From cgra05 at HST.AUC.DK  Thu Jun  1 12:34:31 2006
From: cgra05 at HST.AUC.DK (Carina Graversen)
Date: Thu, 1 Jun 2006 12:34:31 +0200
Subject: SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG
 data ???
In-Reply-To: <003e01c68493$c1b918f0$642dae83@fcdonders.nl>
Message-ID: <THU.1.JUN.2006.123431.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Ingrid,

OH - sorry, I didn't notice the question had already been asked on the
webpage.

However, I still couldn't find the answer on how to create the values for
column 2 and 3, since it says at the webpage "The 2nd and 3rd are the
X-position and Y-position". However, when I generate the layout file from
Neuroscan I get some values for the X and Y coordinates, that are very
different from yours, and the plot ends up in a big mess (see the attached
file).

So I was wondering if you have any idea of how to generate the X- and
Y-positions from Neuroscan ???
(I have attached the generated layout-file from Neuroscan, in case that
helps you. This one is named test128_neuroscan.lay)

We were also wondering about the figure you e-mailed from our data, all
channels appeared to be blue with a green cone (and then some frequency
contributions in some channels). Is it because of some settings not edited
correct, because we would have expected something like in the
documentation - like figure 2 at the "Time-frequency Analysis Using
Multitapers and Wavelets" page.

>>From the test128_neuroscan.lay I tried to create the layout file
test128_fieldtrip.lay, and got the plot shown in figure
test128_fieldtrip.png



Best regards,
Carina Graversen





-----Oprindelig meddelelse-----
Fra: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]Pa vegne
af Ingrid Nieuwenhuis
Sendt: 31. maj 2006 10:23
Til: FIELDTRIP at NIC.SURFNET.NL
Emne: Re: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel
Neuroscan EEG data ???


Hi Carina,

If you look at the FieldTrip page -> documentation -> frequently asked
questions you can find the question (and answer):

What is the format of the layout file, which is used for plotting?

...The 4th and 5th column specify the with and height of the subplot that
will be made in multiplotER and multiplotTFR....

So the two columns with the same value for all channels are those columns.

Bests,
Ingrid

-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Carina Graversen
Sent: Wednesday, May 31, 2006 10:58 AM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan
EEG data ???

Hi Ingrid.

Thanks a lot.

I have tried to generate my own layout file in Neuroscan, but unfortunately
it doesn't work. So I was wondering if you can tell me the format of the
layout-file, because when I look at your file, 2 of the columns contain the
same value for all channels.

I have tried to generate for both cartesian and polor, but none of them
matches. In the generated file I get the format:
<display page><channel number><pos x0><pos y0><pos x1><pos y1>

Can I change my input configuration to either use this format, or how should
I change the format of the layout file ???

Thanks in advance  :o)

/Carina





-----Oprindelig meddelelse-----
Fra: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]Pa vegne
af Ingrid Nieuwenhuis
Sendt: 26. maj 2006 13:29
Til: FIELDTRIP at NIC.SURFNET.NL
Emne: Re: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG data
???


Hi Carina,

Thanks for sending me the data. Indeed the biosemi 128ch layout doesn't
correspond to your layout. You have 128 channels labeled from 1 to 128. If
you open biosemi128.lay in a text-editor you can see that this layout file
has 150 channels labeled from A1 to P7. The labels in your data
(TFRmult.label) and the labels in the layout file don't match, that's why
you got an empty figure (I'll add an error in the plot function, so that
when no labels match you'll get an error message in the future).

So what you have to do now is to make your own layout file that matches the
data; with the correct x and y coordinates of the 128 channels and the same
label names as in your data. Just as an illustration I attached an adapted
version of the biosemi128.lay file, with only the first 128 channels, and
labels 1 to 128, just as in your data. With the following configuration:

cfg8 = [];
cfg8.baseline   = [0 0.1];
cfg8.xlim       = [0 0.3]
cfg8.ylim       = [15 29];
cfg8.zlim       = [-100 100];
cfg8.showlabels = 'yes';
cfg8.layout    = 'testlay128.lay';

I got the attached figure from your data.

Good luck,
Ingrid



-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Robert Oostenveld
Sent: Wednesday, May 24, 2006 8:57 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG data ???

Hi Carina

Are you sure that the biosemi 128ch layout corresponds with your
electrode layout? Open the layout file in a tetx editor and look at
http://www2.ru.nl/fcdonders/fieldtrip/doku.php?
id=fieldtrip:documentation:frequently_asked_questions#what_is_the_format
_of_the_layout_file_which_is_used_for_plotting

I suggest that you try the elec1010.lay or elec1005.lay, or even
better, that you construct your own layout file corresponding with
your own electrode locations.

Robert


On 24 May 2006, at 12:29, Carina Graversen wrote:

> Hi.
>
> I'm trying to use the Fieldtrip program to create a wavelet plot of
> my EEG
> data.
>
> I have used it previously for 64 channel recordings, but now I'm
> working
> with 128 channels of data, which is causing me some problems. The
> only thing
> I have changed is the command:
> cfg8.layout    = 'biosemi128.lay';
>
> But now the figure only outputs a grey page with no Time-Frequency
> distributions at all.
>
> Can anyone tell me what I'm doing wrong - below is a complete list
> of all
> the commands I use  :o).
>
> Best Regards,
> Carina Graversen
>
>
>
>
> %
> **********************************************************************
> ***
> % EVENTRELATEDAVERAGING
> %
> **********************************************************************
> ***
> cfg1 = [];                                                     % empty
> configuration
> cfg1.datafile                      = 'test128.eeg';            %
> 128 channel
> Neuroscan eeg file
> cfg1.headerfile                    = 'test128.eeg';
> cfg1.channel                       = 'all';
>
> dataFIC = preprocessing(cfg1);                                 %
> Preprocess!
>
> cfg2 = [];                                                     % empty
> configuration
>
> avgFIC = timelockanalysis(cfg2, dataFIC);
>
>
> % %
> **********************************************************************
> ***
> % % WAVELET
> % %
> **********************************************************************
> ***
> cfg7 = [];
> cfg7.output     = 'pow';
> cfg7.method     = 'wltconvol'
> cfg7.foi        = 1:2:30;
> cfg7.t_ftimwin  = 5./cfg7.foi;
> cfg7.tapsmofrq  = 0.4 *cfg7.foi;
> cfg7.toi        = 0:0.01:0.5;
>
> TFRmult = freqanalysis(cfg7, avgFIC);
>
> cfg8 = [];
> cfg8.baseline   = [-0.5 0.5];
> cfg8.xlim       = [0 0.5]
> cfg8.zlim       = [-3e-27 0.2];
> cfg8.showlabels = 'yes';
> cfg8.layout    = 'biosemi128.lay';
>
> multiplotTFR(cfg8, TFRmult);
>
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From r.oostenveld at FCDONDERS.RU.NL  Thu Jun  1 12:35:43 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 1 Jun 2006 12:35:43 +0200
Subject: Filtering
In-Reply-To: <000001c683f3$4e30cb30$90514484@dellgx240>
Message-ID: <THU.1.JUN.2006.123543.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Vladimir

On 30 May 2006, at 16:14, Vladimir Litvak wrote:
> As I understand, when I do filtering in preprocessing the filter is
> applied before the data is cut to epochs.

Not completely: a segment of data is read from file that contains the
trial (trl) plus the optional padding. That segment is filtered and
then the padding is thrown away. Eventual filter atrifacts at the
boundaries of the data segment that was read are in the padding and
thus would not affect the data of interest itself. If you apply
padding, the effect is the same as if you would have filtered the
complete data continuously.

> I now want to do some analysis where I want to filter after the
> epochs are cut out (because there are TMS deltas there and I don't
> want them to affect everything around them). Is there a simple way
> to filter epoched data in FT (other than by my own code)?

You can specify cfg.padding=0 in preprocessing and ensure that the
TMS pulse is not inside the trial definition. You can do
preprocessing without any options and then use timelockanalysis (with
keeptrials) on it. Timelockanalysis supports almost all options that
preprocessing has, i.e. all filtering and baselinecorection options,
but of course cannot do the padding. Those additional options are not
documented in timelockanalysis, but look in the code and you will
see  them. Doing it in timelockanalysis has the advantage that it is
easier to play around with filter settings (i.e. it is faster not
having to read the data every time). Also interesting to know perhaps
is that you can also apply timelockanalysis and its filtering to an
average, i.e. timelockanalysis will accept a timelock-structure as
input. So you can average in the first call to timelockanalysis, and
then throw that average into timelockanalysis a second time to see
the effect of the filter. In the latter case only the average is
filtered, i.e. it is very fast.

best
Robert


From ingrid.nieuwenhuis at FCDONDERS.RU.NL  Thu Jun  1 13:21:11 2006
From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis)
Date: Thu, 1 Jun 2006 13:21:11 +0200
Subject: SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG
 data ???
In-Reply-To: <LMELLGAMDIJKNDEFIMFHEECDCHAA.cgra05@hst.auc.dk>
Message-ID: <THU.1.JUN.2006.132111.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Carina,

The problem is that the width and height of the boxes (column 4 and 5) are
too big compared to your x and y coordinates. What multiplotTFR does is that
it plots the TFR boxes at the specified coordinates. The x and y coordinates
are between +/- 0 and 0.7 and the box width/height is 0.18	and 1.14, so
all the plots are plotted on top of each other. That's why it is a mess. So
you could use the x and y coordinates, but the boxes should be smaller, or
you can scale it al up.

What comes out of the plots is just what the data is. Probably depends on
your settings during the TFR analysis. The dark blue at the edges and bottom
are NaN's in the data.

Bests,
Ingrid



-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Carina Graversen
Sent: Thursday, June 01, 2006 12:35 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel
Neuroscan EEG data ???

Hi Ingrid,

OH - sorry, I didn't notice the question had already been asked on the
webpage.

However, I still couldn't find the answer on how to create the values for
column 2 and 3, since it says at the webpage "The 2nd and 3rd are the
X-position and Y-position". However, when I generate the layout file from
Neuroscan I get some values for the X and Y coordinates, that are very
different from yours, and the plot ends up in a big mess (see the attached
file).

So I was wondering if you have any idea of how to generate the X- and
Y-positions from Neuroscan ???
(I have attached the generated layout-file from Neuroscan, in case that
helps you. This one is named test128_neuroscan.lay)

We were also wondering about the figure you e-mailed from our data, all
channels appeared to be blue with a green cone (and then some frequency
contributions in some channels). Is it because of some settings not edited
correct, because we would have expected something like in the
documentation - like figure 2 at the "Time-frequency Analysis Using
Multitapers and Wavelets" page.

>>From the test128_neuroscan.lay I tried to create the layout file
test128_fieldtrip.lay, and got the plot shown in figure
test128_fieldtrip.png



Best regards,
Carina Graversen





-----Oprindelig meddelelse-----
Fra: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]Pa vegne
af Ingrid Nieuwenhuis
Sendt: 31. maj 2006 10:23
Til: FIELDTRIP at NIC.SURFNET.NL
Emne: Re: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel
Neuroscan EEG data ???


Hi Carina,

If you look at the FieldTrip page -> documentation -> frequently asked
questions you can find the question (and answer):

What is the format of the layout file, which is used for plotting?

...The 4th and 5th column specify the with and height of the subplot that
will be made in multiplotER and multiplotTFR....

So the two columns with the same value for all channels are those columns.

Bests,
Ingrid

-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Carina Graversen
Sent: Wednesday, May 31, 2006 10:58 AM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan
EEG data ???

Hi Ingrid.

Thanks a lot.

I have tried to generate my own layout file in Neuroscan, but unfortunately
it doesn't work. So I was wondering if you can tell me the format of the
layout-file, because when I look at your file, 2 of the columns contain the
same value for all channels.

I have tried to generate for both cartesian and polor, but none of them
matches. In the generated file I get the format:
<display page><channel number><pos x0><pos y0><pos x1><pos y1>

Can I change my input configuration to either use this format, or how should
I change the format of the layout file ???

Thanks in advance  :o)

/Carina





-----Oprindelig meddelelse-----
Fra: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]Pa vegne
af Ingrid Nieuwenhuis
Sendt: 26. maj 2006 13:29
Til: FIELDTRIP at NIC.SURFNET.NL
Emne: Re: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG data
???


Hi Carina,

Thanks for sending me the data. Indeed the biosemi 128ch layout doesn't
correspond to your layout. You have 128 channels labeled from 1 to 128. If
you open biosemi128.lay in a text-editor you can see that this layout file
has 150 channels labeled from A1 to P7. The labels in your data
(TFRmult.label) and the labels in the layout file don't match, that's why
you got an empty figure (I'll add an error in the plot function, so that
when no labels match you'll get an error message in the future).

So what you have to do now is to make your own layout file that matches the
data; with the correct x and y coordinates of the 128 channels and the same
label names as in your data. Just as an illustration I attached an adapted
version of the biosemi128.lay file, with only the first 128 channels, and
labels 1 to 128, just as in your data. With the following configuration:

cfg8 = [];
cfg8.baseline   = [0 0.1];
cfg8.xlim       = [0 0.3]
cfg8.ylim       = [15 29];
cfg8.zlim       = [-100 100];
cfg8.showlabels = 'yes';
cfg8.layout    = 'testlay128.lay';

I got the attached figure from your data.

Good luck,
Ingrid



-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Robert Oostenveld
Sent: Wednesday, May 24, 2006 8:57 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG data ???

Hi Carina

Are you sure that the biosemi 128ch layout corresponds with your
electrode layout? Open the layout file in a tetx editor and look at
http://www2.ru.nl/fcdonders/fieldtrip/doku.php?
id=fieldtrip:documentation:frequently_asked_questions#what_is_the_format
_of_the_layout_file_which_is_used_for_plotting

I suggest that you try the elec1010.lay or elec1005.lay, or even
better, that you construct your own layout file corresponding with
your own electrode locations.

Robert


On 24 May 2006, at 12:29, Carina Graversen wrote:

> Hi.
>
> I'm trying to use the Fieldtrip program to create a wavelet plot of
> my EEG
> data.
>
> I have used it previously for 64 channel recordings, but now I'm
> working
> with 128 channels of data, which is causing me some problems. The
> only thing
> I have changed is the command:
> cfg8.layout    = 'biosemi128.lay';
>
> But now the figure only outputs a grey page with no Time-Frequency
> distributions at all.
>
> Can anyone tell me what I'm doing wrong - below is a complete list
> of all
> the commands I use  :o).
>
> Best Regards,
> Carina Graversen
>
>
>
>
> %
> **********************************************************************
> ***
> % EVENTRELATEDAVERAGING
> %
> **********************************************************************
> ***
> cfg1 = [];                                                     % empty
> configuration
> cfg1.datafile                      = 'test128.eeg';            %
> 128 channel
> Neuroscan eeg file
> cfg1.headerfile                    = 'test128.eeg';
> cfg1.channel                       = 'all';
>
> dataFIC = preprocessing(cfg1);                                 %
> Preprocess!
>
> cfg2 = [];                                                     % empty
> configuration
>
> avgFIC = timelockanalysis(cfg2, dataFIC);
>
>
> % %
> **********************************************************************
> ***
> % % WAVELET
> % %
> **********************************************************************
> ***
> cfg7 = [];
> cfg7.output     = 'pow';
> cfg7.method     = 'wltconvol'
> cfg7.foi        = 1:2:30;
> cfg7.t_ftimwin  = 5./cfg7.foi;
> cfg7.tapsmofrq  = 0.4 *cfg7.foi;
> cfg7.toi        = 0:0.01:0.5;
>
> TFRmult = freqanalysis(cfg7, avgFIC);
>
> cfg8 = [];
> cfg8.baseline   = [-0.5 0.5];
> cfg8.xlim       = [0 0.5]
> cfg8.zlim       = [-3e-27 0.2];
> cfg8.showlabels = 'yes';
> cfg8.layout    = 'biosemi128.lay';
>
> multiplotTFR(cfg8, TFRmult);
>


From r.oostenveld at FCDONDERS.RU.NL  Thu Jun  1 13:51:02 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 1 Jun 2006 13:51:02 +0200
Subject: SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG
 data ???
In-Reply-To: <LMELLGAMDIJKNDEFIMFHEECDCHAA.cgra05@hst.auc.dk>
Message-ID: <THU.1.JUN.2006.135102.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Carina,

Please take attached "layoutplot" function and copy it into the
fieldtrip directory. Then do

 >> cfg.layout = 'CTF151.lay'
cfg =
     layout: 'CTF151.lay'

 >> layoutplot(cfg)
reading layout from file CTF151.lay

and you will get the attached figure for the 151 channel CTF system.
Then try plotting the other layouts (the *.lay files) and your own
layout, and modify the values in your own layout file (in a text
editor) untill you like what you see.

Robert

PS when I was looking at the other layouts, I noticed that the
elec1020, elec1010 and elec1005 layouts supplied with fieldtrip are
not optimal, since they also have overlapping boxes.

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From r.oostenveld at FCDONDERS.RU.NL  Thu Jun  1 13:58:48 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 1 Jun 2006 13:58:48 +0200
Subject: query on coherence source analysis
In-Reply-To: <BAY12-F10440EA05E5791B6BF0425CE9D0@phx.gbl>
Message-ID: <THU.1.JUN.2006.135848.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Muthuraman

I have not been able to reproduce your error. I suggest that you get
the latest version of FieldTrip from our FTP server and try again.

best egards,
Robert

PS this is the test script I used. It uses some simulated data, which
again uses a MEG gradiometer definition and a head model from the
tutorial data.


-----------------
% read some data that is required to simulate MEG data, i.e. volume
model,
% sensor positions and MRI (optional, only for plotting)
vol  = read_ctf_hdm('Subject01.hdm');
hdr  = read_fcdc_header('Subject01.ds/Subject01.res4');
grad = hdr.grad;

% construct the simulated MEG data for condition A ("active")
cfg               = [];
cfg.vol           = vol;
cfg.grad          = grad;
cfg.fsample       = 300;
cfg.ntrials       = 2;
cfg.triallength   = 1;
cfg.dip.pos       = [0 7 8];
cfg.dip.mom       = [1 0 0];
cfg.dip.signal    = sin(2*pi*10*(1:cfg.fsample)./cfg.fsample);
cfg.absnoise      = 1e-8;
data = dipolesimulation(cfg);

% add the source signal as fake EMG channel
for i=1:cfg.ntrials
   data.trial{i}(end+1,:) = cfg.dip.signal + randn(size
(cfg.dip.signal));
end
data.label{end+1} = 'EMG';

cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'MEG' 'EMG'},data.label);
cfg.channelcmb={'MEG' 'EMG'};
freq=freqanalysis(cfg,data);





From olga at GRAPHICMIND.INFO  Sat Jun  3 12:45:41 2006
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Sat, 3 Jun 2006 14:45:41 +0400
Subject: deleting two EOG channale from data-stucture
Message-ID: <SAT.3.JUN.2006.144541.0400.FIELDTRIP@NIC.SURFNET.NL>

Dear list members,
I would like to delete two channels from my data. How is it better to do this?
Best Regards,
Olga
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From olga at GRAPHICMIND.INFO  Sat Jun  3 14:16:57 2006
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Sat, 3 Jun 2006 16:16:57 +0400
Subject: and clusterrandomization
Message-ID: <SAT.3.JUN.2006.161657.0400.FIELDTRIP@NIC.SURFNET.NL>

Thank you very much, Eric!
That was an inconsistency in the loci of EOG channels between subjects. Now
I corrected it: HEOG and VEOG data are still presented in the data
structure, but do not have the location (pnt 0 0 0). Is it OK? The results
looks as what I excpected.
Best Regards,
Olga.

----- Original Message -----
From: "Eric Maris" <maris at NICI.RU.NL>
To: <FIELDTRIP at NIC.SURFNET.NL>
Sent: Friday, May 26, 2006 5:35 PM
Subject: Re: [FIELDTRIP] and clusterrandomization


> Dear Olga,
>
>
> But the problems is still in my clusterrandomization.
> Could the fact that the order of the channel in the file (C_vc11.label) is
> not the same as in the C_vc11.elec.label influences the result of
> clusterrandomization (I do not have my neigbouring channel file)?
>
>
> That should not matter. However, the labels in your data structure (.label
> in the output of timelockgrandaverage) should exactly match the labels in
> the elec-structure. If that is OK, then something might have gone wrong
> with the combination of the data of the different subjects. Do they all
> have the same elec-structure? If the same physical channel has different
> labels for different subjects, then this may create inconsistencies
> between EEGlab and Fieldtrip. For Fieldtrip, channels that have the same
> label are assumed to be physically identical, even if they are in
> different positions in the data structure. This is only a guess, of
> course.
>
>
> kind regards,
>
> Eric Maris
>
>
>
>
>
>
>
>
>
> Best Regards,
> Olga.
>  ----- Original Message -----
>  From: Ingrid Nieuwenhuis
>  To: FIELDTRIP at NIC.SURFNET.NL
>  Sent: Wednesday, May 24, 2006 8:45 PM
>  Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>
>
>  Hi Olga,
>
>
>
>  About the z-param:
>
>  This is the field that contains the data to be plotted; for instance
> 'avg', 'powspctrm' or 'cohspctrm'. Normally the function looks in your
> data.dimord to find out which z-param to use. To make the function work
> you could give cfg.zparam = 'avg' (for instance if you want to plot an
> ERF/ERP). But if you could send me what the dimord field of the data that
> you want to plot is, I could look why the plot functions don't extract the
> correct zparam themselves.
>
>
>
>  About the timelockgranaveraging: I also think it should be the same. I
> have no idea what it could be.
>
>
>
>  Good luck,
>
>  Ingrid Nieuwenhuis
>
>
>
>
> ------------------------------------------------------------------------------
>
>  From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf Of Olga Sysoeva
>  Sent: Wednesday, May 24, 2006 5:44 PM
>  To: FIELDTRIP at NIC.SURFNET.NL
>  Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>
>
>
>  Dear List member,
>
>
>
>  Sorry for such dull questions but,
>
>  I am again facing the new problems with Fieldtrip, although did not solve
> some previous one (still can not singleplot and multiplot anything 'cause
> of "unknown zparam field".
>
>
>
>  OK, about new one :-)
>
>
>
>  It seems that I did not use write the timelockgranaveraging.
>
>
>
>   The problem must be here, when I made grand averaging of all my 11
> subject
>   data
>
>                    cfg =[];
>                     cfg.keepindividual = 'yes'
>                     C_vc11  =
>
> timelockgrandaverage(cfg,vc_c_avg1,vc_c_avg2,vc_c_avg3,vc_c_avg4,vc_c_avg5,
> vc_c_avg6,vc_c_avg7,vc_c_avg8,vc_c_avg9,vc_c_avg10,vc_c_avg11 );
>
>  As I understand the
>
>  vc_c_avg11.avg([9],[43]) should be similar with C_vc11.individual ([11],
> [9], [43])
>  But it is not.
>  What can it be?
>
>  Best Regards,
>
>  Olga.
>
>
>
>
>
>    ----- Original Message -----
>
>    From: Olga Sysoeva
>
>    To: FIELDTRIP at NIC.SURFNET.NL
>
>    Sent: Saturday, May 13, 2006 4:34 PM
>
>    Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>
>
>
>    Thank you very much, Lilla!
>
>    Now I knwo what to do but faced the problem with " unknown zparam
> field" when ploting the results. Unfortunatly cfg.zparam does not
> discribed in help file...
>
>    Best Regards, Olga
>
>      ----- Original Message -----
>
>      From: Lilla Magyari
>
>      To: FIELDTRIP at NIC.SURFNET.NL
>
>      Sent: Saturday, May 13, 2006 3:11 PM
>
>      Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data
> within-subject
>
>
>
>      Dear Olga,
>
>
>
>      I am just studying time-frequency analysis but I have done already on
> my data, so perhaps I can help you.
>
>      First, yes, you have to do freqanalysis on the preprocessed data of
> the individual subjects for all conditions that you want to compare (i.e.
> the input for this function contains all trials from one subject in one
> condition.) And it is also important that the other input for this
> function is the cfg where for example, in the cfg.method you have to
> specify what kind of time-frequency analysis you want to use. (You have to
> write 'wltconvol' for wavelet transformation and 'mltconvol' for
> multitaper analysis.)
>
>      When you use freqanalysis as output you can get TFR for one subject
> in one condition (but it is also possible to keep the information for the
> individual trials of the condition by specifying cfg.keeptrials = 'yes').
> When you have the TFRs for each subject you can grandaverage them with
> freqgrandaverage where the input is the TFRs of all subjects (and before
> averaging you can use also freqbaseline for giving a baseline for your
> TFRs).
>
>
>
>      I hope it helps.
>
>
>
>      Best regards,
>
>      Lilla Magyari
>
>
>
>
>
>
>
>
> --------------------------------------------------------------------------
>
>      From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf Of Olga Sysoeva
>      Sent: Saturday, May 13, 2006 9:28 AM
>      To: FIELDTRIP at NIC.SURFNET.NL
>      Subject: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>
>
>
>      Dear list members,
>
>
>
>      Thank you everybody for your help! I've already got interesting
> results using clusterrandomization on my data! Thanks a lot!
>
>
>
>      Now I have a question about using the clusterrandomization on 3-D
> data (channel-time-frequency) in within-subject analysis.
>
>      As I understand it is possible with Fieldtrip, but I really newby in
> time-frequency anlysis, therefore wanted your comments,
>
>      as far as I didn't find the example of the application of
> clusteranalysis on this set of the data in tuturial.
>
>
>
>      I successfully conduct the within-subject clusterrandomization on my
> grand-average data, which does not have the third, frequency demintion.
>
>      Now I want to add it. But I could not apply freqanalyisis on
> grandavarage data, could I? Should I made the TFR of individual data and
> than grand-avarage the result?
>
>      Which function should I use?
>
>
>
>      Best Regards,
>
>      Olga.


