG analysis.
See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
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From batrod at GMAIL.COM  Tue Oct 26 03:04:47 2010
From: batrod at GMAIL.COM (Rodolphe)
Date: Mon, 25 Oct 2010 20:04:47 -0500
Subject: Coherence reference channel for statistical analysis
Message-ID: <MON.25.OCT.2010.200447.0500.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrip users,

Im actually doing analysis on EEG coherence data.
Plotting coherence data is quite easy by choosing  a reference channel
(cfg.cohrefchannel).
But it seems more complicated when it deals with statistical analysis.
Basically my question is: how do i choose a ref channel for an analysis like
the montecarlo (i guess the method is the same for other stat tests).
I tried to look at the code, but i start to be quite confuse between the
different options like 'channelcmb' 'labcmb' 'labelcmb', etc...
Apparently, ft_connectivityanalysis function analyze all possible pairs,
whatever i  specify as channel combinations...

Cheers,

Rodolphe.

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From carsten.wolters at UNI-MUENSTER.DE  Tue Oct 26 09:11:47 2010
From: carsten.wolters at UNI-MUENSTER.DE (Dr. Carsten Wolters)
Date: Tue, 26 Oct 2010 09:11:47 +0200
Subject: Forward model conductivities
In-Reply-To: <AANLkTi=OxhF45FQVM=_H3Y=N57qH-P0irD3b9VDARofc@mail.gmail.com>
Message-ID: <TUE.26.OCT.2010.091147.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Stanley and Paul,

I agree to what Stanley wrote about the skull inhomogeneities, it fits
perfectly
to what we described in a recent publication:
@Article{CHW:Dan2010,
    author = {Dannhauer, M. and Lanfer, B. and Wolters, C.H. and
Kn{\"o}sche, T.},
    title = {Modeling of the Human Skull in {EEG} Source Analysis},
  journal =      "Human Brain Mapping",
  note    =      "DOI: 10.1002/hbm.21114, PMID: 20690140",
  year =         "2010",
}
Best regards
    Carsten

Stanley Klein wrote:
> Dear Paul and Carsten,
> The conductivity ratio of 1/20 that you mention is indeed on the low
> side of
> many present estimates. It is way lower than the Rush  &  Driscoll  1/80
> ratio that we used in our 30 year old "Ary Correction" paper that
> examined
> the effect of skull and scalp thickness. My big worry however is
> not simply to find the ratio (taking individual differences into
> account). but
> also to get estimates of the differences in conductivity across the skull.
> I'm pretty confident that such inhomogeneities are present and that
> they will
> have significant effects on the BEM forward models. The inhomogeneities
> will not only affect the effective depth of sources but also can
> laterally shift
> their locations to places on cortex with very different surface normals.
>
> An important aspect of our EEG/MEG source localization work is to learn
> how to calibrate each individual's conductivity partly based on
> differences
> in EEG vs MEG localizations.
>
> best,
> Stan
>
>
>
> On Mon, Oct 25, 2010 at 4:40 AM, Paul Czienskowski <paul_c at gmx.de
> <mailto:paul_c at gmx.de>> wrote:
>
>     Dear all,
>
>     Alexandre Gramford pointed out to me that there was some
>     discussion ongoing on which conductivities to use for
>     EEG-Forward-Modeling and I'd like to move this discussion more to
>     public for it could be interesting for many of us.
>     I was recently overflying some papers concerned with that very
>     issues and I made some interesting and discoveries, especially in
>
>         Conductivity of living intracranial tissues. by Latikka J,
>         Kuurne T, Eskola H.
>         The electrical conductivity of human cerebrospinal fluid at
>         body temperature by Baumann et al.
>
>     The first one measured the conductivities (or resistivities) of
>     living brain tissue and came to values of 3.51 Ohms*m and 3.91
>     Ohms*m for grey respectively white matter and 0.80 Ohms*m for the
>     CSF (which are about 0.28, 0.256 and 1.25 S/m). In contrary the
>     second one found a value for 1.79 S/m for CSF at body temperature
>     where it was about 1.4 S/m at room temperature. The Skull-To-Brain
>     conductivity ratio was measured for example in
>
>         Estimation of /in vivo/ brain-to-skull conductivity ratio in
>         humans by Yingchun Zhang, Wim van Drongelen, and Bin He
>
>     where they found a ratio of about 1/18.7 which is way larger than
>     the commonly assumed value.
>
>     I would appreciate very much if many of you could contribute to
>     this discussion by telling us which values you use for the
>     conductivities and on which publications the are based.
>
>     Best,
>     Paul
>
>     --
>     Paul Czienskowski
>     Max Planck institute for human development
>     Lentzeallee 94
>     14195 Berlin
>
>     Björnsonstr. 25
>     12163 Berlin
>
>     Tel.: (+49)(0)30/221609359
>     Handy: (+49)(0)1788378772
>
> ------------------------------------------------------------------------
>


--
PD.Dr.rer.nat. Carsten Wolters
Institute for Biomagnetism and Biosignalanalysis
University of Muenster, 48149 Muenster, Germany
Tel.: +49/(0)251-83-56904
Fax:  +49/(0)251-83-56874
http://biomag.uni-muenster.de

---------------------------------------------------------------------------
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between  users of the FieldTrip  toolbox, to share experiences
and to discuss  new ideas for MEG and EEG analysis.
See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
---------------------------------------------------------------------------


From Nina.Kahlbrock at UNI-DUESSELDORF.DE  Tue Oct 26 10:07:33 2010
From: Nina.Kahlbrock at UNI-DUESSELDORF.DE (Nina Kahlbrock)
Date: Tue, 26 Oct 2010 10:07:33 +0200
Subject: AW: [FIELDTRIP] ft_channelrepair with neuromag data
In-Reply-To: <4CC13C4D.3000603@cbs.mpg.de>
Message-ID: <TUE.26.OCT.2010.100733.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Burkhard,
I am also working on NM306 data and I have a specific problem repairing
broken channels using maxfilter. This email might thus be more suited for
the neuromeg discussion list. However, I thought it might be of interest to
other NM users as well...
What I would like to do is pretty much the same as described in the previous
mails: interpolate broken channels and use a standard head position for
multiple recordings in one subject.
I used fieldtrip's automatic and semi-automatic artifact rejection routines
to identify channels that are flat, show jumps and are noisy. I defined
these as bad in maxfilter. Then I used sss/tsss to achieve the desired
steps. It seemed very straight forward. 
However, when looking at the results, the signal seems to be increased (and
more noisy and jumpy) in certain channels (see attached pdfs of bad and
non-bad channel (1st page: raw data, 2nd page: sss data, 3rd page: tsss
data). Have you ever experienced anything like this? The only reason I can
come up with is that in maxfilter I used the continuous raw data file and
not as in fieldtrip, only trials. Between trials there are pauses, where the
channels could have been affected by a few movements. Could this explain my
difficulties?
Is there a way to 'only' interpolate channels and realign the head, without
impacting other non-broken channels?
Thank you very much for your answer!
Nina   