From olga at GRAPHICMIND.INFO  Sat Jun  3 14:26:35 2006
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Sat, 3 Jun 2006 16:26:35 +0400
Subject: clusrand: 19 channels 0 minnbchan
Message-ID: <SAT.3.JUN.2006.162635.0400.FIELDTRIP@NIC.SURFNET.NL>

Dear experts,

Does it make sense to make clusterrandomization if I put "0" in the min number of neibouring channels if I have only 19 of them (10-20 system)?
As I understand in this case just the time is considered when clustering. How many consequent time point is requiered to build a cluster? 

Best Regards,
Olga.
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From maris at NICI.RU.NL  Sat Jun  3 18:47:21 2006
From: maris at NICI.RU.NL (Eric Maris)
Date: Sat, 3 Jun 2006 18:47:21 +0200
Subject: deleting two EOG channale from data-stucture
Message-ID: <SAT.3.JUN.2006.184721.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Olga,


I would like to delete two channels from my data. How is it better to do
this?


Type "help channelselection" at the Matlab command line. This will give you
information on how the Fieldtrip functions perform channelselection on the
basis of the input in cfg.channel. I don't have Matlab running now, but I
think that '-EOG' in cfg.channel will do the job you request.


greetings,

Eric


From maris at NICI.RU.NL  Sat Jun  3 18:50:06 2006
From: maris at NICI.RU.NL (Eric Maris)
Date: Sat, 3 Jun 2006 18:50:06 +0200
Subject: and clusterrandomization
Message-ID: <SAT.3.JUN.2006.185006.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Olga,

> That was an inconsistency in the loci of EOG channels between subjects.
> Now I corrected it: HEOG and VEOG data are still presented in the data
> structure, but do not have the location (pnt 0 0 0). Is it OK? The results
> looks as what I excpected.

Because you never will include the EOG-channels in an analysis of the
EEG-channels, the location of the EOG is not required by
clusterrandanalysis.

greetings,

Eric Maris



> Best Regards,
> Olga.
>
> ----- Original Message -----
> From: "Eric Maris" <maris at NICI.RU.NL>
> To: <FIELDTRIP at NIC.SURFNET.NL>
> Sent: Friday, May 26, 2006 5:35 PM
> Subject: Re: [FIELDTRIP] and clusterrandomization
>
>
>> Dear Olga,
>>
>>
>> But the problems is still in my clusterrandomization.
>> Could the fact that the order of the channel in the file (C_vc11.label)
>> is not the same as in the C_vc11.elec.label influences the result of
>> clusterrandomization (I do not have my neigbouring channel file)?
>>
>>
>> That should not matter. However, the labels in your data structure
>> (.label in the output of timelockgrandaverage) should exactly match the
>> labels in the elec-structure. If that is OK, then something might have
>> gone wrong with the combination of the data of the different subjects. Do
>> they all have the same elec-structure? If the same physical channel has
>> different labels for different subjects, then this may create
>> inconsistencies between EEGlab and Fieldtrip. For Fieldtrip, channels
>> that have the same label are assumed to be physically identical, even if
>> they are in different positions in the data structure. This is only a
>> guess, of course.
>>
>>
>> kind regards,
>>
>> Eric Maris
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Best Regards,
>> Olga.
>>  ----- Original Message -----
>>  From: Ingrid Nieuwenhuis
>>  To: FIELDTRIP at NIC.SURFNET.NL
>>  Sent: Wednesday, May 24, 2006 8:45 PM
>>  Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>>
>>
>>  Hi Olga,
>>
>>
>>
>>  About the z-param:
>>
>>  This is the field that contains the data to be plotted; for instance
>> 'avg', 'powspctrm' or 'cohspctrm'. Normally the function looks in your
>> data.dimord to find out which z-param to use. To make the function work
>> you could give cfg.zparam = 'avg' (for instance if you want to plot an
>> ERF/ERP). But if you could send me what the dimord field of the data that
>> you want to plot is, I could look why the plot functions don't extract
>> the correct zparam themselves.
>>
>>
>>
>>  About the timelockgranaveraging: I also think it should be the same. I
>> have no idea what it could be.
>>
>>
>>
>>  Good luck,
>>
>>  Ingrid Nieuwenhuis
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>>  From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
>> Behalf Of Olga Sysoeva
>>  Sent: Wednesday, May 24, 2006 5:44 PM
>>  To: FIELDTRIP at NIC.SURFNET.NL
>>  Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>>
>>
>>
>>  Dear List member,
>>
>>
>>
>>  Sorry for such dull questions but,
>>
>>  I am again facing the new problems with Fieldtrip, although did not
>> solve some previous one (still can not singleplot and multiplot anything
>> 'cause of "unknown zparam field".
>>
>>
>>
>>  OK, about new one :-)
>>
>>
>>
>>  It seems that I did not use write the timelockgranaveraging.
>>
>>
>>
>>   The problem must be here, when I made grand averaging of all my 11
>> subject
>>   data
>>
>>                    cfg =[];
>>                     cfg.keepindividual = 'yes'
>>                     C_vc11  =
>>
>> timelockgrandaverage(cfg,vc_c_avg1,vc_c_avg2,vc_c_avg3,vc_c_avg4,vc_c_avg5,
>> vc_c_avg6,vc_c_avg7,vc_c_avg8,vc_c_avg9,vc_c_avg10,vc_c_avg11 );
>>
>>  As I understand the
>>
>>  vc_c_avg11.avg([9],[43]) should be similar with C_vc11.individual ([11],
>> [9], [43])
>>  But it is not.
>>  What can it be?
>>
>>  Best Regards,
>>
>>  Olga.
>>
>>
>>
>>
>>
>>    ----- Original Message -----
>>
>>    From: Olga Sysoeva
>>
>>    To: FIELDTRIP at NIC.SURFNET.NL
>>
>>    Sent: Saturday, May 13, 2006 4:34 PM
>>
>>    Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data
>> within-subject
>>
>>
>>
>>    Thank you very much, Lilla!
>>
>>    Now I knwo what to do but faced the problem with " unknown zparam
>> field" when ploting the results. Unfortunatly cfg.zparam does not
>> discribed in help file...
>>
>>    Best Regards, Olga
>>
>>      ----- Original Message -----
>>
>>      From: Lilla Magyari
>>
>>      To: FIELDTRIP at NIC.SURFNET.NL
>>
>>      Sent: Saturday, May 13, 2006 3:11 PM
>>
>>      Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data
>> within-subject
>>
>>
>>
>>      Dear Olga,
>>
>>
>>
>>      I am just studying time-frequency analysis but I have done already
>> on my data, so perhaps I can help you.
>>
>>      First, yes, you have to do freqanalysis on the preprocessed data of
>> the individual subjects for all conditions that you want to compare (i.e.
>> the input for this function contains all trials from one subject in one
>> condition.) And it is also important that the other input for this
>> function is the cfg where for example, in the cfg.method you have to
>> specify what kind of time-frequency analysis you want to use. (You have
>> to write 'wltconvol' for wavelet transformation and 'mltconvol' for
>> multitaper analysis.)
>>
>>      When you use freqanalysis as output you can get TFR for one subject
>> in one condition (but it is also possible to keep the information for the
>> individual trials of the condition by specifying cfg.keeptrials = 'yes').
>> When you have the TFRs for each subject you can grandaverage them with
>> freqgrandaverage where the input is the TFRs of all subjects (and before
>> averaging you can use also freqbaseline for giving a baseline for your
>> TFRs).
>>
>>
>>
>>      I hope it helps.
>>
>>
>>
>>      Best regards,
>>
>>      Lilla Magyari
>>
>>
>>
>>
>>
>>
>>
>>
>> --------------------------------------------------------------------------
>>
>>      From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
>> Behalf Of Olga Sysoeva
>>      Sent: Saturday, May 13, 2006 9:28 AM
>>      To: FIELDTRIP at NIC.SURFNET.NL
>>      Subject: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>>
>>
>>
>>      Dear list members,
>>
>>
>>
>>      Thank you everybody for your help! I've already got interesting
>> results using clusterrandomization on my data! Thanks a lot!
>>
>>
>>
>>      Now I have a question about using the clusterrandomization on 3-D
>> data (channel-time-frequency) in within-subject analysis.
>>
>>      As I understand it is possible with Fieldtrip, but I really newby in
>> time-frequency anlysis, therefore wanted your comments,
>>
>>      as far as I didn't find the example of the application of
>> clusteranalysis on this set of the data in tuturial.
>>
>>
>>
>>      I successfully conduct the within-subject clusterrandomization on my
>> grand-average data, which does not have the third, frequency demintion.
>>
>>      Now I want to add it. But I could not apply freqanalyisis on
>> grandavarage data, could I? Should I made the TFR of individual data and
>> than grand-avarage the result?
>>
>>      Which function should I use?
>>
>>
>>
>>      Best Regards,
>>
>>      Olga.


From maris at NICI.RU.NL  Sat Jun  3 18:53:19 2006
From: maris at NICI.RU.NL (Eric Maris)
Date: Sat, 3 Jun 2006 18:53:19 +0200
Subject: clusrand: 19 channels 0 minnbchan
Message-ID: <SAT.3.JUN.2006.185319.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Olga,


Does it make sense to make clusterrandomization if I put "0" in the min
number of neibouring channels if I have only 19 of them (10-20 system)?
As I understand in this case just the time is considered when clustering.
How many consequent time point is requiered to build a cluster?


Yes, it makes sense. The cfg.minnbchan-field is a way to suppress the
tendency of the cluster-growing algorithm to connect everything with
everything, even on the basis of noise. The FA-rate is not affect by the
value of cfg.minnbchan.


greetings,

Eric Maris


From pchris at UNC.EDU  Mon Jun  5 19:05:30 2006
From: pchris at UNC.EDU (Punita Christopher)
Date: Mon, 5 Jun 2006 19:05:30 +0200
Subject: dipole model
Message-ID: <MON.5.JUN.2006.190530.0200.FIELDTRIP@NIC.SURFNET.NL>

Has anyone seen any literature that deals with a spherical multiple layer 
head model in which the dipole spans across layers i.e. the source and 
sink of the dipole are in separate layers.  
Thanks,
Punita


From r.oostenveld at FCDONDERS.RU.NL  Tue Jun  6 10:50:02 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Tue, 6 Jun 2006 10:50:02 +0200
Subject: dipole model
In-Reply-To: <LISTSERV%200606051905308600.5C84@NIC.SURFNET.NL>
Message-ID: <TUE.6.JUN.2006.105002.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Punita,

On 5 Jun 2006, at 19:05, Punita Christopher wrote:
> Has anyone seen any literature that deals with a spherical multiple
> layer
> head model in which the dipole spans across layers i.e. the source and
> sink of the dipole are in separate layers.

In the dipole model the source and sink are infintely close together.
The difference on the scalp between a dipole and a source+sink model
with only a few mm in between will be negligible. A source+sink model
with more distance between them can be modelled as such, it requires
the solution of the monopole in a sphere (i.e. the desired source
+sink consists of the superposition of two monopoles). I am not sure
whether an analytical solution for that exsists in a 3- or 4-shell
model, but I would would guess that it does (*). For a BEM model it
is trivial to replace the dipole infinite medium potential with a
monopole infinite medium potential, i.e the BEM formulation
(separation of source and volume conduction) allows the specification
of arbitrary sources.

best
Robert

*) I don't know literature for a monopole in a multi-shell sphere,
but I would expect it to be in either textbooks as a didactical
example or in older articles (70s or 80s). You may want to search for
multipole expansions, which are described in more recent literature,
the monopole is the first term (0th order) of that, the dipole the
second term. Perhaps "Phys Med Biol. 2001 Aug;46(8):2255-66. A study
of equivalent source techniques for high-resolution EEG imaging. Yao
D, Zhou Y, Zeng M, Fan S, Lian J, Wu D, Ao X, Chen L, He B." could
provide more insight.


From muthuraman10 at HOTMAIL.COM  Tue Jun  6 11:19:56 2006
From: muthuraman10 at HOTMAIL.COM (Muthuraman Muthuraman)
Date: Tue, 6 Jun 2006 09:19:56 +0000
Subject: query on coherence analysis
In-Reply-To: <FA431909-950B-4EC2-9598-1C6C49250100@fcdonders.ru.nl>
Message-ID: <TUE.6.JUN.2006.091956.0000.FIELDTRIP@NIC.SURFNET.NL>

Hello

Thanks for the comments, i have downloaded the latest version
and now i am able to calculate using mtmwelch

but i get a error when i am plotting
i will included the matlab commands

>>cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
cfg.channelcmb={'EEG' 'EMG2'};
freq=freqanalysis(cfg,data);

>>fd=freqdescriptives([],freq);

cfg=[];
cfg.xparam='foi';
cfg.yparam='cohspctrm';
cfg.xlim=[0 30];
cfg.cohrefchannel='EMG2';
cfg.box='yes';
cfg.showlabels='yes';
cfg.channelname='EEG26';
singleplotER(cfg,fd);

??? Reference to non-existent field 'foi'.

Error in ==> singleplotER at 272
  plot(varargin{k-1}.(cfg.xparam), P, style);

with regards
muthu


>From: Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>
>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence source analysis
>Date: Thu, 1 Jun 2006 13:58:48 +0200
>
>Dear Muthuraman
>
>I have not been able to reproduce your error. I suggest that you get  the
>latest version of FieldTrip from our FTP server and try again.
>
>best egards,
>Robert
>
>PS this is the test script I used. It uses some simulated data, which
>again uses a MEG gradiometer definition and a head model from the  tutorial
>data.
>
>
>-----------------
>% read some data that is required to simulate MEG data, i.e. volume  model,
>% sensor positions and MRI (optional, only for plotting)
>vol  = read_ctf_hdm('Subject01.hdm');
>hdr  = read_fcdc_header('Subject01.ds/Subject01.res4');
>grad = hdr.grad;
>
>% construct the simulated MEG data for condition A ("active")
>cfg               = [];
>cfg.vol           = vol;
>cfg.grad          = grad;
>cfg.fsample       = 300;
>cfg.ntrials       = 2;
>cfg.triallength   = 1;
>cfg.dip.pos       = [0 7 8];
>cfg.dip.mom       = [1 0 0];
>cfg.dip.signal    = sin(2*pi*10*(1:cfg.fsample)./cfg.fsample);
>cfg.absnoise      = 1e-8;
>data = dipolesimulation(cfg);
>
>% add the source signal as fake EMG channel
>for i=1:cfg.ntrials
>   data.trial{i}(end+1,:) = cfg.dip.signal + randn(size (cfg.dip.signal));
>end
>data.label{end+1} = 'EMG';
>
>cfg=[];
>cfg.output='powandcsd';
>cfg.method='mtmwelch';
>cfg.foi=1:2:30;
>numfoi = length(cfg.foi);
>cfg.taper='hanning';
>cfg.t_ftimwin=zeros(1,numfoi);
>cfg.t_ftimwin(:)=0.5;
>cfg.channel=channelselection({'MEG' 'EMG'},data.label);
>cfg.channelcmb={'MEG' 'EMG'};
>freq=freqanalysis(cfg,data);
>
>
>


From ingrid.nieuwenhuis at FCDONDERS.RU.NL  Tue Jun  6 13:33:28 2006
From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis)
Date: Tue, 6 Jun 2006 13:33:28 +0200
Subject: query on coherence analysis
In-Reply-To: <BAY121-F232E75D5ACD864CFE8389CCE950@phx.gbl>
Message-ID: <TUE.6.JUN.2006.133328.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Muthuraman,

cfg.xparam should not be 'foi', but 'freq' (see help singleplotER)

Bests,
Ingrid


-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Muthuraman Muthuraman
Sent: Tuesday, June 06, 2006 11:20 AM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] query on coherence analysis

Hello

Thanks for the comments, i have downloaded the latest version
and now i am able to calculate using mtmwelch

but i get a error when i am plotting
i will included the matlab commands

>>cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
cfg.channelcmb={'EEG' 'EMG2'};
freq=freqanalysis(cfg,data);

>>fd=freqdescriptives([],freq);

cfg=[];
cfg.xparam='foi';
cfg.yparam='cohspctrm';
cfg.xlim=[0 30];
cfg.cohrefchannel='EMG2';
cfg.box='yes';
cfg.showlabels='yes';
cfg.channelname='EEG26';
singleplotER(cfg,fd);

??? Reference to non-existent field 'foi'.

Error in ==> singleplotER at 272
  plot(varargin{k-1}.(cfg.xparam), P, style);

with regards
muthu


>From: Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>
>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence source analysis
>Date: Thu, 1 Jun 2006 13:58:48 +0200
>
>Dear Muthuraman
>
>I have not been able to reproduce your error. I suggest that you get  the
>latest version of FieldTrip from our FTP server and try again.
>
>best egards,
>Robert
>
>PS this is the test script I used. It uses some simulated data, which
>again uses a MEG gradiometer definition and a head model from the  tutorial

>data.
>
>
>-----------------
>% read some data that is required to simulate MEG data, i.e. volume  model,
>% sensor positions and MRI (optional, only for plotting)
>vol  = read_ctf_hdm('Subject01.hdm');
>hdr  = read_fcdc_header('Subject01.ds/Subject01.res4');
>grad = hdr.grad;
>
>% construct the simulated MEG data for condition A ("active")
>cfg               = [];
>cfg.vol           = vol;
>cfg.grad          = grad;
>cfg.fsample       = 300;
>cfg.ntrials       = 2;
>cfg.triallength   = 1;
>cfg.dip.pos       = [0 7 8];
>cfg.dip.mom       = [1 0 0];
>cfg.dip.signal    = sin(2*pi*10*(1:cfg.fsample)./cfg.fsample);
>cfg.absnoise      = 1e-8;
>data = dipolesimulation(cfg);
>
>% add the source signal as fake EMG channel
>for i=1:cfg.ntrials
>   data.trial{i}(end+1,:) = cfg.dip.signal + randn(size (cfg.dip.signal));
>end
>data.label{end+1} = 'EMG';
>
>cfg=[];
>cfg.output='powandcsd';
>cfg.method='mtmwelch';
>cfg.foi=1:2:30;
>numfoi = length(cfg.foi);
>cfg.taper='hanning';
>cfg.t_ftimwin=zeros(1,numfoi);
>cfg.t_ftimwin(:)=0.5;
>cfg.channel=channelselection({'MEG' 'EMG'},data.label);
>cfg.channelcmb={'MEG' 'EMG'};
>freq=freqanalysis(cfg,data);
>
>
>


From ingrid.nieuwenhuis at FCDONDERS.RU.NL  Wed Jun 14 11:55:53 2006
From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis)
Date: Wed, 14 Jun 2006 11:55:53 +0200
Subject: missing cumtapcnt field
Message-ID: <WED.14.JUN.2006.115553.0200.FIELDTRIP@NIC.SURFNET.NL>

I'm (trying to) beamform, but I get the following error:

reference to non-existent field 'cumtapcnt' 
In prepare_freq_matrices line 124.
Ntrials = length(freq.cumtapcnt)

I used freqanalysis method 'mtmconvol' to do make the freq, and it indeed 
doesn't contain a 'cumtapcnt'

      cfg = [];
      cfg.method = 'mtmconvol';
      cfg.output = 'powandcsd';
      cfg.foi             = 90;
      cfg.t_ftimwin       = 0.5;
      cfg.tapsmofrq       = 30;
      cfg.pad             = 'maxperlen';
      cfg.taper           = 'dpss';
      cfg.keeptrials      = 'yes';
      cfg.keeptapers      = 'no';
      cfg.toi             = 0.75 
        
      freq_BF = freqanalysis(cfg, data);

So my questions: 
- Why doesn't my freq contain a cumtapcnt field. Should I have kept my 
tapers (cfg.keeptapers = 'yes')?
- Can I solve this without having to freqanalysis my data all over again, I 
can see in my freq.crsspctrm = [76 x 11476 double] that I have 76 trials. 
Can I for instance just make a vector of ones with length 76 and put that 
in my freq, or will that create problems?

Thanks a lot,
Ingrid 


From Jan.Schoffelen at FCDONDERS.RU.NL  Wed Jun 14 12:42:08 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Wed, 14 Jun 2006 12:42:08 +0200
Subject: missing cumtapcnt field
In-Reply-To: <LISTSERV%200606141155536310.74A7@NIC.SURFNET.NL>
Message-ID: <WED.14.JUN.2006.124208.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Ingrid,


>Can I for instance just make a vector of ones with length 76 and put that
>in my freq, or will that create problems?