-----Ursprüngliche Nachricht-----
Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag
von Burkhard Maess
Gesendet: Freitag, 22. Oktober 2010 09:25
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: Re: [FIELDTRIP] ft_channelrepair with neuromag data

Dear David,

I agree with Jan-Mathijs.

variant a: apply maxfilter - that will repair all broken channels. You 
also can manually define certain channels as broken. Maxfilter may also 
align data of different headpositions to a single position.

variant b: use megrealign - it includes a minimum norm localization and 
from there MEG data is forward computed. In this way, you can repair 
channels, align different head positions to the same and even convert 
data between different systems.

all the best,
Burkhard


jan-mathijs schoffelen wrote:
> Dear David,
>
> This is a good point. As far as I can see from the code, no 
> distinction is made between gradiometers and magnetometers.
> Naively, I would propose the following: first indeed split the data 
> into two subset: gradiometers only and magnetometers only, only then 
> apply the channel reparation routine. Yet, for the gradiometer subset 
> data, it is questionable whether as such the replacement of a bad 
> channel with its neighbours makes sense, because this would lead to 
> averaging gradients of the magnetic field with an orthogonal orientation.
>  
> In other words, this is probably not the most sensible approach. I 
> don't think repairing after combining the planar gradients is 
>  desired, because this leads to an unwanted amplification of the noise 
> (because the combination step results in taking an absolute value). 
> Alternatively, you could consider using ft_megrealign, which in 
> principle could be used to repair bad channels. The recipe would be to 
> only use the data with the clean channels in the input, and you would 
> want to interpolate the data back onto the original sensor-array. An 
> example for interpolating between two types of CTF-systems is shown 
> here http://fieldtrip.fcdonders.nl/example/megrealign.
>
> Just out of curiosity: doesn't the maxfilter in the Neuromag software 
> allow for similar things?
>
> Best wishes,
>
> Jan-Mathijs 
>
> On Oct 21, 2010, at 9:49 PM, David Ziegler wrote:
>
>> Hi Fieldtrippers,
>>
>> I would like to use ft_channelrepair to interpolate data for some 
>> missing/deleted channels with Neuromag 306 data.  I am just wondering 
>> whether there are any potential problems with using the nearest 
>> neighbor interpolation, given the triplet format of the Neuromag 
>> system (two planar gradiometers and one magnetometer).  
>>
>> If this is problematic, are there other options to fixing bad/missing 
>> channels (e.g., can ft_channelrepair be run on just a subset of the 
>> channels, say the gradiometers after I run ft_combineplanar)?
>>
>> Thanks!
>> David
>>
>> -- 
>> David A. Ziegler
>> Department of Brain and Cognitive Sciences 
>> Massachusetts Institute of Technology 
>> 43 Vassar St,  46-5121 
>> Cambridge, MA  02139
>> Tel: 617-258-0765
>> Fax: 617-253-1504
>> daz at mit.edu <mailto:daz at mit.edu>
>>
>>  
>>
>>  
>>
>>
--------------------------------------------------------------------------- 
>> You are receiving this message because you are subscribed to 
>> the FieldTrip list. The aim of this list is to facilitate the discussion 
>> between users of the FieldTrip toolbox, to share experiences 
>> and to discuss new ideas for MEG and EEG analysis. 
>> See also http://listserv.surfnet.nl/archives/fieldtrip.html 
>> and http://www.ru.nl/neuroimaging/fieldtrip.
>>
---------------------------------------------------------------------------
>>
>
> Dr. J.M. (Jan-Mathijs) Schoffelen 
> Donders Institute for Brain, Cognition and Behaviour, 
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
> Telephone: 0031-24-3614793
>
>
--------------------------------------------------------------------------- 
> You are receiving this message because you are subscribed to
> the FieldTrip list. The aim of this list is to facilitate the discussion
> between users of the FieldTrip toolbox, to share experiences
> and to discuss new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
>
---------------------------------------------------------------------------
>

-- 
------------------------------------------------------------
Dr. Burkhard Maess
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig
Aussenstelle Bennewitz, phone/fax: +49(3425)887525-26/-11   
mail: maess 'at' cbs.mpg.de,           http://www.cbs.mpg.de
------------------------------------------------------------
Please do not attach files which may contain executable code, 
e.g. .rtf is preferred over .doc(x)

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between  users of the FieldTrip  toolbox, to share experiences
and to discuss  new ideas for MEG and EEG analysis.
See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
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See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
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From maess at CBS.MPG.DE  Tue Oct 26 10:46:46 2010
From: maess at CBS.MPG.DE (Burkhard Maess)
Date: Tue, 26 Oct 2010 10:46:46 +0200
Subject: AW: [FIELDTRIP] ft_channelrepair with neuromag data
In-Reply-To: <000d01cb74e4$d7ccf490$cd136386@VMED.UKD>
Message-ID: <TUE.26.OCT.2010.104646.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Nina,

indeed this looks funny. I have seen that maxfilter sometimes has 
produced unexpected results, but usually the channels have less noise 
after transformation. Your displays demonstrate the problem, but provide 
insufficient information to search for origin of it. I think, it is 
necessary to place one of these files to an ftp-server together with the 
list of bad channels you have used and the version of maxfilter. I would 
recommend to ask Jukka Nennonen for help because he is the maxfilter-pro 
and the displayed result should not show up. We shall continue the 
discussion here when we know the reason for this strange behavior.