The answer to this question is yes. Indeed, no cumtapcnt is passed back when
using freqanalysis_mtmconvol. Should be fixed, though.
In your case I think it is sufficient just to provide a vector which has a
dimensionality of Nx1, N being the number of epoch. The content of this
vector will not be used later on in this case.
On the other hand, the cumtapcnt-vector, as outputted by for example
freqanalysis_mtmfft contains for each epoch the number of tapers which have
been used for the estimation of the spectra for that particular epoch.
Please note that if you set the option cfg.keeptapers = 'yes', the vector
consists only of ones (or if you use e.g. a single hanning-taper, or such a
low amount of smoothing, that you only need one 'dpss'-taper, in which case
by the way it does not make sense to use the 'dpss'). In any other case, the
cumtapcnt-vector contains a number, which can be different for each epoch
(when you have trials of different lengths). You can easily compute the
number of tapers, this will be: 2xNxK-1, with N being the length of your
data segment (in seconds), and K being the taper-smoothing you specified in
cfg.tapsmofrq.

Yours,

JM


From nathanweisz at MAC.COM  Thu Jun 15 11:42:43 2006
From: nathanweisz at MAC.COM (Nathan Weisz)
Date: Thu, 15 Jun 2006 11:42:43 +0200
Subject: source positions - brain regions
Message-ID: <THU.15.JUN.2006.114243.0200.FIELDTRIP@NIC.SURFNET.NL>

dear help-list,

sorry for what appears to be a very basic question.
i'm just starting to explore the source analysis possibilities that
fieldtrip offers. for this i downloaded a EEG tutorial dataset from
eeglab, did eeglab2fieldtrip, and the timelockanalysis. now i wanted
to estimate the source waveforms of the erp.

%this is my input:
vol   = [];
vol.r = 12 * [0.88 0.92 1.00]; % radii of spheres, the head radius is
12 cm
vol.c = [1 1/80 1];            % conductivity
vol.o = [0 0 0];

tmp=data.elec;
tmp.pnt=tmp.pnt*12;


cfg=[];
cfg.method='lcmv';
cfg.vol=vol;
cfg.elec=tmp;
cfg.resolution=1;

datamn=sourceanalysis(cfg,dataav);

%this is the output
datamn =

       xgrid: [-10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10]
       ygrid: [-10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10]
       zgrid: [-8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10]
         dim: [21 21 19]
         vol: [1x1 struct]
        time: [1x256 double]
         pos: [8379x3 double]
      inside: [1x4811 double]
     outside: [1x3568 double]
      method: 'average'
         avg: [1x1 struct]
         cfg: [1x1 struct]

there were no error or warning messages, so from the basic structure
things seem to be ok.
the time courses of my source activity appears to be saved in
datamn.avg.mom.

 >> size(datamn.avg.mom{datamn.inside(1)})

ans =

      3   256


however now i'm a little bit stuck. from here, what is the best
method of finding out which dipoles correspond (very roughly) to
which brain regions, so i can extract specifically those to look at
the sourcewaveforms? unfortunatley no mri.
I am aware of the sourceplot function, but was uncapable of producing
a meaningful output.

thanks in advance for any hints & best wishes,
nathan



--------------------------------
Dr. Nathan Weisz
Dept. of Psychology
University of Konstanz
P.O. Box D25
78457 Konstanz, Germany

Tel: ++49-7531-884612
Email & Chat-AV: nathanweisz at mac.com
Homepage: http://homepage.mac.com/nathanweisz/start/research.html


From muthuraman10 at HOTMAIL.COM  Thu Jun 15 15:59:54 2006
From: muthuraman10 at HOTMAIL.COM (Muthuraman Muthuraman)
Date: Thu, 15 Jun 2006 13:59:54 +0000
Subject: query on coherence analysis
In-Reply-To: <002201c6895d$07c0d680$642dae83@fcdonders.nl>
Message-ID: <THU.15.JUN.2006.135954.0000.FIELDTRIP@NIC.SURFNET.NL>

Hello

Thankyou for the previous help it works now
i am able to proceed further to calculate the coherence

The problem now the coherence obtained using the mtmwelch
when i plot the coherence figures for the channels
all the coherence figures for the different channel looks the same
is there is a bug in how i am calculating the coherence

These are the steps i carried out in calculating the coherence

headerfile='pd_mof_tr0_c_0306.cnt';
hdr = read_fcdc_header(headerfile);
cfg.trl = [];
for i=1:floor(hdr.nSamples/hdr.Fs)
  cfg.trl(i,1) = (i-1)*hdr.Fs + 1;
  cfg.trl(i,2) = (i  )*hdr.Fs;
  cfg.trl(i,3) = 0;
end

cfg.headerfile=headerfile;
>>cfg.datafile=headerfile;
>>[data] = preprocessing(cfg);

-and after the data is preprocessed i change the channel labels from actual
cz to eeg26 and so on



cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
cfg.channelcmb={'EEG' 'EMG2'};
freq=freqanalysis(cfg,data);


-when i calculate using freqanalysis i get these warnings

1.000 Hz : WARNING - using only one taper for specified smoothing
Warning: Size vector should be a row vector with integer elements.
>In freqanalysis_mtmconvol at 360
  In freqanalysis at 182
  In freqanalysis_mtmwelch at 67
  In freqanalysis at 182
and so on till 30.000 hz

-and while processing

processing trial 2: 1000 samples
Warning: Size vector should be a row vector with integer elements.
>In freqanalysis_mtmconvol at 398
  In freqanalysis at 182
  In freqanalysis_mtmwelch at 67
  In freqanalysis at 182



fd=freqdescriptives([],freq);


cfg=[];
cfg.xparam='freq';
cfg.yparam='cohspctrm';
cfg.xlim=[3 30];
cfg.cohrefchannel='EMG2';
cfg.box='yes';
cfg.showlabels='yes';

cfg.channelname='EEG27';
singleplotER(cfg,fd);
-when i try to plot i get this error
??? Error using ==> char
Cell elements must be character arrays.

Error in ==> singleplotER at 326
  t=[char(cfg.channelname) ' / ' num2str(cfg.channelindex) ];


please , look at it and help me in this regard

thanking you
with regards
muthuraman

>From: Ingrid Nieuwenhuis <ingrid.nieuwenhuis at FCDONDERS.RU.NL>
>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence analysis
>Date: Tue, 6 Jun 2006 13:33:28 +0200
>
>Dear Muthuraman,
>
>cfg.xparam should not be 'foi', but 'freq' (see help singleplotER)
>
>Bests,
>Ingrid
>
>
>-----Original Message-----
>From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
>Of Muthuraman Muthuraman
>Sent: Tuesday, June 06, 2006 11:20 AM
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence analysis
>
>Hello
>
>Thanks for the comments, i have downloaded the latest version
>and now i am able to calculate using mtmwelch
>
>but i get a error when i am plotting
>i will included the matlab commands
>
> >>cfg=[];
>cfg.output='powandcsd';
>cfg.method='mtmwelch';
>cfg.foi=1:2:30;
>numfoi = length(cfg.foi);
>cfg.taper='hanning';
>cfg.t_ftimwin=zeros(1,numfoi);
>cfg.t_ftimwin(:)=0.5;
>cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
>cfg.channelcmb={'EEG' 'EMG2'};
>freq=freqanalysis(cfg,data);
>
> >>fd=freqdescriptives([],freq);
>
>cfg=[];
>cfg.xparam='foi';
>cfg.yparam='cohspctrm';
>cfg.xlim=[0 30];
>cfg.cohrefchannel='EMG2';
>cfg.box='yes';
>cfg.showlabels='yes';
>cfg.channelname='EEG26';
>singleplotER(cfg,fd);
>
>??? Reference to non-existent field 'foi'.
>
>Error in ==> singleplotER at 272
>   plot(varargin{k-1}.(cfg.xparam), P, style);
>
>with regards
>muthu
>
>
> >From: Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>
> >Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
> >To: FIELDTRIP at NIC.SURFNET.NL
> >Subject: Re: [FIELDTRIP] query on coherence source analysis
> >Date: Thu, 1 Jun 2006 13:58:48 +0200
> >
> >Dear Muthuraman
> >
> >I have not been able to reproduce your error. I suggest that you get  the
> >latest version of FieldTrip from our FTP server and try again.
> >
> >best egards,
> >Robert
> >
> >PS this is the test script I used. It uses some simulated data, which
> >again uses a MEG gradiometer definition and a head model from the
>tutorial
>
> >data.
> >
> >
> >-----------------
> >% read some data that is required to simulate MEG data, i.e. volume
>model,
> >% sensor positions and MRI (optional, only for plotting)
> >vol  = read_ctf_hdm('Subject01.hdm');
> >hdr  = read_fcdc_header('Subject01.ds/Subject01.res4');
> >grad = hdr.grad;
> >
> >% construct the simulated MEG data for condition A ("active")
> >cfg               = [];
> >cfg.vol           = vol;
> >cfg.grad          = grad;
> >cfg.fsample       = 300;
> >cfg.ntrials       = 2;
> >cfg.triallength   = 1;
> >cfg.dip.pos       = [0 7 8];
> >cfg.dip.mom       = [1 0 0];
> >cfg.dip.signal    = sin(2*pi*10*(1:cfg.fsample)./cfg.fsample);
> >cfg.absnoise      = 1e-8;
> >data = dipolesimulation(cfg);
> >
> >% add the source signal as fake EMG channel
> >for i=1:cfg.ntrials
> >   data.trial{i}(end+1,:) = cfg.dip.signal + randn(size
>(cfg.dip.signal));
> >end
> >data.label{end+1} = 'EMG';
> >
> >cfg=[];
> >cfg.output='powandcsd';
> >cfg.method='mtmwelch';
> >cfg.foi=1:2:30;
> >numfoi = length(cfg.foi);
> >cfg.taper='hanning';
> >cfg.t_ftimwin=zeros(1,numfoi);
> >cfg.t_ftimwin(:)=0.5;
> >cfg.channel=channelselection({'MEG' 'EMG'},data.label);
> >cfg.channelcmb={'MEG' 'EMG'};
> >freq=freqanalysis(cfg,data);
> >
> >
> >


From linpe at NINDS.NIH.GOV  Thu Jun 15 22:08:19 2006
From: linpe at NINDS.NIH.GOV (Lin, Peter (NIH/NINDS) [E])
Date: Thu, 15 Jun 2006 16:08:19 -0400
Subject: No subject
Message-ID: <THU.15.JUN.2006.160819.0400.FIELDTRIP@NIC.SURFNET.NL>

I am trying to import neuroscan data into fieldtrip for analysis.  I
tried using eeglab to load my epoch's neuroscan file and then used the
eeglab2fieldtrip command on the EEG structure to generate a new data
file.  My question is how to process the data further using the
frequencyanalysis method.  

 

>>[data]=eeglab2fieldtrip(EEG,'preprocessing')

 

data = 

 

      label: {1x64 cell}

    fsample: 1000

       elec: [1x1 struct]

      trial: {1x224 cell}

       time: {1x224 cell}

        cfg: [1x1 struct]

 

I'm wondering if my created data file is not correct.  Any help on how
to proceed would be great.  

 

Thanks,

 

Peter

 

Peter Lin, MD

Clinical Fellow, Human Motor Control Section

Phone: 301-402-0703

email: linpe at ninds.nih.gov

 

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From Jan.Schoffelen at FCDONDERS.RU.NL  Fri Jun 16 09:05:50 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Fri, 16 Jun 2006 09:05:50 +0200
Subject: No subject
In-Reply-To: <C95F8E297215B6489AC8E595CF2239B0053B989F@NIHCESMLBX.nih.gov>
Message-ID: <FRI.16.JUN.2006.090550.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Peter,



As far as I can see, the data looks OK. At least it contains the fields
subsequent analysis steps need to know. However, I cannot judge the content
of these fields, but there's no reason to assume that's not fine.

To proceed, I would first advice you to have a look at the fieldtrip
website. If you follow the link documentation, and then
tutorial-documentation, there's already some stuff regarding frequency
analysis. Moreover, the website also contains the documentation of all
fieldtrip functions, which you can also access from the matlab command line,
by typing help functionname. For example, try help freqanalysis, or help
freqanalysis_mtmconvol. There's already quite some information in there, as
well as all the options you can play with.



Good luck



Jan-mathijs



  _____

From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Lin, Peter (NIH/NINDS) [E]
Sent: Thursday, June 15, 2006 10:08 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: [FIELDTRIP]



I am trying to import neuroscan data into fieldtrip for analysis.  I tried
using eeglab to load my epoch's neuroscan file and then used the
eeglab2fieldtrip command on the EEG structure to generate a new data file.
My question is how to process the data further using the frequencyanalysis
method.



>>[data]=eeglab2fieldtrip(EEG,'preprocessing')



data =



      label: {1x64 cell}

    fsample: 1000

       elec: [1x1 struct]

      trial: {1x224 cell}

       time: {1x224 cell}

        cfg: [1x1 struct]



I'm wondering if my created data file is not correct.  Any help on how to
proceed would be great.



Thanks,



Peter



Peter Lin, MD

Clinical Fellow, Human Motor Control Section

Phone: 301-402-0703

email: linpe at ninds.nih.gov



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From Jan.Schoffelen at FCDONDERS.RU.NL  Fri Jun 16 09:15:15 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Fri, 16 Jun 2006 09:15:15 +0200
Subject: query on coherence analysis
In-Reply-To: <BAY121-F19F3FD6B01B619882BC777CE820@phx.gbl>
Message-ID: <FRI.16.JUN.2006.091515.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Muthuraman,

At first glance I don't have a clue what's going on.
Did you have a look into fd.powspctrm, and fd.cohspctrm?
Does it contain normal numbers, zeros, or nan?
It might be a bug in freqanalysis_mtmwelch.
Did you try out other methods, to be specified in cfg.method?
If yes, did this also give strange results? If no, could you try out
cfg.method = 'mtmconvol' instead of 'mtmwelch'? Please have a look at the
documentation which additional options you have to specify.
What matlab-version do you use? Do you use the latest fieldtrip-version?

One additional thing: please note that you specified the odd frequencies
1:2:29, whereas your time-window is half a second wide. These are not
optimal settings, since the frequency-resolution of your time-window is 2
Hz. This means that your time-window never contains an integer amount of
cycles of the frequency you want to estimate. This might lead to strange
results, though I don't think it has anything to do with your present
problem. However, I would use cfg.freq = 2:2:30 in combination with a
time-window of 0.5 s

Yours,

Jan-Mathijs

-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Muthuraman Muthuraman
Sent: Thursday, June 15, 2006 4:00 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] query on coherence analysis

Hello

Thankyou for the previous help it works now
i am able to proceed further to calculate the coherence

The problem now the coherence obtained using the mtmwelch
when i plot the coherence figures for the channels
all the coherence figures for the different channel looks the same
is there is a bug in how i am calculating the coherence

These are the steps i carried out in calculating the coherence

headerfile='pd_mof_tr0_c_0306.cnt';
hdr = read_fcdc_header(headerfile);
cfg.trl = [];
for i=1:floor(hdr.nSamples/hdr.Fs)
  cfg.trl(i,1) = (i-1)*hdr.Fs + 1;
  cfg.trl(i,2) = (i  )*hdr.Fs;
  cfg.trl(i,3) = 0;
end

cfg.headerfile=headerfile;
>>cfg.datafile=headerfile;
>>[data] = preprocessing(cfg);

-and after the data is preprocessed i change the channel labels from actual
cz to eeg26 and so on



cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
cfg.channelcmb={'EEG' 'EMG2'};
freq=freqanalysis(cfg,data);


-when i calculate using freqanalysis i get these warnings

1.000 Hz : WARNING - using only one taper for specified smoothing
Warning: Size vector should be a row vector with integer elements.
>In freqanalysis_mtmconvol at 360
  In freqanalysis at 182
  In freqanalysis_mtmwelch at 67
  In freqanalysis at 182
and so on till 30.000 hz

-and while processing

processing trial 2: 1000 samples
Warning: Size vector should be a row vector with integer elements.
>In freqanalysis_mtmconvol at 398
  In freqanalysis at 182
  In freqanalysis_mtmwelch at 67
  In freqanalysis at 182



fd=freqdescriptives([],freq);


cfg=[];
cfg.xparam='freq';
cfg.yparam='cohspctrm';
cfg.xlim=[3 30];
cfg.cohrefchannel='EMG2';
cfg.box='yes';
cfg.showlabels='yes';

cfg.channelname='EEG27';
singleplotER(cfg,fd);
-when i try to plot i get this error
??? Error using ==> char
Cell elements must be character arrays.

Error in ==> singleplotER at 326
  t=[char(cfg.channelname) ' / ' num2str(cfg.channelindex) ];


please , look at it and help me in this regard

thanking you
with regards
muthuraman


From r.oostenveld at FCDONDERS.RU.NL  Fri Jun 16 10:39:48 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 16 Jun 2006 10:39:48 +0200
Subject: source positions - brain regions
In-Reply-To: <5E221385-C805-4FFA-BE76-F2C0DF9BEE72@mac.com>
Message-ID: <FRI.16.JUN.2006.103948.0200.FIELDTRIP@NIC.SURFNET.NL>

hi Nathan

On 15 Jun 2006, at 11:42, Nathan Weisz wrote:
> however now i'm a little bit stuck. from here, what is the best
> method of finding out which dipoles correspond (very roughly) to
> which brain regions, so i can extract specifically those to look at
> the sourcewaveforms? unfortunatley no mri.
> I am aware of the sourceplot function, but was uncapable of
> producing a meaningful output.

So far it seems ok. The headmodel is in cm, the electrodes as well (I
presume, otherwise it would have given warnings and/or errors), so
the source locations are also expressed in cm, since they are
expresed in the same coordinate system. I suggest that you have a
look at http://www2.ru.nl/fcdonders/fieldtrip/doku.php?
id=fieldtrip:documentation:frequently_asked_questions#how_are_the_differ
ent_head_and_mri_coordinate_systems_defined to get a better
understanding in general.

What we normally do in such a case is to use an indivudual headmodel,
and what we thus subsequently would do is to take an anatomical MRI
of the same subject, in which the MRI is aligned to the same head/
model coordinate system (using the ears and nose fiducials). Since
you do not have a MRI, you could take a standard MRI (i.e. the MNI
template in single_subj_T1 from SPM). Some time ago I (or Arno)
posted a homogenous transformation matrix "besa2spm" on the eeglab
mailing list (*). That homogenous transformation matrix transforms
from besa coordinates for a spherical model to MNI coordinates.

besa2spm = [
     0.0101   -0.9400         0    0.5588
     1.1889    0.0080    0.0530  -18.0041
    -0.0005   -0.0000    1.1268    1.8045
          0         0         0    1.0000 ];

spm2besa = inv(besa2spm);

The transformation matrix is for the "besa" spherical model in
EEGLAB, which has different sphere radii (85mm outer sphere) than you
have used. So you should add a scaling from the besa radii to yours.

your2besa = eye(4);
your2besa(1,1) = 8.5/12;
your2besa(2,2) = 8.5/12;
your2besa(3,3) = 8.5/12;

then

your2spm = besa2spm * your2besa
spm2your = inv(your2spm);

It is most convenient to apply the inverse transformation to the MRI
corodinate system. I.e. do
   mri = read_fcdc_mri('single_subj_T1.mnc')
then mri.transform describes the voxels in SPM/MNI coordinates, so
   mri.transform = spm2your * mri.transform;
changes the anatomical MRI into your headmodel coordinates.

Subsequently you can interpolate the functional values onto the
anaomtical voxel locations with SOURCEINTERPOLATE, and plot the
functional values overlaid over the anatomical with SOURCEPLLOT or
SLICEINTERP.

best regards,
Robert

PS (*) the besa2spm coordinate transformation matrix was constructed
using ELECTORDENORMAMALIZE, which warps electrodes. In this case the
spherical 1020 electrodes were warped to the corresponding electrodes
in the MNI template. The homogenous transformation matrix describes
the warp/deformation and can be used as well for the dipoles inside
the head.


From jurij.dreo at GUEST.ARNES.SI  Sat Jun 17 12:18:26 2006
From: jurij.dreo at GUEST.ARNES.SI (Jurij Dreo)
Date: Sat, 17 Jun 2006 11:18:26 +0100
Subject: Statistics for coherence in a within-subject experiment
Message-ID: <SAT.17.JUN.2006.111826.0100.FIELDTRIP@NIC.SURFNET.NL>

Hello,

I am using BESA to perform coherence and source coherence 
calculations for a multiple-subject/multiple-condition experiment. In 
the experiment I have 11 subjects, 6 conditions and around 30 sets 
per condition per subject.

In BESA the data was preprocessed and the coherence values in the 
Time-Frequency domain were calculated for each person.

As BESA has no capabilities to calculate statistics in a multiple-
subject study, their support personnel directed me towards FieldTrip.

I´ve been looking over the documentation and tutorials on your web 
page and also downloaded the scrip and ran it in matlab.

The tutorial on Cluster-Lever randomization Tests for the Time-
Frequency domain is quite straight-forward. I am however not quite 
sure which statistic to use for the cfg.statistic variable to analyze 
coherence in a within-subject study such as the one I have.

The documentation on the cfg.statistic variable says it can have 
these values:
1. indepsamplesT' (independent samples T-statistic) 
2. 'indepsamplesregrT' (independent samples regression coefficient T-
statistic)
3. 'indepsamplesZcoh' (independent samples Z-statistic for coherence)
4. 'indepsamplesTsqcrs' (independent samples T-square-statistic for 
the cross-spectrum)
5. 'depsamplesT' (dependent samples T-statistic)
6. 'actvsblT' (activation versus baseline T-statistic)
7. 'depsamplesregrT' (dependent samples regression coefficient T-
statistic) 
8. 'indepsamplesF' (independent samples F-statistic)
9. 'depsamplesF' (dependent samples F-statistic)

I am not sure if any of these options are compatible with a within-
subject multiple condition coherence statistical analysis.

option 3. - indepsamplesZcoh is obviously only suitable for a between-
trial, two-condition experiment

and there are no other options that explicitally say they are used 
for coherence. 

So how can one compare 6 conditions for 11 subjects with regards to 
coherence if one imports the Time-Frequency domain data for each 
person into FieldTrip?

Thank you for your help!

Regards,
Jurij Dreo


From r.oostenveld at FCDONDERS.RU.NL  Mon Jun 19 16:18:55 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Mon, 19 Jun 2006 16:18:55 +0200
Subject: Statistics for coherence in a within-subject experiment
In-Reply-To: <20060617_091826_063328.jurij.dreo@guest.arnes.si>
Message-ID: <MON.19.JUN.2006.161855.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Jurij

> option 3. - indepsamplesZcoh is obviously only suitable for a between-
> trial, two-condition experiment

Yes, that is for testing coherence differences between two conditions
within one subject.