best wishes,
Burkhard



Nina Kahlbrock wrote:
> Dear Burkhard,
> I am also working on NM306 data and I have a specific problem repairing
> broken channels using maxfilter. This email might thus be more suited for
> the neuromeg discussion list. However, I thought it might be of interest to
> other NM users as well...
> What I would like to do is pretty much the same as described in the previous
> mails: interpolate broken channels and use a standard head position for
> multiple recordings in one subject.
> I used fieldtrip's automatic and semi-automatic artifact rejection routines
> to identify channels that are flat, show jumps and are noisy. I defined
> these as bad in maxfilter. Then I used sss/tsss to achieve the desired
> steps. It seemed very straight forward. 
> However, when looking at the results, the signal seems to be increased (and
> more noisy and jumpy) in certain channels (see attached pdfs of bad and
> non-bad channel (1st page: raw data, 2nd page: sss data, 3rd page: tsss
> data). Have you ever experienced anything like this? The only reason I can
> come up with is that in maxfilter I used the continuous raw data file and
> not as in fieldtrip, only trials. Between trials there are pauses, where the
> channels could have been affected by a few movements. Could this explain my
> difficulties?
> Is there a way to 'only' interpolate channels and realign the head, without
> impacting other non-broken channels?
> Thank you very much for your answer!
> Nina   
>
>
>
> -----Ursprüngliche Nachricht-----
> Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag
> von Burkhard Maess
> Gesendet: Freitag, 22. Oktober 2010 09:25
> An: FIELDTRIP at NIC.SURFNET.NL
> Betreff: Re: [FIELDTRIP] ft_channelrepair with neuromag data
>
> Dear David,
>
> I agree with Jan-Mathijs.
>
> variant a: apply maxfilter - that will repair all broken channels. You 
> also can manually define certain channels as broken. Maxfilter may also 
> align data of different headpositions to a single position.
>
> variant b: use megrealign - it includes a minimum norm localization and 
> from there MEG data is forward computed. In this way, you can repair 
> channels, align different head positions to the same and even convert 
> data between different systems.
>
> all the best,
> Burkhard
>
>
> jan-mathijs schoffelen wrote:
>   
>> Dear David,
>>
>> This is a good point. As far as I can see from the code, no 
>> distinction is made between gradiometers and magnetometers.
>> Naively, I would propose the following: first indeed split the data 
>> into two subset: gradiometers only and magnetometers only, only then 
>> apply the channel reparation routine. Yet, for the gradiometer subset 
>> data, it is questionable whether as such the replacement of a bad 
>> channel with its neighbours makes sense, because this would lead to 
>> averaging gradients of the magnetic field with an orthogonal orientation.
>>  
>> In other words, this is probably not the most sensible approach. I 
>> don't think repairing after combining the planar gradients is 
>>  desired, because this leads to an unwanted amplification of the noise 
>> (because the combination step results in taking an absolute value). 
>> Alternatively, you could consider using ft_megrealign, which in 
>> principle could be used to repair bad channels. The recipe would be to 
>> only use the data with the clean channels in the input, and you would 
>> want to interpolate the data back onto the original sensor-array. An 
>> example for interpolating between two types of CTF-systems is shown 
>> here http://fieldtrip.fcdonders.nl/example/megrealign.
>>
>> Just out of curiosity: doesn't the maxfilter in the Neuromag software 
>> allow for similar things?
>>
>> Best wishes,
>>
>> Jan-Mathijs 
>>
>> On Oct 21, 2010, at 9:49 PM, David Ziegler wrote:
>>
>>     
>>> Hi Fieldtrippers,
>>>
>>> I would like to use ft_channelrepair to interpolate data for some 
>>> missing/deleted channels with Neuromag 306 data.  I am just wondering 
>>> whether there are any potential problems with using the nearest 
>>> neighbor interpolation, given the triplet format of the Neuromag 
>>> system (two planar gradiometers and one magnetometer).  
>>>
>>> If this is problematic, are there other options to fixing bad/missing 
>>> channels (e.g., can ft_channelrepair be run on just a subset of the 
>>> channels, say the gradiometers after I run ft_combineplanar)?
>>>
>>> Thanks!
>>> David
>>>
>>> -- 
>>> David A. Ziegler
>>> Department of Brain and Cognitive Sciences 
>>> Massachusetts Institute of Technology 
>>> 43 Vassar St,  46-5121 
>>> Cambridge, MA  02139
>>> Tel: 617-258-0765
>>> Fax: 617-253-1504
>>> daz at mit.edu <mailto:daz at mit.edu>
>>>
>>>  
>>>
>>>  
>>>
>>>
>>>       
> --------------------------------------------------------------------------- 
>   
>>> You are receiving this message because you are subscribed to 
>>> the FieldTrip list. The aim of this list is to facilitate the discussion 
>>> between users of the FieldTrip toolbox, to share experiences 
>>> and to discuss new ideas for MEG and EEG analysis. 
>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html 
>>> and http://www.ru.nl/neuroimaging/fieldtrip.
>>>
>>>       
> ---------------------------------------------------------------------------
>   
>> Dr. J.M. (Jan-Mathijs) Schoffelen 
>> Donders Institute for Brain, Cognition and Behaviour, 
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>> J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
>> Telephone: 0031-24-3614793
>>
>>
>>     
> --------------------------------------------------------------------------- 
>   
>> You are receiving this message because you are subscribed to
>> the FieldTrip list. The aim of this list is to facilitate the discussion
>> between users of the FieldTrip toolbox, to share experiences
>> and to discuss new ideas for MEG and EEG analysis.
>> See also http://listserv.surfnet.nl/archives/fieldtrip.html
>> and http://www.ru.nl/neuroimaging/fieldtrip.
>>
>>     
> ---------------------------------------------------------------------------
>   
>
>   

-- 
------------------------------------------------------------
Dr. Burkhard Maess
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig
Aussenstelle Bennewitz, phone/fax: +49(3425)887525-26/-11   
mail: maess 'at' cbs.mpg.de,           http://www.cbs.mpg.de
------------------------------------------------------------
Please do not attach files which may contain executable code, 
e.g. .rtf is preferred over .doc(x)

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


From e.vandenbroeke at ANES.UMCN.NL  Tue Oct 26 16:25:24 2010
From: e.vandenbroeke at ANES.UMCN.NL (Emanuel van den Broeke)
Date: Tue, 26 Oct 2010 16:25:24 +0200
Subject: non-parametric cluster-based analysis
Message-ID: <TUE.26.OCT.2010.162524.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear fieldtrip users,

I would like to know if I it is allowed to do three single non-parametric cluster 
based analyses and use IndepT-statistics, if I will test three groups (group A 
vs B, B vs C and A vs C) by . And  is it then nescessarily to adjust post-hoc 
the p-value of all three comparisons because of multiple comparisons?

Thanx!
Emanuel

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


From batrod at GMAIL.COM  Wed Oct 27 01:08:23 2010
From: batrod at GMAIL.COM (Rodolphe Nenert)
Date: Wed, 27 Oct 2010 01:08:23 +0200
Subject: non-parametric cluster-based analysis
Message-ID: <WED.27.OCT.2010.010823.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Emmanuel, 

If i understand correctly you want to rank your 3 groups on a particular 
condition using the cluster correction. On normal data you would face the 
multiple comparison problem and would need to correct. Here, this need to be 
confirmed, the problem is you're doing cluster correction. Therefore, the 
significant cluster you may find between your groups may vary in "shape". 
Ranking is thus probably nonsense. 
Still, this analysis will tell you what is significantly different between two 
groups. If you want to rank your 3 groups you can choose relevant electrodes 
and make an ANOVA, or if you want to stay with non-parametric, a Kruskal-
Wallis.
Hope this helps, maybe someone else will have a better answer to your 
problem, 

Rodolphe.