> and there are no other options that explicitally say they are used
> for coherence.
>
> So how can one compare 6 conditions for 11 subjects with regards to
> coherence if one imports the Time-Frequency domain data for each
> person into FieldTrip?

In your case you have observed a "value" in 11 subjects, over 6
conditions. That value happens to be coherence, but could as well
have been something else. Since you have manipulated the conditions
with each subject, you can use a dependent-samples test: the observed
values depend on the subject (an example of a dependent-samples test
is a paired-t test).

If the number of trials varies between subjects and/or sessions, it
will be preferable to transform your coherence values to z-scores
manually prior to submitting the values to clusterrandanalysis.

Now about the 6 conditions, am I right that you have a 1x6 factorial
design, or is there more strucure in the design? Do you have a
specific hypothesis about the different conditions? If you only want
to reject the null-hypothesis "the observed value (coherence) is the
same (more accurately: stems from the same distribution) in all my 6
conditions", you would use an omnibus F-statistic, i.e.
'depsamplesF'. It might be that your hypothesis is more specific, or
also in case you find an omnibus effect, then you would probably want
to perform explicit tests between two subsets of your 6 conditions
using a 'depsamplesT' test.

best regards,
Robert


From jurij.dreo at GUEST.ARNES.SI  Mon Jun 19 17:31:46 2006
From: jurij.dreo at GUEST.ARNES.SI (Jurij Dreo)
Date: Mon, 19 Jun 2006 17:31:46 +0200
Subject: Statistics for coherence in a within-subject experiment
Message-ID: <MON.19.JUN.2006.173146.0200.FIELDTRIP@NIC.SURFNET.NL>

Hello!

Thank you for your answers. Here are my replies to them:

To avoid any misunderstandings here is again a summary of my study design
- I have 11 subjects. 
- Each of them performed 6 tasks related to working memory.
- Each subject performed anywehere from 25 to 60 repeats (trial) of each condition (the standard number of trials per task was 30 - but some subjects performed the entire experiment twice (ergo 60 potential trials) .... and in some some of their trials are unusable - artifacts ... ergo 25 min number of possible trials)

Given my study design I thought something like a one-way ANOVA for correlated samples would be in order.
(as I am comparing 6 conditions within-subjects as every subject performed all sets)


-----------------
> In your case you have observed a "value" in 11 subjects, over 6  
> conditions. That value happens to be coherence, but could as well  
> have been something else. Since you have manipulated the conditions  
> with each subject, you can use a dependent-samples test: the observed  
> values depend on the subject (an example of a dependent-samples test  
> is a paired-t test).
-------------------

I´m not sure what you are saying here.... I agree with the dependent samples idea... but I cannot preform a t-test ... ie. more of them as that would inflate my p-rate overall.

I thought that I would first do an ANOVA and then something like the Tukey HSD Test to cimpare individual conditions

--------------------
> If the number of trials varies between subjects and/or sessions, it  
> will be preferable to transform your coherence values to z-scores  
> manually prior to submitting the values to clusterrandanalysis.
--------------------
Yes I agree that would need to be done manually.

-----------
> Now about the 6 conditions, am I right that you have a 1x6 factorial  
> design, or is there more strucure in the design? Do you have a  
> specific hypothesis about the different conditions? If you only want  
> to reject the null-hypothesis "the observed value (coherence) is the  
> same (more accurately: stems from the same distribution) in all my 6  
> conditions", you would use an omnibus F-statistic, i.e.  
> 'depsamplesF'. It might be that your hypothesis is more specific, or  
> also in case you find an omnibus effect, then you would probably want  
> to perform explicit tests between two subsets of your 6 conditions  
> using a 'depsamplesT' test.
> 
----------

I want to contrast all conditions at once (f -test anova) AND also each combination of conditions (say a post- ANOVA Q-test)

But Im still not sure which statistic to use and even if the one I use will be able to deal with the fact that I have a different number of conditions per condition per subject

As far as I understand it... we must use some kind of ANOVA here... A simple "paired" t-test will not do... as we are comparing more than 2 conditions at once and I do not want to inflate my p-rate.

Thank you for your help!

Regards,
Jurij Dreo
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From muthuraman10 at HOTMAIL.COM  Tue Jun 20 10:40:17 2006
From: muthuraman10 at HOTMAIL.COM (Muthuraman Muthuraman)
Date: Tue, 20 Jun 2006 08:40:17 +0000
Subject: query on coherence analysis
Message-ID: <TUE.20.JUN.2006.084017.0000.FIELDTRIP@NIC.SURFNET.NL>

Hello Jan

The answers for the questions you have asked
and also i have attached some figures with this mail
1-using welch periodogram method
2-using fieldtrip 'mtmfft'
3-using fieldtrip 'mtmwelch'

Did you have a look into fd.powspctrm, and fd.cohspctrm?
-yes,both look the same so something is surely going wrong

Does it contain normal numbers, zeros, or nan?
-yes, it has normal numbers but the vlaues are from 1.0 to 10.0 not as
normal in the case of 0.1 to 1 in coherence spectrum

Did you try out other methods, to be specified in cfg.method?
-yes using 'mtmfft' i have attached the figure in the mail in which i dont
get the correct frequency content and the values are less

-In the 'mtmwelch' method i get a error when i am plotting, even then i am
able to see the figure
??? Error using ==> char
Cell elements must be character arrays.

Error in ==> singleplotER at 326
  t=[char(cfg.channelname) ' / ' num2str(cfg.channelindex) ];

-In the 'mtmconvol' i am not able to plot i get a error
selected 60 channels for coherence
??? Error using ==> plot
Vectors must be the same lengths.

Error in ==> singleplotER at 272
  plot(varargin{k-1}.(cfg.xparam), P, style);


please go through it and give your comments

and one more question for the source analysis
what are the values we need,when i open the elec1010 there are four values
x,y,z values and what is the fourth value

with regards
muthu

>From: Jan Mathijs Schoffelen <Jan.Schoffelen at FCDONDERS.RU.NL>
>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence analysis
>Date: Fri, 16 Jun 2006 09:15:15 +0200
>
>Dear Muthuraman,
>
>At first glance I don't have a clue what's going on.
>Did you have a look into fd.powspctrm, and fd.cohspctrm?
>Does it contain normal numbers, zeros, or nan?
>It might be a bug in freqanalysis_mtmwelch.
>Did you try out other methods, to be specified in cfg.method?
>If yes, did this also give strange results? If no, could you try out
>cfg.method = 'mtmconvol' instead of 'mtmwelch'? Please have a look at the
>documentation which additional options you have to specify.
>What matlab-version do you use? Do you use the latest fieldtrip-version?
>
>One additional thing: please note that you specified the odd frequencies
>1:2:29, whereas your time-window is half a second wide. These are not
>optimal settings, since the frequency-resolution of your time-window is 2
>Hz. This means that your time-window never contains an integer amount of
>cycles of the frequency you want to estimate. This might lead to strange
>results, though I don't think it has anything to do with your present
>problem. However, I would use cfg.freq = 2:2:30 in combination with a
>time-window of 0.5 s
>
>Yours,
>
>Jan-Mathijs
>
>-----Original Message-----
>From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
>Of Muthuraman Muthuraman
>Sent: Thursday, June 15, 2006 4:00 PM
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence analysis
>
>Hello
>
>Thankyou for the previous help it works now
>i am able to proceed further to calculate the coherence
>
>The problem now the coherence obtained using the mtmwelch
>when i plot the coherence figures for the channels
>all the coherence figures for the different channel looks the same
>is there is a bug in how i am calculating the coherence
>
>These are the steps i carried out in calculating the coherence
>
>headerfile='pd_mof_tr0_c_0306.cnt';
>hdr = read_fcdc_header(headerfile);
>cfg.trl = [];
>for i=1:floor(hdr.nSamples/hdr.Fs)
>   cfg.trl(i,1) = (i-1)*hdr.Fs + 1;
>   cfg.trl(i,2) = (i  )*hdr.Fs;
>   cfg.trl(i,3) = 0;
>end
>
>cfg.headerfile=headerfile;
> >>cfg.datafile=headerfile;
> >>[data] = preprocessing(cfg);
>
>-and after the data is preprocessed i change the channel labels from actual
>cz to eeg26 and so on
>
>
>
>cfg=[];
>cfg.output='powandcsd';
>cfg.method='mtmwelch';
>cfg.foi=1:2:30;
>numfoi = length(cfg.foi);
>cfg.taper='hanning';
>cfg.t_ftimwin=zeros(1,numfoi);
>cfg.t_ftimwin(:)=0.5;
>cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
>cfg.channelcmb={'EEG' 'EMG2'};
>freq=freqanalysis(cfg,data);
>
>
>-when i calculate using freqanalysis i get these warnings
>
>1.000 Hz : WARNING - using only one taper for specified smoothing
>Warning: Size vector should be a row vector with integer elements.
> >In freqanalysis_mtmconvol at 360
>   In freqanalysis at 182
>   In freqanalysis_mtmwelch at 67
>   In freqanalysis at 182
>and so on till 30.000 hz
>
>-and while processing
>
>processing trial 2: 1000 samples
>Warning: Size vector should be a row vector with integer elements.
> >In freqanalysis_mtmconvol at 398
>   In freqanalysis at 182
>   In freqanalysis_mtmwelch at 67
>   In freqanalysis at 182
>
>
>
>fd=freqdescriptives([],freq);
>
>
>cfg=[];
>cfg.xparam='freq';
>cfg.yparam='cohspctrm';
>cfg.xlim=[3 30];
>cfg.cohrefchannel='EMG2';
>cfg.box='yes';
>cfg.showlabels='yes';
>
>cfg.channelname='EEG27';
>singleplotER(cfg,fd);
>-when i try to plot i get this error
>??? Error using ==> char
>Cell elements must be character arrays.
>
>Error in ==> singleplotER at 326
>   t=[char(cfg.channelname) ' / ' num2str(cfg.channelindex) ];
>
>
>please , look at it and help me in this regard
>
>thanking you
>with regards
>muthuraman

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From Jan.Schoffelen at FCDONDERS.RU.NL  Wed Jun 21 11:31:07 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Wed, 21 Jun 2006 11:31:07 +0200
Subject: query on coherence analysis
In-Reply-To: <BAY121-F3382C80D92ABF19D39C798CE840@phx.gbl>
Message-ID: <WED.21.JUN.2006.113107.0200.FIELDTRIP@NIC.SURFNET.NL>

>the other question i have asked in the previous mail
>i would like to do the source analysis
>and the values specified in for ex:elec1010
>it has four values and the channel label
>the first three values are x,y,z position values
>what is the fourth value?

Dear Muthuraman,

Please have a look at the FAQ-section of the fieldtrip-website. It is
explained what is specified in the layout-files.

Yours,

Jan-M


From Jan.Schoffelen at FCDONDERS.RU.NL  Wed Jun 21 12:32:15 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Wed, 21 Jun 2006 12:32:15 +0200
Subject: query on coherence analysis
In-Reply-To: <BAY121-F3382C80D92ABF19D39C798CE840@phx.gbl>
Message-ID: <WED.21.JUN.2006.123215.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Muthuraman,

Please find attached a script and a figure.
I compared the 'mtmfft' with 'mtmwelch', and the results look very similar.
I did not test the 'mtmconvol' method, since this function is called when
you specify 'mtmwelch'. I guess you have to check your configuration in that
respect. I would say that the code is doing what it should do.
Please make sure that you use the latest fieldtrip-version.

Yours,

Jan-Mathijs

-----Original Message-----
From: Muthuraman Muthuraman [mailto:muthuraman10 at hotmail.com]
Sent: Wednesday, June 21, 2006 11:05 AM
To: Jan.Schoffelen at fcdonders.ru.nl
Subject: RE: [FIELDTRIP] query on coherence analysis

Hello Jan

Thanks for the suggestions

I have tried 'mtmconvol' and also plotting using singleplotTFR
the figure looks totally blue
i have attached the figure with this mail for the same channel combination
Figure-mtmconvol

and also i have uploaded two files
one is the CNT file of a patient
and the other file is data structure after preprocessing and changing the
channel label

If u have any different results from the data
please let me know
my aim is to do the coherence analysis followed by the source analysis using

'DICS'


the other question i have asked in the previous mail
i would like to do the source analysis
and the values specified in for ex:elec1010
it has four values and the channel label
the first three values are x,y,z position values
what is the fourth value?


thanking you
with regards
muthu
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From srampp at TISCALI.DE  Wed Jun 21 23:07:50 2006
From: srampp at TISCALI.DE (Stefan Rampp)
Date: Wed, 21 Jun 2006 23:07:50 +0200
Subject: Missing minimumnormestimate etc
Message-ID: <WED.21.JUN.2006.230750.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi everyone,

I was just trying to do source localization of epilepsy MEG data using mne, however, it appears that some functions are missing: minimumnormestimate, music, loreta and rv are used in sourceanalysis.m, but I can't find the implementations (and neither can matlab). Do I need to download additional libraries/toolboxes?

Thank you,
Stefan Rampp.
Epilepsycenter Erlangen
Germany
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From t.montez at VUMC.NL  Thu Jun 22 01:27:29 2006
From: t.montez at VUMC.NL (Montez, T.)
Date: Thu, 22 Jun 2006 01:27:29 +0200
Subject: channel location file to import planar to EEGLAB
Message-ID: <THU.22.JUN.2006.012729.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtripers,

I am using EEGLAB to compute ICA of CTF 151 channels data.

I used to read the data in EEGLAB directly from the CTF format, 
but some components are affected by the bad channels. 

Since removing the bad channels will reduce the number of components
and will give problems later at the planar transformation;
I tried using megrepair first and then importing the matlab array
of data.trial{1}. I use the channel locations of a previous 
dataset opened from the CTF format.

- I still get some components reflecting the bad channels, 
should I increase the cfg.neighbourdist?  
(I was using the default of 4 cm).

- To import the data after the planar transformation I need 
a channel location file for the dH and dV pairs, 
can you help me with that? 

Thanks in advance,
Teresa Montez

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From srampp at TISCALI.DE  Thu Jun 22 01:51:25 2006
From: srampp at TISCALI.DE (Stefan Rampp)
Date: Thu, 22 Jun 2006 01:51:25 +0200
Subject: channel location file to import planar to EEGLAB
Message-ID: <THU.22.JUN.2006.015125.0200.FIELDTRIP@NIC.SURFNET.NL>

channel location file to import planar to EEGLABDear Teresa,

I can't really provide much info regarding your first question, however, I might be able to help you with the second: 
Have you applied 'combineplanar' after the planar transformation? This will combine the dH and dV pairs into one channel per pair, e.g.

cfg = [];
combplan = combineplanar(cfg, plan);

were plan is the planar transformed data set. combineplanar allows to choose the method for combination of the pairs. For further details, you might want to have a look at the tutorial about event related averaging:
http://www2.ru.nl/fcdonders/fieldtrip/doku.php?id=fieldtrip:documentation:tutorial:eventrelatedaveraging

Sincerely,
Stefan Rampp
Epilepsycenter Erlangen
Germany.
  ----- Original Message ----- 
  From: Montez, T. 
  To: FIELDTRIP at NIC.SURFNET.NL 
  Sent: Thursday, June 22, 2006 1:27 AM
  Subject: [FIELDTRIP] channel location file to import planar to EEGLAB


  Dear Fieldtripers,

  I am using EEGLAB to compute ICA of CTF 151 channels data.

  I used to read the data in EEGLAB directly from the CTF format,
  but some components are affected by the bad channels.

  Since removing the bad channels will reduce the number of components
  and will give problems later at the planar transformation;
  I tried using megrepair first and then importing the matlab array
  of data.trial{1}. I use the channel locations of a previous
  dataset opened from the CTF format.

  - I still get some components reflecting the bad channels,
  should I increase the cfg.neighbourdist? 
  (I was using the default of 4 cm).

  - To import the data after the planar transformation I need
  a channel location file for the dH and dV pairs,
  can you help me with that?

  Thanks in advance,
  Teresa Montez


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From r.oostenveld at FCDONDERS.RU.NL  Thu Jun 22 09:25:56 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 22 Jun 2006 09:25:56 +0200
Subject: Statistics for coherence in a within-subject experiment
In-Reply-To: <000901c693b5$79d47c10$0200a8c0@laptop>
Message-ID: <THU.22.JUN.2006.092556.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Jurij

The parametric tests that you suggest are not implemented in  
FieldTrip. In the clusterrandanalysis function we use a randomization  
approach for statistical testing. It is a non-parametrical approach,  
and the test statistic consists of a parametrtical statistic per time- 
frequency-channel, which is clustered and summed over neighbouring  
timepoints/frequencies/channels. Not the single-sample statistic, but  
the clustersum is used for the statistical test, thereby increasing  
sensitivity and controlling for  multiple comparisons. The single  
sample (time-frequency-channel) statistic has to be chosen to match  
with the experimental design (e.g. F or F) and the randomization/ 
permutation of the data between the subjects and conditions has to be  
adequate (in your case you want to shuffle data between conditions  
but only within each subject). That determines the statistic to use.  
I suggest that you go over the clusterrandanalysis tutorial at
http://www2.ru.nl/fcdonders/fieldtrip/doku.php? 
id=fieldtrip:documentation:tutorial:clusterrandanalysis

best regards,
Robert


On 19 Jun 2006, at 17:31, Jurij Dreo wrote:

> Hello!
>
> Thank you for your answers. Here are my replies to them:
>
> To avoid any misunderstandings here is again a summary of my study  
> design
> - I have 11 subjects.
> - Each of them performed 6 tasks related to working memory.
> - Each subject performed anywehere from 25 to 60 repeats (trial) of  
> each condition (the standard number of trials per task was 30 - but  
> some subjects performed the entire experiment twice (ergo 60  
> potential trials) .... and in some some of their trials are  
> unusable - artifacts ... ergo 25 min number of possible trials)
>
> Given my study design I thought something like a one-way ANOVA for  
> correlated samples would be in order.
> (as I am comparing 6 conditions within-subjects as every subject  
> performed all sets)
>
>
> -----------------
> > In your case you have observed a "value" in 11 subjects, over 6
> > conditions. That value happens to be coherence, but could as well
> > have been something else. Since you have manipulated the conditions
> > with each subject, you can use a dependent-samples test: the  
> observed
> > values depend on the subject (an example of a dependent-samples test
> > is a paired-t test).
> -------------------
>
> I´m not sure what you are saying here.... I agree with the  
> dependent samples idea... but I cannot preform a t-test ... ie.  
> more of them as that would inflate my p-rate overall.
>
> I thought that I would first do an ANOVA and then something like  
> the Tukey HSD Test to cimpare individual conditions
>
> --------------------
> > If the number of trials varies between subjects and/or sessions, it
> > will be preferable to transform your coherence values to z-scores
> > manually prior to submitting the values to clusterrandanalysis.
> --------------------
> Yes I agree that would need to be done manually.
>
> -----------
> > Now about the 6 conditions, am I right that you have a 1x6 factorial
> > design, or is there more strucure in the design? Do you have a
> > specific hypothesis about the different conditions? If you only want
> > to reject the null-hypothesis "the observed value (coherence) is the
> > same (more accurately: stems from the same distribution) in all my 6
> > conditions", you would use an omnibus F-statistic, i.e.
> > 'depsamplesF'. It might be that your hypothesis is more specific, or
> > also in case you find an omnibus effect, then you would probably  
> want
> > to perform explicit tests between two subsets of your 6 conditions
> > using a 'depsamplesT' test.
> >
> ----------
>
> I want to contrast all conditions at once (f -test anova) AND also  
> each combination of conditions (say a post- ANOVA Q-test)
>
> But Im still not sure which statistic to use and even if the one I  
> use will be able to deal with the fact that I have a different  
> number of conditions per condition per subject
>
> As far as I understand it... we must use some kind of ANOVA here...  
> A simple "paired" t-test will not do... as we are comparing more  
> than 2 conditions at once and I do not want to inflate my p-rate.
>
> Thank you for your help!
>
> Regards,
> Jurij Dreo
>


From r.oostenveld at FCDONDERS.RU.NL  Thu Jun 22 09:31:10 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 22 Jun 2006 09:31:10 +0200
Subject: Missing minimumnormestimate etc
In-Reply-To: <006c01c69576$c1d13270$14b2a8c0@mirandola>
Message-ID: <THU.22.JUN.2006.093110.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Stefan,

The SOURCEANALYSIS function is used as wrapper for various
distributed or scanning inverse approaches, and DIPOLEFITTING is used
for underdetermined model fitting to the data. The only underlying
functions for SOURCEANALYSIS that are released on the ftp server are
the lcmv and the dics beamformer methods. The functions that you
refer to are implemented in our in-house version of FieldTrip but
have not been tested thouroughly. I can give you a pre-release if you
are willing to aid in the testing of those functions.

best regards,
Robert


On 21 Jun 2006, at 23:07, Stefan Rampp wrote:

> Hi everyone,
>
> I was just trying to do source localization of epilepsy MEG data
> using mne, however, it appears that some functions are missing:
> minimumnormestimate, music, loreta and rv are used in
> sourceanalysis.m, but I can't find the implementations (and neither
> can matlab). Do I need to download additional libraries/toolboxes?
>
> Thank you,
> Stefan Rampp.
> Epilepsycenter Erlangen
> Germany
>


From r.oostenveld at FCDONDERS.RU.NL  Thu Jun 22 09:40:31 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 22 Jun 2006 09:40:31 +0200
Subject: channel location file to import planar to EEGLAB
In-Reply-To: <28FF6B8D22C94B44A55E4E1325A94AF2348059@vumc-mb02.vumc.nl>
Message-ID: <THU.22.JUN.2006.094031.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Theresa

On 22 Jun 2006, at 1:27, Montez, T. wrote:
> I am using EEGLAB to compute ICA of CTF 151 channels data.
>
> I used to read the data in EEGLAB directly from the CTF format,
> but some components are affected by the bad channels.
The bad channels do not reflect a linear mixture of underlying
sources, therefore you should remove them prior to ICA. You should
also remove all trials containing anomalous artifacts.
> Since removing the bad channels will reduce the number of components
> and will give problems later at the planar transformation;
> I tried using megrepair first and then importing the matlab array
> of data.trial{1}. I use the channel locations of a previous
> dataset opened from the CTF format.
MEGREPAIR uses a nearest-neighbour approach for fixing the missing
channels. The "repaired" channels are linear combinations (i.e. a
linear mixture) of the neighbours and hence do not add any
information (i.e. components) to the data, doing ICA on the repaired
dataset does not give you all 151 components.
> - I still get some components reflecting the bad channels,
> should I increase the cfg.neighbourdist?
> (I was using the default of 4 cm).
>
> - To import the data after the planar transformation I need
> a channel location file for the dH and dV pairs,
> can you help me with that?
The planar transformation in MEGPLANAR also results in a linear
estimation of the horizontal and vertical gradients, i.e. if you
start with 151 axial channels and you do MEGPLANAR, you will have 302
planar channels, but the dimensionality of that data will still be
151. That means that ICA on the 302-channel planar data will result
in a maximum of 151 components.