On Tue, 26 Oct 2010 16:25:24 +0200, <Emanuel van den Broeke> 
<e.vandenbroeke at ANES.UMCN.NL> wrote:

>Dear fieldtrip users,
>
>I would like to know if I it is allowed to do three single non-parametric 
cluster 
>based analyses and use IndepT-statistics, if I will test three groups (group A 
>vs B, B vs C and A vs C) by . And  is it then nescessarily to adjust post-hoc 
>the p-value of all three comparisons because of multiple comparisons?
>
>Thanx!
>Emanuel
>
>---------------------------------------------------------------------------
>You are receiving this message because you are subscribed to
>the  FieldTrip list. The aim of this list is to facilitate the discussion
>between  users of the FieldTrip  toolbox, to share experiences
>and to discuss  new ideas for MEG and EEG analysis.
>See also http://listserv.surfnet.nl/archives/fieldtrip.html
>and http://www.ru.nl/neuroimaging/fieldtrip.
>---------------------------------------------------------------------------

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


From e.maris at DONDERS.RU.NL  Wed Oct 27 07:33:36 2010
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Wed, 27 Oct 2010 07:33:36 +0200
Subject: non-parametric cluster-based analysis
In-Reply-To: <LISTSERV%201010261625249140.8B40@NIC.SURFNET.NL>
Message-ID: <WED.27.OCT.2010.073336.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Emanuel,


> I would like to know if I it is allowed to do three single non-
> parametric cluster
> based analyses and use IndepT-statistics, if I will test three groups
> (group A
> vs B, B vs C and A vs C) by . And  is it then nescessarily to adjust
> post-hoc
> the p-value of all three comparisons because of multiple comparisons?

Yes, this is required.

Alternatively, you may run a single three-group analysis using the
indepsamplesF statistic. Here, you test the null hypothesis that the
observations in the three groups are all drawn from the same probability
distribution.


Best,

Eric





>
> Thanx!
> Emanuel
>
> -----------------------------------------------------------------------
> ----
> You are receiving this message because you are subscribed to
> the  FieldTrip list. The aim of this list is to facilitate the
> discussion
> between  users of the FieldTrip  toolbox, to share experiences
> and to discuss  new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> -----------------------------------------------------------------------
> ----

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


From daz at MIT.EDU  Wed Oct 27 17:01:46 2010
From: daz at MIT.EDU (David Ziegler)
Date: Wed, 27 Oct 2010 11:01:46 -0400
Subject: AW: [FIELDTRIP] ft_channelrepair with neuromag data
In-Reply-To: <4CC69576.5090501@cbs.mpg.de>
Message-ID: <WED.27.OCT.2010.110146.0400.FIELDTRIP@NIC.SURFNET.NL>

Hi Burkdard and Nina,

First off, thanks for the great advice Burkhard (and Jan-Mathijs).
Following your advice, I processed my raw neuromag data with maxfilter,
and I ended up with some results that are quite similar to what Nina is
seeing.  This doesn't happen for all of my subjects, but for about half
of them, I get increased noise in select channels following maxfilter.
I believe I used maxfilter v2.0 and my command line was:

maxfilter -f $f_i{each subject's fif file} -origin 0 0 40 -frame head
-autobad 30 -badlimit 7 -in 8 -out 3 -trans default

You mentioned that this should probably be posted to the neuromag list,
but I am not currently on that list and wasn't able to find it with a
quick search.  I'd be happy to repost there if you point me to the
sign-up page.

Thanks!
David


On 10/26/2010 4:46 AM, Burkhard Maess wrote:
> Dear Nina,
>
> indeed this looks funny. I have seen that maxfilter sometimes has
> produced unexpected results, but usually the channels have less noise
> after transformation. Your displays demonstrate the problem, but
> provide insufficient information to search for origin of it. I think,
> it is necessary to place one of these files to an ftp-server together
> with the list of bad channels you have used and the version of
> maxfilter. I would recommend to ask Jukka Nennonen for help because he
> is the maxfilter-pro and the displayed result should not show up. We
> shall continue the discussion here when we know the reason for this
> strange behavior.
>
> best wishes,
> Burkhard
>
>
>
> Nina Kahlbrock wrote:
>> Dear Burkhard,
>> I am also working on NM306 data and I have a specific problem repairing
>> broken channels using maxfilter. This email might thus be more suited
>> for
>> the neuromeg discussion list. However, I thought it might be of
>> interest to
>> other NM users as well...
>> What I would like to do is pretty much the same as described in the
>> previous
>> mails: interpolate broken channels and use a standard head position for
>> multiple recordings in one subject.
>> I used fieldtrip's automatic and semi-automatic artifact rejection
>> routines
>> to identify channels that are flat, show jumps and are noisy. I defined
>> these as bad in maxfilter. Then I used sss/tsss to achieve the desired
>> steps. It seemed very straight forward. However, when looking at the
>> results, the signal seems to be increased (and
>> more noisy and jumpy) in certain channels (see attached pdfs of bad and
>> non-bad channel (1st page: raw data, 2nd page: sss data, 3rd page: tsss
>> data). Have you ever experienced anything like this? The only reason
>> I can
>> come up with is that in maxfilter I used the continuous raw data file
>> and
>> not as in fieldtrip, only trials. Between trials there are pauses,
>> where the
>> channels could have been affected by a few movements. Could this
>> explain my
>> difficulties?
>> Is there a way to 'only' interpolate channels and realign the head,
>> without
>> impacting other non-broken channels?
>> Thank you very much for your answer!
>> Nina
>>
>>
>> -----Ursprüngliche Nachricht-----
>> Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im
>> Auftrag
>> von Burkhard Maess
>> Gesendet: Freitag, 22. Oktober 2010 09:25
>> An: FIELDTRIP at NIC.SURFNET.NL
>> Betreff: Re: [FIELDTRIP] ft_channelrepair with neuromag data
>>
>> Dear David,
>>
>> I agree with Jan-Mathijs.
>>
>> variant a: apply maxfilter - that will repair all broken channels.
>> You also can manually define certain channels as broken. Maxfilter
>> may also align data of different headpositions to a single position.
>>
>> variant b: use megrealign - it includes a minimum norm localization
>> and from there MEG data is forward computed. In this way, you can
>> repair channels, align different head positions to the same and even
>> convert data between different systems.
>>
>> all the best,
>> Burkhard
>>
>>
>> jan-mathijs schoffelen wrote:
>>> Dear David,
>>>
>>> This is a good point. As far as I can see from the code, no
>>> distinction is made between gradiometers and magnetometers.
>>> Naively, I would propose the following: first indeed split the data
>>> into two subset: gradiometers only and magnetometers only, only then
>>> apply the channel reparation routine. Yet, for the gradiometer
>>> subset data, it is questionable whether as such the replacement of a
>>> bad channel with its neighbours makes sense, because this would lead
>>> to averaging gradients of the magnetic field with an orthogonal
>>> orientation.
>>>
>>> In other words, this is probably not the most sensible approach. I
>>> don't think repairing after combining the planar gradients is
>>>  desired, because this leads to an unwanted amplification of the
>>> noise (because the combination step results in taking an absolute
>>> value). Alternatively, you could consider using ft_megrealign, which
>>> in principle could be used to repair bad channels. The recipe would
>>> be to only use the data with the clean channels in the input, and
>>> you would want to interpolate the data back onto the original
>>> sensor-array. An example for interpolating between two types of
>>> CTF-systems is shown here
>>> http://fieldtrip.fcdonders.nl/example/megrealign.
>>>
>>> Just out of curiosity: doesn't the maxfilter in the Neuromag
>>> software allow for similar things?
>>>
>>> Best wishes,
>>>
>>> Jan-Mathijs
>>> On Oct 21, 2010, at 9:49 PM, David Ziegler wrote:
>>>
>>>> Hi Fieldtrippers,
>>>>
>>>> I would like to use ft_channelrepair to interpolate data for some
>>>> missing/deleted channels with Neuromag 306 data.  I am just
>>>> wondering whether there are any potential problems with using the
>>>> nearest neighbor interpolation, given the triplet format of the
>>>> Neuromag system (two planar gradiometers and one magnetometer).
>>>> If this is problematic, are there other options to fixing
>>>> bad/missing channels (e.g., can ft_channelrepair be run on just a
>>>> subset of the channels, say the gradiometers after I run
>>>> ft_combineplanar)?
>>>>
>>>> Thanks!
>>>> David
>>>>
>>>> --
>>>> David A. Ziegler
>>>> Department of Brain and Cognitive Sciences Massachusetts Institute
>>>> of Technology 43 Vassar St,  46-5121 Cambridge, MA  02139
>>>> Tel: 617-258-0765
>>>> Fax: 617-253-1504
>>>> daz at mit.edu <mailto:daz at mit.edu>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>> ---------------------------------------------------------------------------
>>
>>>> You are receiving this message because you are subscribed to the
>>>> FieldTrip list. The aim of this list is to facilitate the
>>>> discussion between users of the FieldTrip toolbox, to share
>>>> experiences and to discuss new ideas for MEG and EEG analysis. See
>>>> also http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>> http://www.ru.nl/neuroimaging/fieldtrip.
>>>>
>> ---------------------------------------------------------------------------
>>
>>> Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain,
>>> Cognition and Behaviour, Centre for Cognitive Neuroimaging,
>>> Radboud University Nijmegen, The Netherlands
>>> J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
>>> Telephone: 0031-24-3614793
>>>
>>>
>> ---------------------------------------------------------------------------
>>
>>> You are receiving this message because you are subscribed to
>>> the FieldTrip list. The aim of this list is to facilitate the
>>> discussion
>>> between users of the FieldTrip toolbox, to share experiences
>>> and to discuss new ideas for MEG and EEG analysis.
>>> See also http://listserv.surfnet.nl/archives/fieldtrip.html
>>> and http://www.ru.nl/neuroimaging/fieldtrip.
>>>
>> ---------------------------------------------------------------------------
>>
>>
>

--

David A. Ziegler

Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St,46-5121
Cambridge, MA 02139

Tel: 617-258-0765

Fax: 617-253-1504

daz at mit.edu <mailto:daz at mit.edu>


---------------------------------------------------------------------------
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between  users of the FieldTrip  toolbox, to share experiences
and to discuss  new ideas for MEG and EEG analysis.
See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
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From Nina.Kahlbrock at UNI-DUESSELDORF.DE  Wed Oct 27 17:26:34 2010
From: Nina.Kahlbrock at UNI-DUESSELDORF.DE (Nina Kahlbrock)
Date: Wed, 27 Oct 2010 17:26:34 +0200
Subject: AW: [FIELDTRIP] AW: [FIELDTRIP] ft_channelrepair with neuromag
 data
In-Reply-To: <4CC83EDA.8070708@mit.edu>
Message-ID: <WED.27.OCT.2010.172634.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi David, 

the link for the neuromeg discussion list is:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=NEUROMEG

I am currently discussing those problems with the Elekta Neuromag support. I
will let you know as soon as this has come to a conclusion.

Cheers, 

Nina

 

 

  _____  

Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag
von David Ziegler
Gesendet: Mittwoch, 27. Oktober 2010 17:02
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: Re: [FIELDTRIP] AW: [FIELDTRIP] ft_channelrepair with neuromag data

 

Hi Burkdard and Nina,

First off, thanks for the great advice Burkhard (and Jan-Mathijs).
Following your advice, I processed my raw neuromag data with maxfilter, and
I ended up with some results that are quite similar to what Nina is seeing.
This doesn't happen for all of my subjects, but for about half of them, I
get increased noise in select channels following maxfilter.  I believe I
used maxfilter v2.0 and my command line was:

maxfilter -f $f_i{each subject's fif file} -origin 0 0 40 -frame head
-autobad 30 -badlimit 7 -in 8 -out 3 -trans default 

You mentioned that this should probably be posted to the neuromag list, but
I am not currently on that list and wasn't able to find it with a quick
search.  I'd be happy to repost there if you point me to the sign-up page.  