I suggest to do the ICA on the axial data with the bad channels
removed. Subsequently you can switch from EEGLAB to FieldTrip and
compute the planar representation of the ICA components using the
MEGPLANAR function (I am not sure whether megplanar knows how to deal
with ICA data, but it is easy to convert the ICA data into something
that resembles an average ERF or alternatively to add support for the
ICA data in megplanar).

best regards,
Robert


From srampp at TISCALI.DE  Thu Jun 22 10:43:01 2006
From: srampp at TISCALI.DE (Stefan Rampp)
Date: Thu, 22 Jun 2006 10:43:01 +0200
Subject: Missing minimumnormestimate etc
Message-ID: <THU.22.JUN.2006.104301.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Robert,

Thank you for the fast answer. Since I'm interested in comparing various
methods, I'd greatly appreciate a pre-release version. And of course I could
contribute to Fieldtrip as a betatester for these functions like that.

Sincerely,
Stefan Rampp
Epilepsycenter Erlangen
Germany


----- Original Message -----
From: "Robert Oostenveld" <r.oostenveld at FCDONDERS.RU.NL>
To: <FIELDTRIP at NIC.SURFNET.NL>
Sent: Thursday, June 22, 2006 9:31 AM
Subject: Re: [FIELDTRIP] Missing minimumnormestimate etc


> Dear Stefan,
>
> The SOURCEANALYSIS function is used as wrapper for various  distributed or
> scanning inverse approaches, and DIPOLEFITTING is used  for
> underdetermined model fitting to the data. The only underlying  functions
> for SOURCEANALYSIS that are released on the ftp server are  the lcmv and
> the dics beamformer methods. The functions that you  refer to are
> implemented in our in-house version of FieldTrip but  have not been tested
> thouroughly. I can give you a pre-release if you  are willing to aid in
> the testing of those functions.
>
> best regards,
> Robert
>
>
> On 21 Jun 2006, at 23:07, Stefan Rampp wrote:
>
>> Hi everyone,
>>
>> I was just trying to do source localization of epilepsy MEG data  using
>> mne, however, it appears that some functions are missing:
>> minimumnormestimate, music, loreta and rv are used in  sourceanalysis.m,
>> but I can't find the implementations (and neither  can matlab). Do I need
>> to download additional libraries/toolboxes?
>>
>> Thank you,
>> Stefan Rampp.
>> Epilepsycenter Erlangen
>> Germany
>>


From MZvyagintsev at UKAACHEN.DE  Thu Jun 22 18:08:43 2006
From: MZvyagintsev at UKAACHEN.DE (Mikhail Zvyagintsev)
Date: Thu, 22 Jun 2006 18:08:43 +0200
Subject: Missing minimumnormestimate etc
In-Reply-To: <21EE19CF-BE60-4719-BC9E-C1F3737F26B5@fcdonders.ru.nl>
Message-ID: <THU.22.JUN.2006.180843.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Robert,

Would be also nice to have an implementaion of LORETA approach for
source analysis from your in-house software. I would appreciate if you
could send it to me as well.

Best regards,

Mikhail Zvyagintsev

MZvyagintsev at UKAachen.de



Robert Oostenveld wrote:

> Dear Stefan,
>
> The SOURCEANALYSIS function is used as wrapper for various
> distributed or scanning inverse approaches, and DIPOLEFITTING is used
> for underdetermined model fitting to the data. The only underlying
> functions for SOURCEANALYSIS that are released on the ftp server are
> the lcmv and the dics beamformer methods. The functions that you
> refer to are implemented in our in-house version of FieldTrip but
> have not been tested thouroughly. I can give you a pre-release if you
> are willing to aid in the testing of those functions.
>
> best regards,
> Robert


From muthuraman10 at HOTMAIL.COM  Fri Jun 23 12:54:57 2006
From: muthuraman10 at HOTMAIL.COM (Muthuraman Muthuraman)
Date: Fri, 23 Jun 2006 10:54:57 +0000
Subject: query on CTF software!!!
Message-ID: <FRI.23.JUN.2006.105457.0000.FIELDTRIP@NIC.SURFNET.NL>

Hello

For the Beamformer source analysis, do we need the CTF software
because when i am trying out the tutorial in beamforming

Matlab
>>freq=19.0;
>>Ncycles=10;
>>dTimeWin=Ncycles/freq;
>>cfg=[];
>>cfg.dataset='Subject01.ds';
>>cfg.channel={'MEG' 'STIM'};
>>cfg.trialdef.excludeConditions={'BAD'};
>>cfg.trialdef.includeTrigger=3;
>>cfg.trialdef.prestim=0.1+dTimeWin;
>>cfg.trialdef.poststim=-0.1;
>>datapre=preprocessing(cfg);

CTF_READ_RES4 [v  1.12]
....done (  0.67 sec)

i get the error

??? Error using ==> read_fcdc_header
could not read CTF res4 header file

Error in ==> preprocessing at 263
hdr = read_fcdc_header(cfg.headerfile);


with regards
muthu


From r.oostenveld at FCDONDERS.RU.NL  Fri Jun 23 15:23:22 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 23 Jun 2006 15:23:22 +0200
Subject: query on CTF software!!!
In-Reply-To: <BAY121-F290E321E30CF71939F2A00CE7A0@phx.gbl>
Message-ID: <FRI.23.JUN.2006.152322.0200.FIELDTRIP@NIC.SURFNET.NL>

dear Muthuraman

On 23 Jun 2006, at 12:54, Muthuraman Muthuraman wrote:
> For the Beamformer source analysis, do we need the CTF software
> because when i am trying out the tutorial in beamforming

You do not need the ctf software to follow the tutorial. The tutorial
is based however on a ctf MEG dataset.

> CTF_READ_RES4 [v  1.12]
> ....done (  0.67 sec)
>
> i get the error
>
> ??? Error using ==> read_fcdc_header
> could not read CTF res4 header file
>
> Error in ==> preprocessing at 263
> hdr = read_fcdc_header(cfg.headerfile);

Based on your error I suspect that matlab/fieldtrip cannot find the
dataset that you are trying to analyze, or that you matlab path is
incorrect. The function "CTF_READ_RES4" is not supposed to be called
(it is part of the NIH ctf import routines, e.g. used in EEGLAB),
since the default private/read_ctf_res4.m function can deal with the
tutorial dataset just fine. Please look into the code of
read_fcdc_header (using the matlab debugger) to figure out what your
exact problem is.

best
Robert


From r.oostenveld at FCDONDERS.RU.NL  Fri Jun 23 15:28:03 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 23 Jun 2006 15:28:03 +0200
Subject: Missing minimumnormestimate etc
In-Reply-To: <449AC08B.4080202@UKAachen.de>
Message-ID: <FRI.23.JUN.2006.152803.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Mikhail

My loreta implementation still has some problems and is not 100%
correct. I first want to fix it before I release it. If you know how
to work with KEY-LORETA (the software from Pasqual Marqui) and could
compare the two implementations, you could get a pre-release version
and help fix the bugs.

Robert


On 22 Jun 2006, at 18:08, Mikhail Zvyagintsev wrote:

> Dear Robert,
>
> Would be also nice to have an implementaion of LORETA approach for
> source analysis from your in-house software. I would appreciate if
> you could send it to me as well.
>
> Best regards,
>
> Mikhail Zvyagintsev
>
> MZvyagintsev at UKAachen.de


From MZvyagintsev at UKAACHEN.DE  Mon Jun 26 13:15:34 2006
From: MZvyagintsev at UKAACHEN.DE (Mikhail Zvyagintsev)
Date: Mon, 26 Jun 2006 13:15:34 +0200
Subject: Missing minimumnormestimate etc
In-Reply-To: <29758FB9-8B0E-4C41-8067-BF39410560A0@fcdonders.ru.nl>
Message-ID: <MON.26.JUN.2006.131534.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Robert,
Thank you for this encouragement. I was working with LORETA from Pasqual
Marqui only with EEG data. I hope it will help me to be useful with
fixing bugs.
Kindly,
Mikhail.

MZvyagintsev at UKAachen.de

Robert Oostenveld wrote:

> Dear Mikhail
>
> My loreta implementation still has some problems and is not 100%
> correct. I first want to fix it before I release it. If you know how
> to work with KEY-LORETA (the software from Pasqual Marqui) and could
> compare the two implementations, you could get a pre-release version
> and help fix the bugs.
>
> Robert


From esther.meeuwissen at FCDONDERS.RU.NL  Mon Jun 26 15:04:27 2006
From: esther.meeuwissen at FCDONDERS.RU.NL (Esther Meeuwissen)
Date: Mon, 26 Jun 2006 15:04:27 +0200
Subject: artifact rejection
Message-ID: <MON.26.JUN.2006.150427.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi all,

A few weeks ago I started to work with Fieldtrip. I would like use it to 
analyze EEG data.

I have a question concerning preprocessing of EEG data. I would like to do 
a artifact rejection during preprocessing partly using the functions in 
fieldtrip (detection and rejection of  muscle artifacts) and partly 
reading in artifact markers that are exported out of brain vision analyser 
(I used the raw data inspector to detect eye blinks).

I used the following script:

EEGchans = 
{'Fp2', 'F7', 'F3', 'Fz', 'F4', 'F8', 'FC5', 'FC1', 'FCz', 'FC2', 'FC6', 'T
7', 'C3', 'Cz', 'C4', 'T8', 'CP5', 'CP1', 'CP2', 'CP6', 'TP10', 'P7', 'P3',
 'Pz', 'P4', 'P8', 'O1', 'O2'};
EOGchans = {'VB','HL', 'HR', 'VO'};

files = {'GOS10B'...
    'GOS11C'};
for subject=1:2,
   
% Parameters
cfg = [];
cfg.datafile            = strcat('',files{subject},'.eeg');
cfg.headerfile          = strcat('',files{subject},'.vhdr');
cfg.trialdef.trgfile    = strcat('',files{subject},'.vmrk');
cfg.rejectfile          = strcat('',files{subject},'_Reject.Marker');
cfg.icaresultfile       = strcat('',files{subject},'.ica');
cfg.outdatafile         = strcat('',files{subject},'.mat');

cfg.channel    = {'all'};
cfg.padding    = 1.5;
cfg.bpfilter   = 'yes';
cfg.bpfreq     = [0.3 30];
cfg.blc        = 'yes';
cfg.blcwindow  = [-0.1 0.0];

% EEG options
cfg.reref      = 'no';
cfg.implicitref = [];
cfg.refchannel  = {};

% Trial definition
cfg.trialdef.stim = [1 2 3 4];   
cfg.trialdef.prestim    = 0.200;
cfg.trialdef.poststim   = 1.000;

% Artifact options (preprocessing)
cfg.artfctdef.reject            = 'complete';
cfg.artfctdef.muscle.sgn        = EEGchans;
cfg.artfctdef.muscle.feedback   = 'no';
cfg.artfctdef.muscle.cutoff     = 15;

% Do preprocessing
cfg = definetrial(cfg);
cfg = artifact_muscle(cfg)
cfg = rejectartifact(cfg);
data = preprocessing(cfg);

%Save intermediate result
save(cfg.outdatafile,'data');
clear data;
pack;
end;

and get the following error message:

 Error using ==> horzcat
CAT arguments dimensions are not consistent.

Error in ==> rejectartifact at 182
    cfg.artfctdef.type = [{'file'} cfg.artfctdef.type];

Error in ==> preprocessing at 317
[cfg] = rejectartifact(cfg);

Error in ==> preproesther1 at 45
data = preprocessing(cfg);

By trying to make it work I figured out that it is possible to do both the 
artifact rejection parts separately using (parts of) the script above but  
(Fieldtrip wants to combine two matrices to 1 matrix and that is what goes 
wrong). Does anyone know how (/whether) it is possible to do a artifact 
detection/rejection in Fieldtrip partly using functions of Fieldtrip 
itself and partly read markers of EEG parts containing a artifact (the 
file made by brain vision analyzer)?

Thanks in advance for the answer(s)!
Esther Meeuwissen


From r.oostenveld at FCDONDERS.RU.NL  Mon Jun 26 17:17:49 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Mon, 26 Jun 2006 17:17:49 +0200
Subject: artifact rejection
In-Reply-To: <LISTSERV%200606261504275190.1F7B@NIC.SURFNET.NL>
Message-ID: <MON.26.JUN.2006.171749.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Esther,

On 26 Jun 2006, at 15:04, Esther Meeuwissen wrote:
> and get the following error message:
>
>  Error using ==> horzcat
> CAT arguments dimensions are not consistent.
>
> Error in ==> rejectartifact at 182
>     cfg.artfctdef.type = [{'file'} cfg.artfctdef.type];

I suspect here that cfg.artfctdef.type is a cell-array with strings
represented as a vertical cell-vector, and that line 182 tries to
combine it with something that Matlab treats as horizontal cell-
vector. It is unclear to me why it does that, since the
cfg.artfctdef.type is built up internally (you did not explicitely
specify it).

> Error in ==> preprocessing at 317
> [cfg] = rejectartifact(cfg);
>
> Error in ==> preproesther1 at 45
> data = preprocessing(cfg);
>
> By trying to make it work I figured out that it is possible to do
> both the
> artifact rejection parts separately using (parts of) the script
> above but
> (Fieldtrip wants to combine two matrices to 1 matrix and that is
> what goes
> wrong). Does anyone know how (/whether) it is possible to do a
> artifact
> detection/rejection in Fieldtrip partly using functions of Fieldtrip
> itself and partly read markers of EEG parts containing a artifact (the
> file made by brain vision analyzer)?

I have tried replicating your problem (with the data that I found on /
home/electromag/estmee/GOs/analyses/datagoed), but did not encounter
any problems up to the definetrial, artifatc_muscle and
rejectartifact. However, the problem comes only in when preprocessing
is called. For backward compatibility with other peoples old scripts,
preprocessing is also calling definetrial and rejhectartifact, and
rejectartifact seems confused by being called twice.

I made a small change to rejectartifact that hopefully fixes the
problem. The updated version is on home/common now and will be on the
ftp this evening.

best regards,
Robert


From Esther.Meeuwissen at FCDONDERS.RU.NL  Tue Jun 27 09:05:21 2006
From: Esther.Meeuwissen at FCDONDERS.RU.NL (Esther Meeuwissen)
Date: Tue, 27 Jun 2006 09:05:21 +0200
Subject: artifact rejection
In-Reply-To: <442FC113-07E9-4479-9237-6D20F1D026C8@fcdonders.ru.nl>
Message-ID: <TUE.27.JUN.2006.090521.0200.FIELDTRIP@NIC.SURFNET.NL>

Robert Oostenveld wrote:
> Hi Esther,
>
> On 26 Jun 2006, at 15:04, Esther Meeuwissen wrote:
>> and get the following error message:
>>
>>  Error using ==> horzcat
>> CAT arguments dimensions are not consistent.
>>
>> Error in ==> rejectartifact at 182
>>     cfg.artfctdef.type = [{'file'} cfg.artfctdef.type];
>
> I suspect here that cfg.artfctdef.type is a cell-array with strings
> represented as a vertical cell-vector, and that line 182 tries to
> combine it with something that Matlab treats as horizontal
> cell-vector. It is unclear to me why it does that, since the
> cfg.artfctdef.type is built up internally (you did not explicitely
> specify it).
>
>> Error in ==> preprocessing at 317
>> [cfg] = rejectartifact(cfg);
>>
>> Error in ==> preproesther1 at 45
>> data = preprocessing(cfg);
>>
>> By trying to make it work I figured out that it is possible to do
>> both the
>> artifact rejection parts separately using (parts of) the script above
>> but
>> (Fieldtrip wants to combine two matrices to 1 matrix and that is what
>> goes
>> wrong). Does anyone know how (/whether) it is possible to do a artifact
>> detection/rejection in Fieldtrip partly using functions of Fieldtrip
>> itself and partly read markers of EEG parts containing a artifact (the
>> file made by brain vision analyzer)?
>
> I have tried replicating your problem (with the data that I found on
> /home/electromag/estmee/GOs/analyses/datagoed), but did not encounter
> any problems up to the definetrial, artifatc_muscle and
> rejectartifact. However, the problem comes only in when preprocessing
> is called. For backward compatibility with other peoples old scripts,
> preprocessing is also calling definetrial and rejhectartifact, and
> rejectartifact seems confused by being called twice.
>
> I made a small change to rejectartifact that hopefully fixes the
> problem. The updated version is on home/common now and will be on the
> ftp this evening.
>
> best regards,
> Robert
>



From cgra05 at HST.AUC.DK  Thu Jun  1 12:34:31 2006
From: cgra05 at HST.AUC.DK (Carina Graversen)
Date: Thu, 1 Jun 2006 12:34:31 +0200
Subject: SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG
 data ???
In-Reply-To: <003e01c68493$c1b918f0$642dae83@fcdonders.nl>
Message-ID: <THU.1.JUN.2006.123431.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Ingrid,

OH - sorry, I didn't notice the question had already been asked on the
webpage.

However, I still couldn't find the answer on how to create the values for
column 2 and 3, since it says at the webpage "The 2nd and 3rd are the
X-position and Y-position". However, when I generate the layout file from
Neuroscan I get some values for the X and Y coordinates, that are very
different from yours, and the plot ends up in a big mess (see the attached
file).

So I was wondering if you have any idea of how to generate the X- and
Y-positions from Neuroscan ???
(I have attached the generated layout-file from Neuroscan, in case that
helps you. This one is named test128_neuroscan.lay)

We were also wondering about the figure you e-mailed from our data, all
channels appeared to be blue with a green cone (and then some frequency
contributions in some channels). Is it because of some settings not edited
correct, because we would have expected something like in the
documentation - like figure 2 at the "Time-frequency Analysis Using
Multitapers and Wavelets" page.

>>From the test128_neuroscan.lay I tried to create the layout file
test128_fieldtrip.lay, and got the plot shown in figure
test128_fieldtrip.png



Best regards,
Carina Graversen





-----Oprindelig meddelelse-----
Fra: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]Pa vegne
af Ingrid Nieuwenhuis
Sendt: 31. maj 2006 10:23
Til: FIELDTRIP at NIC.SURFNET.NL
Emne: Re: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel
Neuroscan EEG data ???


Hi Carina,

If you look at the FieldTrip page -> documentation -> frequently asked
questions you can find the question (and answer):

What is the format of the layout file, which is used for plotting?

...The 4th and 5th column specify the with and height of the subplot that
will be made in multiplotER and multiplotTFR....

So the two columns with the same value for all channels are those columns.

Bests,
Ingrid

-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Carina Graversen
Sent: Wednesday, May 31, 2006 10:58 AM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan
EEG data ???

Hi Ingrid.

Thanks a lot.

I have tried to generate my own layout file in Neuroscan, but unfortunately
it doesn't work. So I was wondering if you can tell me the format of the
layout-file, because when I look at your file, 2 of the columns contain the
same value for all channels.

I have tried to generate for both cartesian and polor, but none of them
matches. In the generated file I get the format:
<display page><channel number><pos x0><pos y0><pos x1><pos y1>

Can I change my input configuration to either use this format, or how should
I change the format of the layout file ???

Thanks in advance  :o)

/Carina





-----Oprindelig meddelelse-----
Fra: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]Pa vegne
af Ingrid Nieuwenhuis
Sendt: 26. maj 2006 13:29
Til: FIELDTRIP at NIC.SURFNET.NL
Emne: Re: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG data
???


Hi Carina,

Thanks for sending me the data. Indeed the biosemi 128ch layout doesn't
correspond to your layout. You have 128 channels labeled from 1 to 128. If
you open biosemi128.lay in a text-editor you can see that this layout file
has 150 channels labeled from A1 to P7. The labels in your data
(TFRmult.label) and the labels in the layout file don't match, that's why
you got an empty figure (I'll add an error in the plot function, so that
when no labels match you'll get an error message in the future).

So what you have to do now is to make your own layout file that matches the
data; with the correct x and y coordinates of the 128 channels and the same
label names as in your data. Just as an illustration I attached an adapted
version of the biosemi128.lay file, with only the first 128 channels, and
labels 1 to 128, just as in your data. With the following configuration:

cfg8 = [];
cfg8.baseline   = [0 0.1];
cfg8.xlim       = [0 0.3]
cfg8.ylim       = [15 29];
cfg8.zlim       = [-100 100];
cfg8.showlabels = 'yes';
cfg8.layout    = 'testlay128.lay';

I got the attached figure from your data.

Good luck,
Ingrid



-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Robert Oostenveld
Sent: Wednesday, May 24, 2006 8:57 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG data ???

Hi Carina

Are you sure that the biosemi 128ch layout corresponds with your
electrode layout? Open the layout file in a tetx editor and look at
http://www2.ru.nl/fcdonders/fieldtrip/doku.php?
id=fieldtrip:documentation:frequently_asked_questions#what_is_the_format
_of_the_layout_file_which_is_used_for_plotting

I suggest that you try the elec1010.lay or elec1005.lay, or even
better, that you construct your own layout file corresponding with
your own electrode locations.

Robert


On 24 May 2006, at 12:29, Carina Graversen wrote:

> Hi.
>
> I'm trying to use the Fieldtrip program to create a wavelet plot of
> my EEG
> data.
>
> I have used it previously for 64 channel recordings, but now I'm
> working
> with 128 channels of data, which is causing me some problems. The
> only thing
> I have changed is the command:
> cfg8.layout    = 'biosemi128.lay';
>
> But now the figure only outputs a grey page with no Time-Frequency
> distributions at all.
>
> Can anyone tell me what I'm doing wrong - below is a complete list
> of all
> the commands I use  :o).
>
> Best Regards,
> Carina Graversen
>
>
>
>
> %
> **********************************************************************
> ***
> % EVENTRELATEDAVERAGING
> %
> **********************************************************************
> ***
> cfg1 = [];                                                     % empty
> configuration
> cfg1.datafile                      = 'test128.eeg';            %
> 128 channel
> Neuroscan eeg file
> cfg1.headerfile                    = 'test128.eeg';
> cfg1.channel                       = 'all';
>
> dataFIC = preprocessing(cfg1);                                 %
> Preprocess!
>
> cfg2 = [];                                                     % empty
> configuration
>
> avgFIC = timelockanalysis(cfg2, dataFIC);
>
>
> % %
> **********************************************************************
> ***
> % % WAVELET
> % %
> **********************************************************************
> ***
> cfg7 = [];
> cfg7.output     = 'pow';
> cfg7.method     = 'wltconvol'
> cfg7.foi        = 1:2:30;
> cfg7.t_ftimwin  = 5./cfg7.foi;
> cfg7.tapsmofrq  = 0.4 *cfg7.foi;
> cfg7.toi        = 0:0.01:0.5;
>
> TFRmult = freqanalysis(cfg7, avgFIC);
>
> cfg8 = [];
> cfg8.baseline   = [-0.5 0.5];
> cfg8.xlim       = [0 0.5]
> cfg8.zlim       = [-3e-27 0.2];
> cfg8.showlabels = 'yes';
> cfg8.layout    = 'biosemi128.lay';
>
> multiplotTFR(cfg8, TFRmult);
>
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From r.oostenveld at FCDONDERS.RU.NL  Thu Jun  1 12:35:43 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 1 Jun 2006 12:35:43 +0200
Subject: Filtering
In-Reply-To: <000001c683f3$4e30cb30$90514484@dellgx240>
Message-ID: <THU.1.JUN.2006.123543.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Vladimir

On 30 May 2006, at 16:14, Vladimir Litvak wrote:
> As I understand, when I do filtering in preprocessing the filter is
> applied before the data is cut to epochs.