Thanks!
David


On 10/26/2010 4:46 AM, Burkhard Maess wrote: 

Dear Nina, 

indeed this looks funny. I have seen that maxfilter sometimes has produced
unexpected results, but usually the channels have less noise after
transformation. Your displays demonstrate the problem, but provide
insufficient information to search for origin of it. I think, it is
necessary to place one of these files to an ftp-server together with the
list of bad channels you have used and the version of maxfilter. I would
recommend to ask Jukka Nennonen for help because he is the maxfilter-pro and
the displayed result should not show up. We shall continue the discussion
here when we know the reason for this strange behavior. 

best wishes, 
Burkhard 



Nina Kahlbrock wrote: 



Dear Burkhard, 
I am also working on NM306 data and I have a specific problem repairing 
broken channels using maxfilter. This email might thus be more suited for 
the neuromeg discussion list. However, I thought it might be of interest to 
other NM users as well... 
What I would like to do is pretty much the same as described in the previous

mails: interpolate broken channels and use a standard head position for 
multiple recordings in one subject. 
I used fieldtrip's automatic and semi-automatic artifact rejection routines 
to identify channels that are flat, show jumps and are noisy. I defined 
these as bad in maxfilter. Then I used sss/tsss to achieve the desired 
steps. It seemed very straight forward. However, when looking at the
results, the signal seems to be increased (and 
more noisy and jumpy) in certain channels (see attached pdfs of bad and 
non-bad channel (1st page: raw data, 2nd page: sss data, 3rd page: tsss 
data). Have you ever experienced anything like this? The only reason I can 
come up with is that in maxfilter I used the continuous raw data file and 
not as in fieldtrip, only trials. Between trials there are pauses, where the

channels could have been affected by a few movements. Could this explain my 
difficulties? 
Is there a way to 'only' interpolate channels and realign the head, without 
impacting other non-broken channels? 
Thank you very much for your answer! 
Nina   


-----Ursprüngliche Nachricht----- 
Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag 
von Burkhard Maess 
Gesendet: Freitag, 22. Oktober 2010 09:25 
An: FIELDTRIP at NIC.SURFNET.NL 
Betreff: Re: [FIELDTRIP] ft_channelrepair with neuromag data 

Dear David, 

I agree with Jan-Mathijs. 

variant a: apply maxfilter - that will repair all broken channels. You also
can manually define certain channels as broken. Maxfilter may also align
data of different headpositions to a single position. 

variant b: use megrealign - it includes a minimum norm localization and from
there MEG data is forward computed. In this way, you can repair channels,
align different head positions to the same and even convert data between
different systems. 

all the best, 
Burkhard 


jan-mathijs schoffelen wrote: 
  

Dear David, 

This is a good point. As far as I can see from the code, no distinction is
made between gradiometers and magnetometers. 
Naively, I would propose the following: first indeed split the data into two
subset: gradiometers only and magnetometers only, only then apply the
channel reparation routine. Yet, for the gradiometer subset data, it is
questionable whether as such the replacement of a bad channel with its
neighbours makes sense, because this would lead to averaging gradients of
the magnetic field with an orthogonal orientation. 
  
In other words, this is probably not the most sensible approach. I don't
think repairing after combining the planar gradients is  desired, because
this leads to an unwanted amplification of the noise (because the
combination step results in taking an absolute value). Alternatively, you
could consider using ft_megrealign, which in principle could be used to
repair bad channels. The recipe would be to only use the data with the clean
channels in the input, and you would want to interpolate the data back onto
the original sensor-array. An example for interpolating between two types of
CTF-systems is shown here http://fieldtrip.fcdonders.nl/example/megrealign. 

Just out of curiosity: doesn't the maxfilter in the Neuromag software allow
for similar things? 

Best wishes, 

Jan-Mathijs 
On Oct 21, 2010, at 9:49 PM, David Ziegler wrote: 

    

Hi Fieldtrippers, 

I would like to use ft_channelrepair to interpolate data for some
missing/deleted channels with Neuromag 306 data.  I am just wondering
whether there are any potential problems with using the nearest neighbor
interpolation, given the triplet format of the Neuromag system (two planar
gradiometers and one magnetometer).  
If this is problematic, are there other options to fixing bad/missing
channels (e.g., can ft_channelrepair be run on just a subset of the
channels, say the gradiometers after I run ft_combineplanar)? 

Thanks! 
David 

-- 
David A. Ziegler 
Department of Brain and Cognitive Sciences Massachusetts Institute of
Technology 43 Vassar St,  46-5121 Cambridge, MA  02139 
Tel: 617-258-0765 
Fax: 617-253-1504 
daz at mit.edu  <mailto:daz at mit.edu> <mailto:daz at mit.edu> 

  

  


      

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


You are receiving this message because you are subscribed to the FieldTrip
list. The aim of this list is to facilitate the discussion between users of
the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG
and EEG analysis. See also
http://listserv.surfnet.nl/archives/fieldtrip.html and
http://www.ru.nl/neuroimaging/fieldtrip. 

      

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

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


    

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


You are receiving this message because you are subscribed to 
the FieldTrip list. The aim of this list is to facilitate the discussion 
between users of the FieldTrip toolbox, to share experiences 
and to discuss new ideas for MEG and EEG analysis. 
See also http://listserv.surfnet.nl/archives/fieldtrip.html 
and http://www.ru.nl/neuroimaging/fieldtrip. 

    

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

 

 

-- 



David A. Ziegler

Department of Brain and Cognitive Sciences 
Massachusetts Institute of Technology 
43 Vassar St,  46-5121 
Cambridge, MA  02139

Tel: 617-258-0765

Fax: 617-253-1504

daz at mit.edu

 

 

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See also http://listserv.surfnet.nl/archives/fieldtrip.html 
and http://www.ru.nl/neuroimaging/fieldtrip.
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From daz at MIT.EDU  Wed Oct 27 17:40:12 2010
From: daz at MIT.EDU (David Ziegler)
Date: Wed, 27 Oct 2010 11:40:12 -0400
Subject: AW: [FIELDTRIP] AW: [FIELDTRIP] ft_channelrepair with
 neuromag data
In-Reply-To: <000a01cb75eb$573904b0$cd136386@VMED.UKD>
Message-ID: <WED.27.OCT.2010.114012.0400.FIELDTRIP@NIC.SURFNET.NL>

Thanks, Nina, for the link and in advance for anything you find out from
Neuromag support.  Did you use a similar command as mine?

Cheers!
David


On 10/27/2010 11:26 AM, Nina Kahlbrock wrote:
>
> Hi David,
>
> the link for the neuromeg discussion list is:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=NEUROMEG
>
> I am currently discussing those problems with the Elekta Neuromag
> support. I will let you know as soon as this has come to a conclusion.
>
> Cheers,
>
> Nina
>
> ------------------------------------------------------------------------
>
> *Von:*FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] *Im
> Auftrag von *David Ziegler
> *Gesendet:* Mittwoch, 27. Oktober 2010 17:02
> *An:* FIELDTRIP at NIC.SURFNET.NL
> *Betreff:* Re: [FIELDTRIP] AW: [FIELDTRIP] ft_channelrepair with
> neuromag data
>
> Hi Burkdard and Nina,
>
> First off, thanks for the great advice Burkhard (and Jan-Mathijs).
> Following your advice, I processed my raw neuromag data with
> maxfilter, and I ended up with some results that are quite similar to
> what Nina is seeing.  This doesn't happen for all of my subjects, but
> for about half of them, I get increased noise in select channels
> following maxfilter.  I believe I used maxfilter v2.0 and my command
> line was:
>
> maxfilter -f $f_i{each subject's fif file} -origin 0 0 40 -frame head
> -autobad 30 -badlimit 7 -in 8 -out 3 -trans default
>
> You mentioned that this should probably be posted to the neuromag
> list, but I am not currently on that list and wasn't able to find it
> with a quick search.  I'd be happy to repost there if you point me to
> the sign-up page.
>
> Thanks!
> David
>
>
> On 10/26/2010 4:46 AM, Burkhard Maess wrote:
>
> Dear Nina,
>
> indeed this looks funny. I have seen that maxfilter sometimes has
> produced unexpected results, but usually the channels have less noise
> after transformation. Your displays demonstrate the problem, but
> provide insufficient information to search for origin of it. I think,
> it is necessary to place one of these files to an ftp-server together
> with the list of bad channels you have used and the version of
> maxfilter. I would recommend to ask Jukka Nennonen for help because he
> is the maxfilter-pro and the displayed result should not show up. We
> shall continue the discussion here when we know the reason for this
> strange behavior.
>
> best wishes,
> Burkhard
>
>
>
> Nina Kahlbrock wrote:
>
> Dear Burkhard,
> I am also working on NM306 data and I have a specific problem repairing
> broken channels using maxfilter. This email might thus be more suited for
> the neuromeg discussion list. However, I thought it might be of
> interest to
> other NM users as well...
> What I would like to do is pretty much the same as described in the
> previous
> mails: interpolate broken channels and use a standard head position for
> multiple recordings in one subject.
> I used fieldtrip's automatic and semi-automatic artifact rejection
> routines
> to identify channels that are flat, show jumps and are noisy. I defined
> these as bad in maxfilter. Then I used sss/tsss to achieve the desired
> steps. It seemed very straight forward. However, when looking at the
> results, the signal seems to be increased (and
> more noisy and jumpy) in certain channels (see attached pdfs of bad and
> non-bad channel (1st page: raw data, 2nd page: sss data, 3rd page: tsss
> data). Have you ever experienced anything like this? The only reason I
> can
> come up with is that in maxfilter I used the continuous raw data file and
> not as in fieldtrip, only trials. Between trials there are pauses,
> where the
> channels could have been affected by a few movements. Could this
> explain my
> difficulties?
> Is there a way to 'only' interpolate channels and realign the head,
> without
> impacting other non-broken channels?
> Thank you very much for your answer!
> Nina
>
>
> -----Ursprüngliche Nachricht-----
> Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im
> Auftrag
> von Burkhard Maess
> Gesendet: Freitag, 22. Oktober 2010 09:25
> An: FIELDTRIP at NIC.SURFNET.NL <mailto:FIELDTRIP at NIC.SURFNET.NL>
> Betreff: Re: [FIELDTRIP] ft_channelrepair with neuromag data
>
> Dear David,
>
> I agree with Jan-Mathijs.
>
> variant a: apply maxfilter - that will repair all broken channels. You
> also can manually define certain channels as broken. Maxfilter may
> also align data of different headpositions to a single position.
>
> variant b: use megrealign - it includes a minimum norm localization
> and from there MEG data is forward computed. In this way, you can
> repair channels, align different head positions to the same and even
> convert data between different systems.
>
> all the best,
> Burkhard
>
>
> jan-mathijs schoffelen wrote:
>
> Dear David,
>
> This is a good point. As far as I can see from the code, no
> distinction is made between gradiometers and magnetometers.
> Naively, I would propose the following: first indeed split the data
> into two subset: gradiometers only and magnetometers only, only then
> apply the channel reparation routine. Yet, for the gradiometer subset
> data, it is questionable whether as such the replacement of a bad
> channel with its neighbours makes sense, because this would lead to
> averaging gradients of the magnetic field with an orthogonal orientation.
>
> In other words, this is probably not the most sensible approach. I
> don't think repairing after combining the planar gradients is
>  desired, because this leads to an unwanted amplification of the noise
> (because the combination step results in taking an absolute value).
> Alternatively, you could consider using ft_megrealign, which in
> principle could be used to repair bad channels. The recipe would be to
> only use the data with the clean channels in the input, and you would
> want to interpolate the data back onto the original sensor-array. An
> example for interpolating between two types of CTF-systems is shown
> here http://fieldtrip.fcdonders.nl/example/megrealign.
>
> Just out of curiosity: doesn't the maxfilter in the Neuromag software
> allow for similar things?
>
> Best wishes,
>
> Jan-Mathijs
> On Oct 21, 2010, at 9:49 PM, David Ziegler wrote:
>
> Hi Fieldtrippers,
>
> I would like to use ft_channelrepair to interpolate data for some
> missing/deleted channels with Neuromag 306 data.  I am just wondering
> whether there are any potential problems with using the nearest
> neighbor interpolation, given the triplet format of the Neuromag
> system (two planar gradiometers and one magnetometer).
> If this is problematic, are there other options to fixing bad/missing
> channels (e.g., can ft_channelrepair be run on just a subset of the
> channels, say the gradiometers after I run ft_combineplanar)?
>
> Thanks!
> David
>
> --
> David A. Ziegler
> Department of Brain and Cognitive Sciences Massachusetts Institute of
> Technology 43 Vassar St,  46-5121 Cambridge, MA  02139
> Tel: 617-258-0765
> Fax: 617-253-1504
> daz at mit.edu <mailto:daz at mit.edu> <mailto:daz at mit.edu>
>
>
>
>
>
>
> ---------------------------------------------------------------------------
>
>
>> You are receiving this message because you are subscribed to the
>> FieldTrip list. The aim of this list is to facilitate the discussion
>> between users of the FieldTrip toolbox, to share experiences and to
>> discuss new ideas for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/neuroimaging/fieldtrip.
>>
> ---------------------------------------------------------------------------
>
>
> Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain,
> Cognition and Behaviour, Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
> <mailto:J.Schoffelen at donders.ru.nl>
> Telephone: 0031-24-3614793
>
>
> ---------------------------------------------------------------------------
>
>
> You are receiving this message because you are subscribed to
> the FieldTrip list. The aim of this list is to facilitate the discussion
> between users of the FieldTrip toolbox, to share experiences
> and to discuss new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
>
> ---------------------------------------------------------------------------
>
>
> --
>
> David A. Ziegler
>
> Department of Brain and Cognitive Sciences
> Massachusetts Institute of Technology
> 43 Vassar St,  46-5121
> Cambridge, MA 02139
>
> Tel: 617-258-0765
>
> Fax: 617-253-1504
>
> daz at mit.edu <mailto:daz at mit.edu>
>
> ---------------------------------------------------------------------------
> You are receiving this message because you are subscribed to
> the FieldTrip list. The aim of this list is to facilitate the discussion
> between users of the FieldTrip toolbox, to share experiences
> and to discuss new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------
>
> ---------------------------------------------------------------------------
> You are receiving this message because you are subscribed to
> the FieldTrip list. The aim of this list is to facilitate the discussion
> between users of the FieldTrip toolbox, to share experiences
> and to discuss new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------
>