Not completely: a segment of data is read from file that contains the
trial (trl) plus the optional padding. That segment is filtered and
then the padding is thrown away. Eventual filter atrifacts at the
boundaries of the data segment that was read are in the padding and
thus would not affect the data of interest itself. If you apply
padding, the effect is the same as if you would have filtered the
complete data continuously.

> I now want to do some analysis where I want to filter after the
> epochs are cut out (because there are TMS deltas there and I don't
> want them to affect everything around them). Is there a simple way
> to filter epoched data in FT (other than by my own code)?

You can specify cfg.padding=0 in preprocessing and ensure that the
TMS pulse is not inside the trial definition. You can do
preprocessing without any options and then use timelockanalysis (with
keeptrials) on it. Timelockanalysis supports almost all options that
preprocessing has, i.e. all filtering and baselinecorection options,
but of course cannot do the padding. Those additional options are not
documented in timelockanalysis, but look in the code and you will
see  them. Doing it in timelockanalysis has the advantage that it is
easier to play around with filter settings (i.e. it is faster not
having to read the data every time). Also interesting to know perhaps
is that you can also apply timelockanalysis and its filtering to an
average, i.e. timelockanalysis will accept a timelock-structure as
input. So you can average in the first call to timelockanalysis, and
then throw that average into timelockanalysis a second time to see
the effect of the filter. In the latter case only the average is
filtered, i.e. it is very fast.

best
Robert


From ingrid.nieuwenhuis at FCDONDERS.RU.NL  Thu Jun  1 13:21:11 2006
From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis)
Date: Thu, 1 Jun 2006 13:21:11 +0200
Subject: SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG
 data ???
In-Reply-To: <LMELLGAMDIJKNDEFIMFHEECDCHAA.cgra05@hst.auc.dk>
Message-ID: <THU.1.JUN.2006.132111.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Carina,

The problem is that the width and height of the boxes (column 4 and 5) are
too big compared to your x and y coordinates. What multiplotTFR does is that
it plots the TFR boxes at the specified coordinates. The x and y coordinates
are between +/- 0 and 0.7 and the box width/height is 0.18	and 1.14, so
all the plots are plotted on top of each other. That's why it is a mess. So
you could use the x and y coordinates, but the boxes should be smaller, or
you can scale it al up.

What comes out of the plots is just what the data is. Probably depends on
your settings during the TFR analysis. The dark blue at the edges and bottom
are NaN's in the data.

Bests,
Ingrid



-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Carina Graversen
Sent: Thursday, June 01, 2006 12:35 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel
Neuroscan EEG data ???

Hi Ingrid,

OH - sorry, I didn't notice the question had already been asked on the
webpage.

However, I still couldn't find the answer on how to create the values for
column 2 and 3, since it says at the webpage "The 2nd and 3rd are the
X-position and Y-position". However, when I generate the layout file from
Neuroscan I get some values for the X and Y coordinates, that are very
different from yours, and the plot ends up in a big mess (see the attached
file).

So I was wondering if you have any idea of how to generate the X- and
Y-positions from Neuroscan ???
(I have attached the generated layout-file from Neuroscan, in case that
helps you. This one is named test128_neuroscan.lay)

We were also wondering about the figure you e-mailed from our data, all
channels appeared to be blue with a green cone (and then some frequency
contributions in some channels). Is it because of some settings not edited
correct, because we would have expected something like in the
documentation - like figure 2 at the "Time-frequency Analysis Using
Multitapers and Wavelets" page.

>>From the test128_neuroscan.lay I tried to create the layout file
test128_fieldtrip.lay, and got the plot shown in figure
test128_fieldtrip.png



Best regards,
Carina Graversen





-----Oprindelig meddelelse-----
Fra: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]Pa vegne
af Ingrid Nieuwenhuis
Sendt: 31. maj 2006 10:23
Til: FIELDTRIP at NIC.SURFNET.NL
Emne: Re: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel
Neuroscan EEG data ???


Hi Carina,

If you look at the FieldTrip page -> documentation -> frequently asked
questions you can find the question (and answer):

What is the format of the layout file, which is used for plotting?

...The 4th and 5th column specify the with and height of the subplot that
will be made in multiplotER and multiplotTFR....

So the two columns with the same value for all channels are those columns.

Bests,
Ingrid

-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Carina Graversen
Sent: Wednesday, May 31, 2006 10:58 AM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan
EEG data ???

Hi Ingrid.

Thanks a lot.

I have tried to generate my own layout file in Neuroscan, but unfortunately
it doesn't work. So I was wondering if you can tell me the format of the
layout-file, because when I look at your file, 2 of the columns contain the
same value for all channels.

I have tried to generate for both cartesian and polor, but none of them
matches. In the generated file I get the format:
<display page><channel number><pos x0><pos y0><pos x1><pos y1>

Can I change my input configuration to either use this format, or how should
I change the format of the layout file ???

Thanks in advance  :o)

/Carina





-----Oprindelig meddelelse-----
Fra: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]Pa vegne
af Ingrid Nieuwenhuis
Sendt: 26. maj 2006 13:29
Til: FIELDTRIP at NIC.SURFNET.NL
Emne: Re: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG data
???


Hi Carina,

Thanks for sending me the data. Indeed the biosemi 128ch layout doesn't
correspond to your layout. You have 128 channels labeled from 1 to 128. If
you open biosemi128.lay in a text-editor you can see that this layout file
has 150 channels labeled from A1 to P7. The labels in your data
(TFRmult.label) and the labels in the layout file don't match, that's why
you got an empty figure (I'll add an error in the plot function, so that
when no labels match you'll get an error message in the future).

So what you have to do now is to make your own layout file that matches the
data; with the correct x and y coordinates of the 128 channels and the same
label names as in your data. Just as an illustration I attached an adapted
version of the biosemi128.lay file, with only the first 128 channels, and
labels 1 to 128, just as in your data. With the following configuration:

cfg8 = [];
cfg8.baseline   = [0 0.1];
cfg8.xlim       = [0 0.3]
cfg8.ylim       = [15 29];
cfg8.zlim       = [-100 100];
cfg8.showlabels = 'yes';
cfg8.layout    = 'testlay128.lay';

I got the attached figure from your data.

Good luck,
Ingrid



-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Robert Oostenveld
Sent: Wednesday, May 24, 2006 8:57 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG data ???

Hi Carina

Are you sure that the biosemi 128ch layout corresponds with your
electrode layout? Open the layout file in a tetx editor and look at
http://www2.ru.nl/fcdonders/fieldtrip/doku.php?
id=fieldtrip:documentation:frequently_asked_questions#what_is_the_format
_of_the_layout_file_which_is_used_for_plotting

I suggest that you try the elec1010.lay or elec1005.lay, or even
better, that you construct your own layout file corresponding with
your own electrode locations.

Robert


On 24 May 2006, at 12:29, Carina Graversen wrote:

> Hi.
>
> I'm trying to use the Fieldtrip program to create a wavelet plot of
> my EEG
> data.
>
> I have used it previously for 64 channel recordings, but now I'm
> working
> with 128 channels of data, which is causing me some problems. The
> only thing
> I have changed is the command:
> cfg8.layout    = 'biosemi128.lay';
>
> But now the figure only outputs a grey page with no Time-Frequency
> distributions at all.
>
> Can anyone tell me what I'm doing wrong - below is a complete list
> of all
> the commands I use  :o).
>
> Best Regards,
> Carina Graversen
>
>
>
>
> %
> **********************************************************************
> ***
> % EVENTRELATEDAVERAGING
> %
> **********************************************************************
> ***
> cfg1 = [];                                                     % empty
> configuration
> cfg1.datafile                      = 'test128.eeg';            %
> 128 channel
> Neuroscan eeg file
> cfg1.headerfile                    = 'test128.eeg';
> cfg1.channel                       = 'all';
>
> dataFIC = preprocessing(cfg1);                                 %
> Preprocess!
>
> cfg2 = [];                                                     % empty
> configuration
>
> avgFIC = timelockanalysis(cfg2, dataFIC);
>
>
> % %
> **********************************************************************
> ***
> % % WAVELET
> % %
> **********************************************************************
> ***
> cfg7 = [];
> cfg7.output     = 'pow';
> cfg7.method     = 'wltconvol'
> cfg7.foi        = 1:2:30;
> cfg7.t_ftimwin  = 5./cfg7.foi;
> cfg7.tapsmofrq  = 0.4 *cfg7.foi;
> cfg7.toi        = 0:0.01:0.5;
>
> TFRmult = freqanalysis(cfg7, avgFIC);
>
> cfg8 = [];
> cfg8.baseline   = [-0.5 0.5];
> cfg8.xlim       = [0 0.5]
> cfg8.zlim       = [-3e-27 0.2];
> cfg8.showlabels = 'yes';
> cfg8.layout    = 'biosemi128.lay';
>
> multiplotTFR(cfg8, TFRmult);
>


From r.oostenveld at FCDONDERS.RU.NL  Thu Jun  1 13:51:02 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 1 Jun 2006 13:51:02 +0200
Subject: SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG
 data ???
In-Reply-To: <LMELLGAMDIJKNDEFIMFHEECDCHAA.cgra05@hst.auc.dk>
Message-ID: <THU.1.JUN.2006.135102.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Carina,

Please take attached "layoutplot" function and copy it into the
fieldtrip directory. Then do

 >> cfg.layout = 'CTF151.lay'
cfg =
     layout: 'CTF151.lay'

 >> layoutplot(cfg)
reading layout from file CTF151.lay

and you will get the attached figure for the 151 channel CTF system.
Then try plotting the other layouts (the *.lay files) and your own
layout, and modify the values in your own layout file (in a text
editor) untill you like what you see.

Robert

PS when I was looking at the other layouts, I noticed that the
elec1020, elec1010 and elec1005 layouts supplied with fieldtrip are
not optimal, since they also have overlapping boxes.

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From r.oostenveld at FCDONDERS.RU.NL  Thu Jun  1 13:58:48 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 1 Jun 2006 13:58:48 +0200
Subject: query on coherence source analysis
In-Reply-To: <BAY12-F10440EA05E5791B6BF0425CE9D0@phx.gbl>
Message-ID: <THU.1.JUN.2006.135848.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Muthuraman

I have not been able to reproduce your error. I suggest that you get
the latest version of FieldTrip from our FTP server and try again.

best egards,
Robert

PS this is the test script I used. It uses some simulated data, which
again uses a MEG gradiometer definition and a head model from the
tutorial data.


-----------------
% read some data that is required to simulate MEG data, i.e. volume
model,
% sensor positions and MRI (optional, only for plotting)
vol  = read_ctf_hdm('Subject01.hdm');
hdr  = read_fcdc_header('Subject01.ds/Subject01.res4');
grad = hdr.grad;

% construct the simulated MEG data for condition A ("active")
cfg               = [];
cfg.vol           = vol;
cfg.grad          = grad;
cfg.fsample       = 300;
cfg.ntrials       = 2;
cfg.triallength   = 1;
cfg.dip.pos       = [0 7 8];
cfg.dip.mom       = [1 0 0];
cfg.dip.signal    = sin(2*pi*10*(1:cfg.fsample)./cfg.fsample);
cfg.absnoise      = 1e-8;
data = dipolesimulation(cfg);

% add the source signal as fake EMG channel
for i=1:cfg.ntrials
   data.trial{i}(end+1,:) = cfg.dip.signal + randn(size
(cfg.dip.signal));
end
data.label{end+1} = 'EMG';

cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'MEG' 'EMG'},data.label);
cfg.channelcmb={'MEG' 'EMG'};
freq=freqanalysis(cfg,data);





From olga at GRAPHICMIND.INFO  Sat Jun  3 12:45:41 2006
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Sat, 3 Jun 2006 14:45:41 +0400
Subject: deleting two EOG channale from data-stucture
Message-ID: <SAT.3.JUN.2006.144541.0400.FIELDTRIP@NIC.SURFNET.NL>

Dear list members,
I would like to delete two channels from my data. How is it better to do this?
Best Regards,
Olga
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From olga at GRAPHICMIND.INFO  Sat Jun  3 14:16:57 2006
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Sat, 3 Jun 2006 16:16:57 +0400
Subject: and clusterrandomization
Message-ID: <SAT.3.JUN.2006.161657.0400.FIELDTRIP@NIC.SURFNET.NL>

Thank you very much, Eric!
That was an inconsistency in the loci of EOG channels between subjects. Now
I corrected it: HEOG and VEOG data are still presented in the data
structure, but do not have the location (pnt 0 0 0). Is it OK? The results
looks as what I excpected.
Best Regards,
Olga.

----- Original Message -----
From: "Eric Maris" <maris at NICI.RU.NL>
To: <FIELDTRIP at NIC.SURFNET.NL>
Sent: Friday, May 26, 2006 5:35 PM
Subject: Re: [FIELDTRIP] and clusterrandomization


> Dear Olga,
>
>
> But the problems is still in my clusterrandomization.
> Could the fact that the order of the channel in the file (C_vc11.label) is
> not the same as in the C_vc11.elec.label influences the result of
> clusterrandomization (I do not have my neigbouring channel file)?
>
>
> That should not matter. However, the labels in your data structure (.label
> in the output of timelockgrandaverage) should exactly match the labels in
> the elec-structure. If that is OK, then something might have gone wrong
> with the combination of the data of the different subjects. Do they all
> have the same elec-structure? If the same physical channel has different
> labels for different subjects, then this may create inconsistencies
> between EEGlab and Fieldtrip. For Fieldtrip, channels that have the same
> label are assumed to be physically identical, even if they are in
> different positions in the data structure. This is only a guess, of
> course.
>
>
> kind regards,
>
> Eric Maris
>
>
>
>
>
>
>
>
>
> Best Regards,
> Olga.
>  ----- Original Message -----
>  From: Ingrid Nieuwenhuis
>  To: FIELDTRIP at NIC.SURFNET.NL
>  Sent: Wednesday, May 24, 2006 8:45 PM
>  Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>
>
>  Hi Olga,
>
>
>
>  About the z-param:
>
>  This is the field that contains the data to be plotted; for instance
> 'avg', 'powspctrm' or 'cohspctrm'. Normally the function looks in your
> data.dimord to find out which z-param to use. To make the function work
> you could give cfg.zparam = 'avg' (for instance if you want to plot an
> ERF/ERP). But if you could send me what the dimord field of the data that
> you want to plot is, I could look why the plot functions don't extract the
> correct zparam themselves.
>
>
>
>  About the timelockgranaveraging: I also think it should be the same. I
> have no idea what it could be.
>
>
>
>  Good luck,
>
>  Ingrid Nieuwenhuis
>
>
>
>
> ------------------------------------------------------------------------------
>
>  From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf Of Olga Sysoeva
>  Sent: Wednesday, May 24, 2006 5:44 PM
>  To: FIELDTRIP at NIC.SURFNET.NL
>  Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>
>
>
>  Dear List member,
>
>
>
>  Sorry for such dull questions but,
>
>  I am again facing the new problems with Fieldtrip, although did not solve
> some previous one (still can not singleplot and multiplot anything 'cause
> of "unknown zparam field".
>
>
>
>  OK, about new one :-)
>
>
>
>  It seems that I did not use write the timelockgranaveraging.
>
>
>
>   The problem must be here, when I made grand averaging of all my 11
> subject
>   data
>
>                    cfg =[];
>                     cfg.keepindividual = 'yes'
>                     C_vc11  =
>
> timelockgrandaverage(cfg,vc_c_avg1,vc_c_avg2,vc_c_avg3,vc_c_avg4,vc_c_avg5,
> vc_c_avg6,vc_c_avg7,vc_c_avg8,vc_c_avg9,vc_c_avg10,vc_c_avg11 );
>
>  As I understand the
>
>  vc_c_avg11.avg([9],[43]) should be similar with C_vc11.individual ([11],
> [9], [43])
>  But it is not.
>  What can it be?
>
>  Best Regards,
>
>  Olga.
>
>
>
>
>
>    ----- Original Message -----
>
>    From: Olga Sysoeva
>
>    To: FIELDTRIP at NIC.SURFNET.NL
>
>    Sent: Saturday, May 13, 2006 4:34 PM
>
>    Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>
>
>
>    Thank you very much, Lilla!
>
>    Now I knwo what to do but faced the problem with " unknown zparam
> field" when ploting the results. Unfortunatly cfg.zparam does not
> discribed in help file...
>
>    Best Regards, Olga
>
>      ----- Original Message -----
>
>      From: Lilla Magyari
>
>      To: FIELDTRIP at NIC.SURFNET.NL
>
>      Sent: Saturday, May 13, 2006 3:11 PM
>
>      Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data
> within-subject
>
>
>
>      Dear Olga,
>
>
>
>      I am just studying time-frequency analysis but I have done already on
> my data, so perhaps I can help you.
>
>      First, yes, you have to do freqanalysis on the preprocessed data of
> the individual subjects for all conditions that you want to compare (i.e.
> the input for this function contains all trials from one subject in one
> condition.) And it is also important that the other input for this
> function is the cfg where for example, in the cfg.method you have to
> specify what kind of time-frequency analysis you want to use. (You have to
> write 'wltconvol' for wavelet transformation and 'mltconvol' for
> multitaper analysis.)
>
>      When you use freqanalysis as output you can get TFR for one subject
> in one condition (but it is also possible to keep the information for the
> individual trials of the condition by specifying cfg.keeptrials = 'yes').
> When you have the TFRs for each subject you can grandaverage them with
> freqgrandaverage where the input is the TFRs of all subjects (and before
> averaging you can use also freqbaseline for giving a baseline for your
> TFRs).
>
>
>
>      I hope it helps.
>
>
>
>      Best regards,
>
>      Lilla Magyari
>
>
>
>
>
>
>
>
> --------------------------------------------------------------------------
>
>      From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf Of Olga Sysoeva
>      Sent: Saturday, May 13, 2006 9:28 AM
>      To: FIELDTRIP at NIC.SURFNET.NL
>      Subject: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>
>
>
>      Dear list members,
>
>
>
>      Thank you everybody for your help! I've already got interesting
> results using clusterrandomization on my data! Thanks a lot!
>
>
>
>      Now I have a question about using the clusterrandomization on 3-D
> data (channel-time-frequency) in within-subject analysis.
>
>      As I understand it is possible with Fieldtrip, but I really newby in
> time-frequency anlysis, therefore wanted your comments,
>
>      as far as I didn't find the example of the application of
> clusteranalysis on this set of the data in tuturial.
>
>
>
>      I successfully conduct the within-subject clusterrandomization on my
> grand-average data, which does not have the third, frequency demintion.
>
>      Now I want to add it. But I could not apply freqanalyisis on
> grandavarage data, could I? Should I made the TFR of individual data and
> than grand-avarage the result?
>
>      Which function should I use?
>
>
>
>      Best Regards,
>
>      Olga.


From olga at GRAPHICMIND.INFO  Sat Jun  3 14:26:35 2006
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Sat, 3 Jun 2006 16:26:35 +0400
Subject: clusrand: 19 channels 0 minnbchan
Message-ID: <SAT.3.JUN.2006.162635.0400.FIELDTRIP@NIC.SURFNET.NL>

Dear experts,

Does it make sense to make clusterrandomization if I put "0" in the min number of neibouring channels if I have only 19 of them (10-20 system)?
As I understand in this case just the time is considered when clustering. How many consequent time point is requiered to build a cluster? 

Best Regards,
Olga.
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From maris at NICI.RU.NL  Sat Jun  3 18:47:21 2006
From: maris at NICI.RU.NL (Eric Maris)
Date: Sat, 3 Jun 2006 18:47:21 +0200
Subject: deleting two EOG channale from data-stucture
Message-ID: <SAT.3.JUN.2006.184721.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Olga,


I would like to delete two channels from my data. How is it better to do
this?


Type "help channelselection" at the Matlab command line. This will give you
information on how the Fieldtrip functions perform channelselection on the
basis of the input in cfg.channel. I don't have Matlab running now, but I
think that '-EOG' in cfg.channel will do the job you request.


greetings,

Eric


From maris at NICI.RU.NL  Sat Jun  3 18:50:06 2006
From: maris at NICI.RU.NL (Eric Maris)
Date: Sat, 3 Jun 2006 18:50:06 +0200
Subject: and clusterrandomization
Message-ID: <SAT.3.JUN.2006.185006.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Olga,

> That was an inconsistency in the loci of EOG channels between subjects.
> Now I corrected it: HEOG and VEOG data are still presented in the data
> structure, but do not have the location (pnt 0 0 0). Is it OK? The results
> looks as what I excpected.