--

David A. Ziegler

Department of Brain and Cognitive Sciences
Massachusetts Institute of Technology
43 Vassar St,46-5121
Cambridge, MA 02139

Tel: 617-258-0765

Fax: 617-253-1504

daz at mit.edu <mailto:daz at mit.edu>


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From r.oostenveld at DONDERS.RU.NL  Thu Oct 28 17:34:48 2010
From: r.oostenveld at DONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 28 Oct 2010 17:34:48 +0200
Subject: fieldtrip list will move to another server
Message-ID: <THU.28.OCT.2010.173448.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear fieldtrip list members

Surfnet, the organization that hosts the fieldtrip email discussion
list, will stop supporting the listserver. Consequently we have to
move the fieldtrip email discussion list and the fieldtrip-news list
to another listserver. We can continue to use it until end of this
year, but already now people cannot subscribe to the list any more
using the webinterface. You can still subscribe by sending an email to FIELDTRIP-request at NIC.SURFNET.NL
, which will then be manually processed by one of the list
administrators. The description on http://fieldtrip.fcdonders.nl/discussion_list
  has been changed accordingly.

We'll keep you posted on the progress of migrating to another
listserver.

best regards,
Robert



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

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You are receiving this message because you are subscribed to
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See also http://listserv.surfnet.nl/archives/fieldtrip.html
and http://www.ru.nl/neuroimaging/fieldtrip.
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From recasensmarc at GMAIL.COM  Thu Oct 28 19:11:55 2010
From: recasensmarc at GMAIL.COM (Marc Recasens)
Date: Thu, 28 Oct 2010 19:11:55 +0200
Subject: Remove muscle artifacts using ICA
Message-ID: <THU.28.OCT.2010.191155.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear all,

I have quite a naive question.
I'm processing some MEG (4-D) datasets in order to use source location
methods afterwards. One of my concerns is that I have some channels (3 in a
row) with a steady high frequency artifact >50Hz (I thought it is muscle
activity, However it is very tonic and present during the whole recording)
which is within my frequencies of interest. This can be seen in the attached
figures: timelocked responses bandpass filtered between 15 and 150 Hz, and
time-frequency activity between 50 and 100 Hz.
As the artefactual channels are put altogether in the right edge of the
sensor array (A148, A147 and A146) interpolation may not be a suitable
method to eliminate those artefactual channels. (?)

I was wondering whether it is possible to correct those artifacts using ICA
in such a way similar to ECG artifact removal using component analysis, that
is, by identifying  and remove those components in the source analysis that
explain the high-frequency artifacts present in some of my channels.

Thanks a lot.









--
Marc Recasens
Tel.: +34 639 24 15 98

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From jan.schoffelen at DONDERS.RU.NL  Fri Oct 29 09:52:57 2010
From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen)
Date: Fri, 29 Oct 2010 09:52:57 +0200
Subject: Remove muscle artifacts using ICA
In-Reply-To: <AANLkTin=xV0tHhf1fVBT29UkGcDyO88O+qUC-r2LKdxM@mail.gmail.com>
Message-ID: <FRI.29.OCT.2010.095257.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Marc,

Your figures seem to be missing, so it is hard to judge what the
artifacts look like exactly. Could it be that one of your head
localization coils was switched on througout the measurement?
In general, if your goal is to do source localization, I would not try
to fix ugly channels, but just omit them from the sensor-array,
because there will be plenty of sensors left.
The fixing operation (whatever way it is done, e.g. nearest neighbour
interpolation, ICA etc) involves replacing each channel's estimate by
a linear combination of a subset of/all other channels. You have to
keep in mind that the solution to the forward model (i.e. the
leadfields for the sources you want to estimate) have to take the same
linear operation into account in order to give correct results.
As such, irrespective of the fact that the noisy channels are on the
edge of the array, interpolation does not really make sense, because
you are not really improving the quality of your total signal array.
Also, in this case, I don't expect that rejecting the independent
component capturing the artifact will be that beneficial, because most
likely the spatial topography of this component of this component will
be confined to the three bad guys, with more or less random loadings
on the rest of the channels. Did you check whether the artifact is
present at the level of the reference sensors? If that's the case, you
could consider applying the cfw and afw (compute fixed weights, and
apply fixed weights) utilities from the 4D software.

Best wishes

Jan-Mathijs


On Oct 28, 2010, at 7:11 PM, Marc Recasens wrote:

> Dear all,
>
> I have quite a naive question.
> I'm processing some MEG (4-D) datasets in order to use source
> location methods afterwards. One of my concerns is that I have some
> channels (3 in a row) with a steady high frequency artifact >50Hz (I
> thought it is muscle activity, However it is very tonic and present
> during the whole recording) which is within my frequencies of
> interest. This can be seen in the attached figures: timelocked
> responses bandpass filtered between 15 and 150 Hz, and time-
> frequency activity between 50 and 100 Hz.
> As the artefactual channels are put altogether in the right edge of
> the sensor array (A148, A147 and A146) interpolation may not be a
> suitable method to eliminate those artefactual channels. (?)
>
> I was wondering whether it is possible to correct those artifacts
> using ICA in such a way similar to ECG artifact removal using
> component analysis, that is, by identifying  and remove those
> components in the source analysis that explain the high-frequency
> artifacts present in some of my channels.
>
> Thanks a lot.
>
>
>
>
>
>
>
>
>
>
> --
> Marc Recasens
> Tel.: +34 639 24 15 98
> --------------------------------------------------------------------------- You
>  are receiving this message because you are subscribed to
> the FieldTrip list. The aim of this list is to facilitate the
> discussion
> between users of the FieldTrip toolbox, to share experiences
> and to discuss new ideas for MEG and EEG analysis.
> See also http://listserv.surfnet.nl/archives/fieldtrip.html
> and http://www.ru.nl/neuroimaging/fieldtrip.
> ---------------------------------------------------------------------------
>

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


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