Because you never will include the EOG-channels in an analysis of the
EEG-channels, the location of the EOG is not required by
clusterrandanalysis.

greetings,

Eric Maris



> Best Regards,
> Olga.
>
> ----- Original Message -----
> From: "Eric Maris" <maris at NICI.RU.NL>
> To: <FIELDTRIP at NIC.SURFNET.NL>
> Sent: Friday, May 26, 2006 5:35 PM
> Subject: Re: [FIELDTRIP] and clusterrandomization
>
>
>> Dear Olga,
>>
>>
>> But the problems is still in my clusterrandomization.
>> Could the fact that the order of the channel in the file (C_vc11.label)
>> is not the same as in the C_vc11.elec.label influences the result of
>> clusterrandomization (I do not have my neigbouring channel file)?
>>
>>
>> That should not matter. However, the labels in your data structure
>> (.label in the output of timelockgrandaverage) should exactly match the
>> labels in the elec-structure. If that is OK, then something might have
>> gone wrong with the combination of the data of the different subjects. Do
>> they all have the same elec-structure? If the same physical channel has
>> different labels for different subjects, then this may create
>> inconsistencies between EEGlab and Fieldtrip. For Fieldtrip, channels
>> that have the same label are assumed to be physically identical, even if
>> they are in different positions in the data structure. This is only a
>> guess, of course.
>>
>>
>> kind regards,
>>
>> Eric Maris
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Best Regards,
>> Olga.
>>  ----- Original Message -----
>>  From: Ingrid Nieuwenhuis
>>  To: FIELDTRIP at NIC.SURFNET.NL
>>  Sent: Wednesday, May 24, 2006 8:45 PM
>>  Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>>
>>
>>  Hi Olga,
>>
>>
>>
>>  About the z-param:
>>
>>  This is the field that contains the data to be plotted; for instance
>> 'avg', 'powspctrm' or 'cohspctrm'. Normally the function looks in your
>> data.dimord to find out which z-param to use. To make the function work
>> you could give cfg.zparam = 'avg' (for instance if you want to plot an
>> ERF/ERP). But if you could send me what the dimord field of the data that
>> you want to plot is, I could look why the plot functions don't extract
>> the correct zparam themselves.
>>
>>
>>
>>  About the timelockgranaveraging: I also think it should be the same. I
>> have no idea what it could be.
>>
>>
>>
>>  Good luck,
>>
>>  Ingrid Nieuwenhuis
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>>  From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
>> Behalf Of Olga Sysoeva
>>  Sent: Wednesday, May 24, 2006 5:44 PM
>>  To: FIELDTRIP at NIC.SURFNET.NL
>>  Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>>
>>
>>
>>  Dear List member,
>>
>>
>>
>>  Sorry for such dull questions but,
>>
>>  I am again facing the new problems with Fieldtrip, although did not
>> solve some previous one (still can not singleplot and multiplot anything
>> 'cause of "unknown zparam field".
>>
>>
>>
>>  OK, about new one :-)
>>
>>
>>
>>  It seems that I did not use write the timelockgranaveraging.
>>
>>
>>
>>   The problem must be here, when I made grand averaging of all my 11
>> subject
>>   data
>>
>>                    cfg =[];
>>                     cfg.keepindividual = 'yes'
>>                     C_vc11  =
>>
>> timelockgrandaverage(cfg,vc_c_avg1,vc_c_avg2,vc_c_avg3,vc_c_avg4,vc_c_avg5,
>> vc_c_avg6,vc_c_avg7,vc_c_avg8,vc_c_avg9,vc_c_avg10,vc_c_avg11 );
>>
>>  As I understand the
>>
>>  vc_c_avg11.avg([9],[43]) should be similar with C_vc11.individual ([11],
>> [9], [43])
>>  But it is not.
>>  What can it be?
>>
>>  Best Regards,
>>
>>  Olga.
>>
>>
>>
>>
>>
>>    ----- Original Message -----
>>
>>    From: Olga Sysoeva
>>
>>    To: FIELDTRIP at NIC.SURFNET.NL
>>
>>    Sent: Saturday, May 13, 2006 4:34 PM
>>
>>    Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data
>> within-subject
>>
>>
>>
>>    Thank you very much, Lilla!
>>
>>    Now I knwo what to do but faced the problem with " unknown zparam
>> field" when ploting the results. Unfortunatly cfg.zparam does not
>> discribed in help file...
>>
>>    Best Regards, Olga
>>
>>      ----- Original Message -----
>>
>>      From: Lilla Magyari
>>
>>      To: FIELDTRIP at NIC.SURFNET.NL
>>
>>      Sent: Saturday, May 13, 2006 3:11 PM
>>
>>      Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data
>> within-subject
>>
>>
>>
>>      Dear Olga,
>>
>>
>>
>>      I am just studying time-frequency analysis but I have done already
>> on my data, so perhaps I can help you.
>>
>>      First, yes, you have to do freqanalysis on the preprocessed data of
>> the individual subjects for all conditions that you want to compare (i.e.
>> the input for this function contains all trials from one subject in one
>> condition.) And it is also important that the other input for this
>> function is the cfg where for example, in the cfg.method you have to
>> specify what kind of time-frequency analysis you want to use. (You have
>> to write 'wltconvol' for wavelet transformation and 'mltconvol' for
>> multitaper analysis.)
>>
>>      When you use freqanalysis as output you can get TFR for one subject
>> in one condition (but it is also possible to keep the information for the
>> individual trials of the condition by specifying cfg.keeptrials = 'yes').
>> When you have the TFRs for each subject you can grandaverage them with
>> freqgrandaverage where the input is the TFRs of all subjects (and before
>> averaging you can use also freqbaseline for giving a baseline for your
>> TFRs).
>>
>>
>>
>>      I hope it helps.
>>
>>
>>
>>      Best regards,
>>
>>      Lilla Magyari
>>
>>
>>
>>
>>
>>
>>
>>
>> --------------------------------------------------------------------------
>>
>>      From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
>> Behalf Of Olga Sysoeva
>>      Sent: Saturday, May 13, 2006 9:28 AM
>>      To: FIELDTRIP at NIC.SURFNET.NL
>>      Subject: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>>
>>
>>
>>      Dear list members,
>>
>>
>>
>>      Thank you everybody for your help! I've already got interesting
>> results using clusterrandomization on my data! Thanks a lot!
>>
>>
>>
>>      Now I have a question about using the clusterrandomization on 3-D
>> data (channel-time-frequency) in within-subject analysis.
>>
>>      As I understand it is possible with Fieldtrip, but I really newby in
>> time-frequency anlysis, therefore wanted your comments,
>>
>>      as far as I didn't find the example of the application of
>> clusteranalysis on this set of the data in tuturial.
>>
>>
>>
>>      I successfully conduct the within-subject clusterrandomization on my
>> grand-average data, which does not have the third, frequency demintion.
>>
>>      Now I want to add it. But I could not apply freqanalyisis on
>> grandavarage data, could I? Should I made the TFR of individual data and
>> than grand-avarage the result?
>>
>>      Which function should I use?
>>
>>
>>
>>      Best Regards,
>>
>>      Olga.


From maris at NICI.RU.NL  Sat Jun  3 18:53:19 2006
From: maris at NICI.RU.NL (Eric Maris)
Date: Sat, 3 Jun 2006 18:53:19 +0200
Subject: clusrand: 19 channels 0 minnbchan
Message-ID: <SAT.3.JUN.2006.185319.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Olga,


Does it make sense to make clusterrandomization if I put "0" in the min
number of neibouring channels if I have only 19 of them (10-20 system)?
As I understand in this case just the time is considered when clustering.
How many consequent time point is requiered to build a cluster?


Yes, it makes sense. The cfg.minnbchan-field is a way to suppress the
tendency of the cluster-growing algorithm to connect everything with
everything, even on the basis of noise. The FA-rate is not affect by the
value of cfg.minnbchan.


greetings,

Eric Maris


From pchris at UNC.EDU  Mon Jun  5 19:05:30 2006
From: pchris at UNC.EDU (Punita Christopher)
Date: Mon, 5 Jun 2006 19:05:30 +0200
Subject: dipole model
Message-ID: <MON.5.JUN.2006.190530.0200.FIELDTRIP@NIC.SURFNET.NL>

Has anyone seen any literature that deals with a spherical multiple layer 
head model in which the dipole spans across layers i.e. the source and 
sink of the dipole are in separate layers.  
Thanks,
Punita


From r.oostenveld at FCDONDERS.RU.NL  Tue Jun  6 10:50:02 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Tue, 6 Jun 2006 10:50:02 +0200
Subject: dipole model
In-Reply-To: <LISTSERV%200606051905308600.5C84@NIC.SURFNET.NL>
Message-ID: <TUE.6.JUN.2006.105002.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Punita,

On 5 Jun 2006, at 19:05, Punita Christopher wrote:
> Has anyone seen any literature that deals with a spherical multiple
> layer
> head model in which the dipole spans across layers i.e. the source and
> sink of the dipole are in separate layers.

In the dipole model the source and sink are infintely close together.
The difference on the scalp between a dipole and a source+sink model
with only a few mm in between will be negligible. A source+sink model
with more distance between them can be modelled as such, it requires
the solution of the monopole in a sphere (i.e. the desired source
+sink consists of the superposition of two monopoles). I am not sure
whether an analytical solution for that exsists in a 3- or 4-shell
model, but I would would guess that it does (*). For a BEM model it
is trivial to replace the dipole infinite medium potential with a
monopole infinite medium potential, i.e the BEM formulation
(separation of source and volume conduction) allows the specification
of arbitrary sources.

best
Robert

*) I don't know literature for a monopole in a multi-shell sphere,
but I would expect it to be in either textbooks as a didactical
example or in older articles (70s or 80s). You may want to search for
multipole expansions, which are described in more recent literature,
the monopole is the first term (0th order) of that, the dipole the
second term. Perhaps "Phys Med Biol. 2001 Aug;46(8):2255-66. A study
of equivalent source techniques for high-resolution EEG imaging. Yao
D, Zhou Y, Zeng M, Fan S, Lian J, Wu D, Ao X, Chen L, He B." could
provide more insight.


From muthuraman10 at HOTMAIL.COM  Tue Jun  6 11:19:56 2006
From: muthuraman10 at HOTMAIL.COM (Muthuraman Muthuraman)
Date: Tue, 6 Jun 2006 09:19:56 +0000
Subject: query on coherence analysis
In-Reply-To: <FA431909-950B-4EC2-9598-1C6C49250100@fcdonders.ru.nl>
Message-ID: <TUE.6.JUN.2006.091956.0000.FIELDTRIP@NIC.SURFNET.NL>

Hello

Thanks for the comments, i have downloaded the latest version
and now i am able to calculate using mtmwelch

but i get a error when i am plotting
i will included the matlab commands

>>cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
cfg.channelcmb={'EEG' 'EMG2'};
freq=freqanalysis(cfg,data);

>>fd=freqdescriptives([],freq);

cfg=[];
cfg.xparam='foi';
cfg.yparam='cohspctrm';
cfg.xlim=[0 30];
cfg.cohrefchannel='EMG2';
cfg.box='yes';
cfg.showlabels='yes';
cfg.channelname='EEG26';
singleplotER(cfg,fd);

??? Reference to non-existent field 'foi'.

Error in ==> singleplotER at 272
  plot(varargin{k-1}.(cfg.xparam), P, style);

with regards
muthu


>From: Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>
>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence source analysis
>Date: Thu, 1 Jun 2006 13:58:48 +0200
>
>Dear Muthuraman
>
>I have not been able to reproduce your error. I suggest that you get  the
>latest version of FieldTrip from our FTP server and try again.
>
>best egards,
>Robert
>
>PS this is the test script I used. It uses some simulated data, which
>again uses a MEG gradiometer definition and a head model from the  tutorial
>data.
>
>
>-----------------
>% read some data that is required to simulate MEG data, i.e. volume  model,
>% sensor positions and MRI (optional, only for plotting)
>vol  = read_ctf_hdm('Subject01.hdm');
>hdr  = read_fcdc_header('Subject01.ds/Subject01.res4');
>grad = hdr.grad;
>
>% construct the simulated MEG data for condition A ("active")
>cfg               = [];
>cfg.vol           = vol;
>cfg.grad          = grad;
>cfg.fsample       = 300;
>cfg.ntrials       = 2;
>cfg.triallength   = 1;
>cfg.dip.pos       = [0 7 8];
>cfg.dip.mom       = [1 0 0];
>cfg.dip.signal    = sin(2*pi*10*(1:cfg.fsample)./cfg.fsample);
>cfg.absnoise      = 1e-8;
>data = dipolesimulation(cfg);
>
>% add the source signal as fake EMG channel
>for i=1:cfg.ntrials
>   data.trial{i}(end+1,:) = cfg.dip.signal + randn(size (cfg.dip.signal));
>end
>data.label{end+1} = 'EMG';
>
>cfg=[];
>cfg.output='powandcsd';
>cfg.method='mtmwelch';
>cfg.foi=1:2:30;
>numfoi = length(cfg.foi);
>cfg.taper='hanning';
>cfg.t_ftimwin=zeros(1,numfoi);
>cfg.t_ftimwin(:)=0.5;
>cfg.channel=channelselection({'MEG' 'EMG'},data.label);
>cfg.channelcmb={'MEG' 'EMG'};
>freq=freqanalysis(cfg,data);
>
>
>


From ingrid.nieuwenhuis at FCDONDERS.RU.NL  Tue Jun  6 13:33:28 2006
From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis)
Date: Tue, 6 Jun 2006 13:33:28 +0200
Subject: query on coherence analysis
In-Reply-To: <BAY121-F232E75D5ACD864CFE8389CCE950@phx.gbl>
Message-ID: <TUE.6.JUN.2006.133328.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Muthuraman,

cfg.xparam should not be 'foi', but 'freq' (see help singleplotER)

Bests,
Ingrid


-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Muthuraman Muthuraman
Sent: Tuesday, June 06, 2006 11:20 AM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] query on coherence analysis

Hello

Thanks for the comments, i have downloaded the latest version
and now i am able to calculate using mtmwelch

but i get a error when i am plotting
i will included the matlab commands

>>cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
cfg.channelcmb={'EEG' 'EMG2'};
freq=freqanalysis(cfg,data);

>>fd=freqdescriptives([],freq);

cfg=[];
cfg.xparam='foi';
cfg.yparam='cohspctrm';
cfg.xlim=[0 30];
cfg.cohrefchannel='EMG2';
cfg.box='yes';
cfg.showlabels='yes';
cfg.channelname='EEG26';
singleplotER(cfg,fd);

??? Reference to non-existent field 'foi'.

Error in ==> singleplotER at 272
  plot(varargin{k-1}.(cfg.xparam), P, style);

with regards
muthu


>From: Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>
>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence source analysis
>Date: Thu, 1 Jun 2006 13:58:48 +0200
>
>Dear Muthuraman
>
>I have not been able to reproduce your error. I suggest that you get  the
>latest version of FieldTrip from our FTP server and try again.
>
>best egards,
>Robert
>
>PS this is the test script I used. It uses some simulated data, which
>again uses a MEG gradiometer definition and a head model from the  tutorial

>data.
>
>
>-----------------
>% read some data that is required to simulate MEG data, i.e. volume  model,
>% sensor positions and MRI (optional, only for plotting)
>vol  = read_ctf_hdm('Subject01.hdm');
>hdr  = read_fcdc_header('Subject01.ds/Subject01.res4');
>grad = hdr.grad;
>
>% construct the simulated MEG data for condition A ("active")
>cfg               = [];
>cfg.vol           = vol;
>cfg.grad          = grad;
>cfg.fsample       = 300;
>cfg.ntrials       = 2;
>cfg.triallength   = 1;
>cfg.dip.pos       = [0 7 8];
>cfg.dip.mom       = [1 0 0];
>cfg.dip.signal    = sin(2*pi*10*(1:cfg.fsample)./cfg.fsample);
>cfg.absnoise      = 1e-8;
>data = dipolesimulation(cfg);
>
>% add the source signal as fake EMG channel
>for i=1:cfg.ntrials
>   data.trial{i}(end+1,:) = cfg.dip.signal + randn(size (cfg.dip.signal));
>end
>data.label{end+1} = 'EMG';
>
>cfg=[];
>cfg.output='powandcsd';
>cfg.method='mtmwelch';
>cfg.foi=1:2:30;
>numfoi = length(cfg.foi);
>cfg.taper='hanning';
>cfg.t_ftimwin=zeros(1,numfoi);
>cfg.t_ftimwin(:)=0.5;
>cfg.channel=channelselection({'MEG' 'EMG'},data.label);
>cfg.channelcmb={'MEG' 'EMG'};
>freq=freqanalysis(cfg,data);
>
>
>


From ingrid.nieuwenhuis at FCDONDERS.RU.NL  Wed Jun 14 11:55:53 2006
From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis)
Date: Wed, 14 Jun 2006 11:55:53 +0200
Subject: missing cumtapcnt field
Message-ID: <WED.14.JUN.2006.115553.0200.FIELDTRIP@NIC.SURFNET.NL>

I'm (trying to) beamform, but I get the following error:

reference to non-existent field 'cumtapcnt' 
In prepare_freq_matrices line 124.
Ntrials = length(freq.cumtapcnt)

I used freqanalysis method 'mtmconvol' to do make the freq, and it indeed 
doesn't contain a 'cumtapcnt'

      cfg = [];
      cfg.method = 'mtmconvol';
      cfg.output = 'powandcsd';
      cfg.foi             = 90;
      cfg.t_ftimwin       = 0.5;
      cfg.tapsmofrq       = 30;
      cfg.pad             = 'maxperlen';
      cfg.taper           = 'dpss';
      cfg.keeptrials      = 'yes';
      cfg.keeptapers      = 'no';
      cfg.toi             = 0.75 
        
      freq_BF = freqanalysis(cfg, data);

So my questions: 
- Why doesn't my freq contain a cumtapcnt field. Should I have kept my 
tapers (cfg.keeptapers = 'yes')?
- Can I solve this without having to freqanalysis my data all over again, I 
can see in my freq.crsspctrm = [76 x 11476 double] that I have 76 trials. 
Can I for instance just make a vector of ones with length 76 and put that 
in my freq, or will that create problems?

Thanks a lot,
Ingrid 


From Jan.Schoffelen at FCDONDERS.RU.NL  Wed Jun 14 12:42:08 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Wed, 14 Jun 2006 12:42:08 +0200
Subject: missing cumtapcnt field
In-Reply-To: <LISTSERV%200606141155536310.74A7@NIC.SURFNET.NL>
Message-ID: <WED.14.JUN.2006.124208.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Ingrid,


>Can I for instance just make a vector of ones with length 76 and put that
>in my freq, or will that create problems?

The answer to this question is yes. Indeed, no cumtapcnt is passed back when
using freqanalysis_mtmconvol. Should be fixed, though.
In your case I think it is sufficient just to provide a vector which has a
dimensionality of Nx1, N being the number of epoch. The content of this
vector will not be used later on in this case.
On the other hand, the cumtapcnt-vector, as outputted by for example
freqanalysis_mtmfft contains for each epoch the number of tapers which have
been used for the estimation of the spectra for that particular epoch.
Please note that if you set the option cfg.keeptapers = 'yes', the vector
consists only of ones (or if you use e.g. a single hanning-taper, or such a
low amount of smoothing, that you only need one 'dpss'-taper, in which case
by the way it does not make sense to use the 'dpss'). In any other case, the
cumtapcnt-vector contains a number, which can be different for each epoch
(when you have trials of different lengths). You can easily compute the
number of tapers, this will be: 2xNxK-1, with N being the length of your
data segment (in seconds), and K being the taper-smoothing you specified in
cfg.tapsmofrq.

Yours,

JM


From nathanweisz at MAC.COM  Thu Jun 15 11:42:43 2006
From: nathanweisz at MAC.COM (Nathan Weisz)
Date: Thu, 15 Jun 2006 11:42:43 +0200
Subject: source positions - brain regions
Message-ID: <THU.15.JUN.2006.114243.0200.FIELDTRIP@NIC.SURFNET.NL>

dear help-list,

sorry for what appears to be a very basic question.
i'm just starting to explore the source analysis possibilities that
fieldtrip offers. for this i downloaded a EEG tutorial dataset from
eeglab, did eeglab2fieldtrip, and the timelockanalysis. now i wanted
to estimate the source waveforms of the erp.

%this is my input:
vol   = [];
vol.r = 12 * [0.88 0.92 1.00]; % radii of spheres, the head radius is
12 cm
vol.c = [1 1/80 1];            % conductivity
vol.o = [0 0 0];

tmp=data.elec;
tmp.pnt=tmp.pnt*12;


cfg=[];
cfg.method='lcmv';
cfg.vol=vol;
cfg.elec=tmp;
cfg.resolution=1;

datamn=sourceanalysis(cfg,dataav);

%this is the output
datamn =

       xgrid: [-10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10]
       ygrid: [-10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10]
       zgrid: [-8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10]
         dim: [21 21 19]
         vol: [1x1 struct]
        time: [1x256 double]
         pos: [8379x3 double]
      inside: [1x4811 double]
     outside: [1x3568 double]
      method: 'average'
         avg: [1x1 struct]
         cfg: [1x1 struct]

there were no error or warning messages, so from the basic structure
things seem to be ok.
the time courses of my source activity appears to be saved in
datamn.avg.mom.

 >> size(datamn.avg.mom{datamn.inside(1)})

ans =

      3   256


however now i'm a little bit stuck. from here, what is the best
method of finding out which dipoles correspond (very roughly) to
which brain regions, so i can extract specifically those to look at
the sourcewaveforms? unfortunatley no mri.
I am aware of the sourceplot function, but was uncapable of producing
a meaningful output.

thanks in advance for any hints & best wishes,
nathan



--------------------------------
Dr. Nathan Weisz
Dept. of Psychology
University of Konstanz
P.O. Box D25
78457 Konstanz, Germany

Tel: ++49-7531-884612
Email & Chat-AV: nathanweisz at mac.com
Homepage: http://homepage.mac.com/nathanweisz/start/research.html


From muthuraman10 at HOTMAIL.COM  Thu Jun 15 15:59:54 2006
From: muthuraman10 at HOTMAIL.COM (Muthuraman Muthuraman)
Date: Thu, 15 Jun 2006 13:59:54 +0000
Subject: query on coherence analysis
In-Reply-To: <002201c6895d$07c0d680$642dae83@fcdonders.nl>
Message-ID: <THU.15.JUN.2006.135954.0000.FIELDTRIP@NIC.SURFNET.NL>

Hello

Thankyou for the previous help it works now
i am able to proceed further to calculate the coherence

The problem now the coherence obtained using the mtmwelch
when i plot the coherence figures for the channels
all the coherence figures for the different channel looks the same
is there is a bug in how i am calculating the coherence

These are the steps i carried out in calculating the coherence

headerfile='pd_mof_tr0_c_0306.cnt';
hdr = read_fcdc_header(headerfile);
cfg.trl = [];
for i=1:floor(hdr.nSamples/hdr.Fs)
  cfg.trl(i,1) = (i-1)*hdr.Fs + 1;
  cfg.trl(i,2) = (i  )*hdr.Fs;
  cfg.trl(i,3) = 0;
end

cfg.headerfile=headerfile;
>>cfg.datafile=headerfile;
>>[data] = preprocessing(cfg);

-and after the data is preprocessed i change the channel labels from actual
cz to eeg26 and so on



cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
cfg.channelcmb={'EEG' 'EMG2'};
freq=freqanalysis(cfg,data);


-when i calculate using freqanalysis i get these warnings

1.000 Hz : WARNING - using only one taper for specified smoothing
Warning: Size vector should be a row vector with integer elements.
>In freqanalysis_mtmconvol at 360
  In freqanalysis at 182
  In freqanalysis_mtmwelch at 67
  In freqanalysis at 182
and so on till 30.000 hz

-and while processing

processing trial 2: 1000 samples
Warning: Size vector should be a row vector with integer elements.
>In freqanalysis_mtmconvol at 398
  In freqanalysis at 182
  In freqanalysis_mtmwelch at 67
  In freqanalysis at 182



fd=freqdescriptives([],freq);


cfg=[];
cfg.xparam='freq';
cfg.yparam='cohspctrm';
cfg.xlim=[3 30];
cfg.cohrefchannel='EMG2';
cfg.box='yes';
cfg.showlabels='yes';

cfg.channelname='EEG27';
singleplotER(cfg,fd);
-when i try to plot i get this error
??? Error using ==> char
Cell elements must be character arrays.

Error in ==> singleplotER at 326
  t=[char(cfg.channelname) ' / ' num2str(cfg.channelindex) ];


please , look at it and help me in this regard

thanking you
with regards
muthuraman

>From: Ingrid Nieuwenhuis <ingrid.nieuwenhuis at FCDONDERS.RU.NL>
>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence analysis
>Date: Tue, 6 Jun 2006 13:33:28 +0200
>
>Dear Muthuraman,
>
>cfg.xparam should not be 'foi', but 'freq' (see help singleplotER)
>
>Bests,
>Ingrid
>
>
>-----Original Message-----
>From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
>Of Muthuraman Muthuraman
>Sent: Tuesday, June 06, 2006 11:20 AM
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence analysis
>
>Hello
>
>Thanks for the comments, i have downloaded the latest version
>and now i am able to calculate using mtmwelch
>
>but i get a error when i am plotting
>i will included the matlab commands
>
> >>cfg=[];
>cfg.output='powandcsd';
>cfg.method='mtmwelch';
>cfg.foi=1:2:30;
>numfoi = length(cfg.foi);
>cfg.taper='hanning';
>cfg.t_ftimwin=zeros(1,numfoi);
>cfg.t_ftimwin(:)=0.5;
>cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
>cfg.channelcmb={'EEG' 'EMG2'};
>freq=freqanalysis(cfg,data);
>
> >>fd=freqdescriptives([],freq);
>
>cfg=[];
>cfg.xparam='foi';
>cfg.yparam='cohspctrm';
>cfg.xlim=[0 30];
>cfg.cohrefchannel='EMG2';
>cfg.box='yes';
>cfg.showlabels='yes';
>cfg.channelname='EEG26';
>singleplotER(cfg,fd);
>
>??? Reference to non-existent field 'foi'.
>
>Error in ==> singleplotER at 272
>   plot(varargin{k-1}.(cfg.xparam), P, style);
>
>with regards
>muthu
>
>
> >From: Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>
> >Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
> >To: FIELDTRIP at NIC.SURFNET.NL
> >Subject: Re: [FIELDTRIP] query on coherence source analysis
> >Date: Thu, 1 Jun 2006 13:58:48 +0200
> >
> >Dear Muthuraman
> >
> >I have not been able to reproduce your error. I suggest that you get  the
> >latest version of FieldTrip from our FTP server and try again.
> >
> >best egards,
> >Robert
> >
> >PS this is the test script I used. It uses some simulated data, which
> >again uses a MEG gradiometer definition and a head model from the
>tutorial
>
> >data.
> >
> >
> >-----------------
> >% read some data that is required to simulate MEG data, i.e. volume
>model,
> >% sensor positions and MRI (optional, only for plotting)
> >vol  = read_ctf_hdm('Subject01.hdm');
> >hdr  = read_fcdc_header('Subject01.ds/Subject01.res4');
> >grad = hdr.grad;
> >
> >% construct the simulated MEG data for condition A ("active")
> >cfg               = [];
> >cfg.vol           = vol;
> >cfg.grad          = grad;
> >cfg.fsample       = 300;
> >cfg.ntrials       = 2;
> >cfg.triallength   = 1;
> >cfg.dip.pos       = [0 7 8];
> >cfg.dip.mom       = [1 0 0];
> >cfg.dip.signal    = sin(2*pi*10*(1:cfg.fsample)./cfg.fsample);
> >cfg.absnoise      = 1e-8;
> >data = dipolesimulation(cfg);
> >
> >% add the source signal as fake EMG channel
> >for i=1:cfg.ntrials
> >   data.trial{i}(end+1,:) = cfg.dip.signal + randn(size
>(cfg.dip.signal));
> >end
> >data.label{end+1} = 'EMG';
> >
> >cfg=[];
> >cfg.output='powandcsd';
> >cfg.method='mtmwelch';
> >cfg.foi=1:2:30;
> >numfoi = length(cfg.foi);
> >cfg.taper='hanning';
> >cfg.t_ftimwin=zeros(1,numfoi);
> >cfg.t_ftimwin(:)=0.5;
> >cfg.channel=channelselection({'MEG' 'EMG'},data.label);
> >cfg.channelcmb={'MEG' 'EMG'};
> >freq=freqanalysis(cfg,data);
> >
> >
> >


From linpe at NINDS.NIH.GOV  Thu Jun 15 22:08:19 2006
From: linpe at NINDS.NIH.GOV (Lin, Peter (NIH/NINDS) [E])
Date: Thu, 15 Jun 2006 16:08:19 -0400
Subject: No subject
Message-ID: <THU.15.JUN.2006.160819.0400.FIELDTRIP@NIC.SURFNET.NL>

I am trying to import neuroscan data into fieldtrip for analysis.  I
tried using eeglab to load my epoch's neuroscan file and then used the
eeglab2fieldtrip command on the EEG structure to generate a new data
file.  My question is how to process the data further using the
frequencyanalysis method.  

 

>>[data]=eeglab2fieldtrip(EEG,'preprocessing')

 

data = 

 

      label: {1x64 cell}

    fsample: 1000

       elec: [1x1 struct]

      trial: {1x224 cell}

       time: {1x224 cell}

        cfg: [1x1 struct]

 

I'm wondering if my created data file is not correct.  Any help on how
to proceed would be great.  

 

Thanks,

 

Peter

 

Peter Lin, MD

Clinical Fellow, Human Motor Control Section

Phone: 301-402-0703

email: linpe at ninds.nih.gov

 

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From Jan.Schoffelen at FCDONDERS.RU.NL  Fri Jun 16 09:05:50 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Fri, 16 Jun 2006 09:05:50 +0200
Subject: No subject
In-Reply-To: <C95F8E297215B6489AC8E595CF2239B0053B989F@NIHCESMLBX.nih.gov>
Message-ID: <FRI.16.JUN.2006.090550.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Peter,



As far as I can see, the data looks OK. At least it contains the fields
subsequent analysis steps need to know. However, I cannot judge the content
of these fields, but there's no reason to assume that's not fine.

To proceed, I would first advice you to have a look at the fieldtrip
website. If you follow the link documentation, and then
tutorial-documentation, there's already some stuff regarding frequency
analysis. Moreover, the website also contains the documentation of all
fieldtrip functions, which you can also access from the matlab command line,
by typing help functionname. For example, try help freqanalysis, or help
freqanalysis_mtmconvol. There's already quite some information in there, as
well as all the options you can play with.



Good luck



Jan-mathijs



  _____

From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Lin, Peter (NIH/NINDS) [E]
Sent: Thursday, June 15, 2006 10:08 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: [FIELDTRIP]



I am trying to import neuroscan data into fieldtrip for analysis.  I tried
using eeglab to load my epoch's neuroscan file and then used the
eeglab2fieldtrip command on the EEG structure to generate a new data file.
My question is how to process the data further using the frequencyanalysis
method.



>>[data]=eeglab2fieldtrip(EEG,'preprocessing')



data =



      label: {1x64 cell}

    fsample: 1000

       elec: [1x1 struct]

      trial: {1x224 cell}

       time: {1x224 cell}

        cfg: [1x1 struct]



I'm wondering if my created data file is not correct.  Any help on how to
proceed would be great.



Thanks,



Peter



Peter Lin, MD

Clinical Fellow, Human Motor Control Section

Phone: 301-402-0703

email: linpe at ninds.nih.gov



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From Jan.Schoffelen at FCDONDERS.RU.NL  Fri Jun 16 09:15:15 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Fri, 16 Jun 2006 09:15:15 +0200
Subject: query on coherence analysis
In-Reply-To: <BAY121-F19F3FD6B01B619882BC777CE820@phx.gbl>
Message-ID: <FRI.16.JUN.2006.091515.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Muthuraman,

At first glance I don't have a clue what's going on.
Did you have a look into fd.powspctrm, and fd.cohspctrm?
Does it contain normal numbers, zeros, or nan?
It might be a bug in freqanalysis_mtmwelch.
Did you try out other methods, to be specified in cfg.method?
If yes, did this also give strange results? If no, could you try out
cfg.method = 'mtmconvol' instead of 'mtmwelch'? Please have a look at the
documentation which additional options you have to specify.
What matlab-version do you use? Do you use the latest fieldtrip-version?

One additional thing: please note that you specified the odd frequencies
1:2:29, whereas your time-window is half a second wide. These are not
optimal settings, since the frequency-resolution of your time-window is 2
Hz. This means that your time-window never contains an integer amount of
cycles of the frequency you want to estimate. This might lead to strange
results, though I don't think it has anything to do with your present
problem. However, I would use cfg.freq = 2:2:30 in combination with a
time-window of 0.5 s

Yours,

Jan-Mathijs

-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Muthuraman Muthuraman
Sent: Thursday, June 15, 2006 4:00 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] query on coherence analysis

Hello

Thankyou for the previous help it works now
i am able to proceed further to calculate the coherence

The problem now the coherence obtained using the mtmwelch
when i plot the coherence figures for the channels
all the coherence figures for the different channel looks the same
is there is a bug in how i am calculating the coherence

These are the steps i carried out in calculating the coherence

headerfile='pd_mof_tr0_c_0306.cnt';
hdr = read_fcdc_header(headerfile);
cfg.trl = [];
for i=1:floor(hdr.nSamples/hdr.Fs)
  cfg.trl(i,1) = (i-1)*hdr.Fs + 1;
  cfg.trl(i,2) = (i  )*hdr.Fs;
  cfg.trl(i,3) = 0;
end

cfg.headerfile=headerfile;
>>cfg.datafile=headerfile;
>>[data] = preprocessing(cfg);

-and after the data is preprocessed i change the channel labels from actual
cz to eeg26 and so on



cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
cfg.channelcmb={'EEG' 'EMG2'};
freq=freqanalysis(cfg,data);


-when i calculate using freqanalysis i get these warnings

1.000 Hz : WARNING - using only one taper for specified smoothing
Warning: Size vector should be a row vector with integer elements.
>In freqanalysis_mtmconvol at 360
  In freqanalysis at 182
  In freqanalysis_mtmwelch at 67
  In freqanalysis at 182
and so on till 30.000 hz

-and while processing

processing trial 2: 1000 samples
Warning: Size vector should be a row vector with integer elements.
>In freqanalysis_mtmconvol at 398
  In freqanalysis at 182
  In freqanalysis_mtmwelch at 67
  In freqanalysis at 182



fd=freqdescriptives([],freq);


cfg=[];
cfg.xparam='freq';
cfg.yparam='cohspctrm';
cfg.xlim=[3 30];
cfg.cohrefchannel='EMG2';
cfg.box='yes';
cfg.showlabels='yes';

cfg.channelname='EEG27';
singleplotER(cfg,fd);
-when i try to plot i get this error
??? Error using ==> char
Cell elements must be character arrays.

Error in ==> singleplotER at 326
  t=[char(cfg.channelname) ' / ' num2str(cfg.channelindex) ];


please , look at it and help me in this regard

thanking you
with regards
muthuraman


From r.oostenveld at FCDONDERS.RU.NL  Fri Jun 16 10:39:48 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 16 Jun 2006 10:39:48 +0200
Subject: source positions - brain regions
In-Reply-To: <5E221385-C805-4FFA-BE76-F2C0DF9BEE72@mac.com>
Message-ID: <FRI.16.JUN.2006.103948.0200.FIELDTRIP@NIC.SURFNET.NL>

hi Nathan

On 15 Jun 2006, at 11:42, Nathan Weisz wrote:
> however now i'm a little bit stuck. from here, what is the best
> method of finding out which dipoles correspond (very roughly) to
> which brain regions, so i can extract specifically those to look at
> the sourcewaveforms? unfortunatley no mri.
> I am aware of the sourceplot function, but was uncapable of
> producing a meaningful output.

So far it seems ok. The headmodel is in cm, the electrodes as well (I
presume, otherwise it would have given warnings and/or errors), so
the source locations are also expressed in cm, since they are
expresed in the same coordinate system. I suggest that you have a
look at http://www2.ru.nl/fcdonders/fieldtrip/doku.php?
id=fieldtrip:documentation:frequently_asked_questions#how_are_the_differ
ent_head_and_mri_coordinate_systems_defined to get a better
understanding in general.

What we normally do in such a case is to use an indivudual headmodel,
and what we thus subsequently would do is to take an anatomical MRI
of the same subject, in which the MRI is aligned to the same head/
model coordinate system (using the ears and nose fiducials). Since
you do not have a MRI, you could take a standard MRI (i.e. the MNI
template in single_subj_T1 from SPM). Some time ago I (or Arno)
posted a homogenous transformation matrix "besa2spm" on the eeglab
mailing list (*). That homogenous transformation matrix transforms
from besa coordinates for a spherical model to MNI coordinates.

besa2spm = [
     0.0101   -0.9400         0    0.5588
     1.1889    0.0080    0.0530  -18.0041
    -0.0005   -0.0000    1.1268    1.8045
          0         0         0    1.0000 ];

spm2besa = inv(besa2spm);

The transformation matrix is for the "besa" spherical model in
EEGLAB, which has different sphere radii (85mm outer sphere) than you
have used. So you should add a scaling from the besa radii to yours.

your2besa = eye(4);
your2besa(1,1) = 8.5/12;
your2besa(2,2) = 8.5/12;
your2besa(3,3) = 8.5/12;

then

your2spm = besa2spm * your2besa
spm2your = inv(your2spm);

It is most convenient to apply the inverse transformation to the MRI
corodinate system. I.e. do
   mri = read_fcdc_mri('single_subj_T1.mnc')
then mri.transform describes the voxels in SPM/MNI coordinates, so
   mri.transform = spm2your * mri.transform;
changes the anatomical MRI into your headmodel coordinates.

Subsequently you can interpolate the functional values onto the
anaomtical voxel locations with SOURCEINTERPOLATE, and plot the
functional values overlaid over the anatomical with SOURCEPLLOT or
SLICEINTERP.

best regards,
Robert

PS (*) the besa2spm coordinate transformation matrix was constructed
using ELECTORDENORMAMALIZE, which warps electrodes. In this case the
spherical 1020 electrodes were warped to the corresponding electrodes
in the MNI template. The homogenous transformation matrix describes
the warp/deformation and can be used as well for the dipoles inside
the head.


From jurij.dreo at GUEST.ARNES.SI  Sat Jun 17 12:18:26 2006
From: jurij.dreo at GUEST.ARNES.SI (Jurij Dreo)
Date: Sat, 17 Jun 2006 11:18:26 +0100
Subject: Statistics for coherence in a within-subject experiment
Message-ID: <SAT.17.JUN.2006.111826.0100.FIELDTRIP@NIC.SURFNET.NL>

Hello,

I am using BESA to perform coherence and source coherence 
calculations for a multiple-subject/multiple-condition experiment. In 
the experiment I have 11 subjects, 6 conditions and around 30 sets 
per condition per subject.

In BESA the data was preprocessed and the coherence values in the 
Time-Frequency domain were calculated for each person.

As BESA has no capabilities to calculate statistics in a multiple-
subject study, their support personnel directed me towards FieldTrip.

I´ve been looking over the documentation and tutorials on your web 
page and also downloaded the scrip and ran it in matlab.

The tutorial on Cluster-Lever randomization Tests for the Time-
Frequency domain is quite straight-forward. I am however not quite 
sure which statistic to use for the cfg.statistic variable to analyze 
coherence in a within-subject study such as the one I have.

The documentation on the cfg.statistic variable says it can have 
these values:
1. indepsamplesT' (independent samples T-statistic) 
2. 'indepsamplesregrT' (independent samples regression coefficient T-
statistic)
3. 'indepsamplesZcoh' (independent samples Z-statistic for coherence)
4. 'indepsamplesTsqcrs' (independent samples T-square-statistic for 
the cross-spectrum)
5. 'depsamplesT' (dependent samples T-statistic)
6. 'actvsblT' (activation versus baseline T-statistic)
7. 'depsamplesregrT' (dependent samples regression coefficient T-
statistic) 
8. 'indepsamplesF' (independent samples F-statistic)
9. 'depsamplesF' (dependent samples F-statistic)

I am not sure if any of these options are compatible with a within-
subject multiple condition coherence statistical analysis.

option 3. - indepsamplesZcoh is obviously only suitable for a between-
trial, two-condition experiment

and there are no other options that explicitally say they are used 
for coherence. 

So how can one compare 6 conditions for 11 subjects with regards to 
coherence if one imports the Time-Frequency domain data for each 
person into FieldTrip?

Thank you for your help!

Regards,
Jurij Dreo


From r.oostenveld at FCDONDERS.RU.NL  Mon Jun 19 16:18:55 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Mon, 19 Jun 2006 16:18:55 +0200
Subject: Statistics for coherence in a within-subject experiment
In-Reply-To: <20060617_091826_063328.jurij.dreo@guest.arnes.si>
Message-ID: <MON.19.JUN.2006.161855.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Jurij

> option 3. - indepsamplesZcoh is obviously only suitable for a between-
> trial, two-condition experiment

Yes, that is for testing coherence differences between two conditions
within one subject.

> and there are no other options that explicitally say they are used
> for coherence.
>
> So how can one compare 6 conditions for 11 subjects with regards to
> coherence if one imports the Time-Frequency domain data for each
> person into FieldTrip?

In your case you have observed a "value" in 11 subjects, over 6
conditions. That value happens to be coherence, but could as well
have been something else. Since you have manipulated the conditions
with each subject, you can use a dependent-samples test: the observed
values depend on the subject (an example of a dependent-samples test
is a paired-t test).

If the number of trials varies between subjects and/or sessions, it
will be preferable to transform your coherence values to z-scores
manually prior to submitting the values to clusterrandanalysis.

Now about the 6 conditions, am I right that you have a 1x6 factorial
design, or is there more strucure in the design? Do you have a
specific hypothesis about the different conditions? If you only want
to reject the null-hypothesis "the observed value (coherence) is the
same (more accurately: stems from the same distribution) in all my 6
conditions", you would use an omnibus F-statistic, i.e.
'depsamplesF'. It might be that your hypothesis is more specific, or
also in case you find an omnibus effect, then you would probably want
to perform explicit tests between two subsets of your 6 conditions
using a 'depsamplesT' test.

best regards,
Robert


From jurij.dreo at GUEST.ARNES.SI  Mon Jun 19 17:31:46 2006
From: jurij.dreo at GUEST.ARNES.SI (Jurij Dreo)
Date: Mon, 19 Jun 2006 17:31:46 +0200
Subject: Statistics for coherence in a within-subject experiment
Message-ID: <MON.19.JUN.2006.173146.0200.FIELDTRIP@NIC.SURFNET.NL>

Hello!

Thank you for your answers. Here are my replies to them:

To avoid any misunderstandings here is again a summary of my study design
- I have 11 subjects. 
- Each of them performed 6 tasks related to working memory.
- Each subject performed anywehere from 25 to 60 repeats (trial) of each condition (the standard number of trials per task was 30 - but some subjects performed the entire experiment twice (ergo 60 potential trials) .... and in some some of their trials are unusable - artifacts ... ergo 25 min number of possible trials)

Given my study design I thought something like a one-way ANOVA for correlated samples would be in order.
(as I am comparing 6 conditions within-subjects as every subject performed all sets)


-----------------
> In your case you have observed a "value" in 11 subjects, over 6  
> conditions. That value happens to be coherence, but could as well  
> have been something else. Since you have manipulated the conditions  
> with each subject, you can use a dependent-samples test: the observed  
> values depend on the subject (an example of a dependent-samples test  
> is a paired-t test).
-------------------

I´m not sure what you are saying here.... I agree with the dependent samples idea... but I cannot preform a t-test ... ie. more of them as that would inflate my p-rate overall.

I thought that I would first do an ANOVA and then something like the Tukey HSD Test to cimpare individual conditions

--------------------
> If the number of trials varies between subjects and/or sessions, it  
> will be preferable to transform your coherence values to z-scores  
> manually prior to submitting the values to clusterrandanalysis.
--------------------
Yes I agree that would need to be done manually.

-----------
> Now about the 6 conditions, am I right that you have a 1x6 factorial  
> design, or is there more strucure in the design? Do you have a  
> specific hypothesis about the different conditions? If you only want  
> to reject the null-hypothesis "the observed value (coherence) is the  
> same (more accurately: stems from the same distribution) in all my 6  
> conditions", you would use an omnibus F-statistic, i.e.  
> 'depsamplesF'. It might be that your hypothesis is more specific, or  
> also in case you find an omnibus effect, then you would probably want  
> to perform explicit tests between two subsets of your 6 conditions  
> using a 'depsamplesT' test.
> 
----------

I want to contrast all conditions at once (f -test anova) AND also each combination of conditions (say a post- ANOVA Q-test)

But Im still not sure which statistic to use and even if the one I use will be able to deal with the fact that I have a different number of conditions per condition per subject

As far as I understand it... we must use some kind of ANOVA here... A simple "paired" t-test will not do... as we are comparing more than 2 conditions at once and I do not want to inflate my p-rate.

Thank you for your help!

Regards,
Jurij Dreo
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From muthuraman10 at HOTMAIL.COM  Tue Jun 20 10:40:17 2006
From: muthuraman10 at HOTMAIL.COM (Muthuraman Muthuraman)
Date: Tue, 20 Jun 2006 08:40:17 +0000
Subject: query on coherence analysis
Message-ID: <TUE.20.JUN.2006.084017.0000.FIELDTRIP@NIC.SURFNET.NL>

Hello Jan

The answers for the questions you have asked
and also i have attached some figures with this mail
1-using welch periodogram method
2-using fieldtrip 'mtmfft'
3-using fieldtrip 'mtmwelch'

Did you have a look into fd.powspctrm, and fd.cohspctrm?
-yes,both look the same so something is surely going wrong

Does it contain normal numbers, zeros, or nan?
-yes, it has normal numbers but the vlaues are from 1.0 to 10.0 not as
normal in the case of 0.1 to 1 in coherence spectrum

Did you try out other methods, to be specified in cfg.method?
-yes using 'mtmfft' i have attached the figure in the mail in which i dont
get the correct frequency content and the values are less

-In the 'mtmwelch' method i get a error when i am plotting, even then i am
able to see the figure
??? Error using ==> char
Cell elements must be character arrays.

Error in ==> singleplotER at 326
  t=[char(cfg.channelname) ' / ' num2str(cfg.channelindex) ];

-In the 'mtmconvol' i am not able to plot i get a error
selected 60 channels for coherence
??? Error using ==> plot
Vectors must be the same lengths.

Error in ==> singleplotER at 272
  plot(varargin{k-1}.(cfg.xparam), P, style);


please go through it and give your comments

and one more question for the source analysis
what are the values we need,when i open the elec1010 there are four values
x,y,z values and what is the fourth value

with regards
muthu

>From: Jan Mathijs Schoffelen <Jan.Schoffelen at FCDONDERS.RU.NL>
>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence analysis
>Date: Fri, 16 Jun 2006 09:15:15 +0200
>
>Dear Muthuraman,
>
>At first glance I don't have a clue what's going on.
>Did you have a look into fd.powspctrm, and fd.cohspctrm?
>Does it contain normal numbers, zeros, or nan?
>It might be a bug in freqanalysis_mtmwelch.
>Did you try out other methods, to be specified in cfg.method?
>If yes, did this also give strange results? If no, could you try out
>cfg.method = 'mtmconvol' instead of 'mtmwelch'? Please have a look at the
>documentation which additional options you have to specify.
>What matlab-version do you use? Do you use the latest fieldtrip-version?
>
>One additional thing: please note that you specified the odd frequencies
>1:2:29, whereas your time-window is half a second wide. These are not
>optimal settings, since the frequency-resolution of your time-window is 2
>Hz. This means that your time-window never contains an integer amount of
>cycles of the frequency you want to estimate. This might lead to strange
>results, though I don't think it has anything to do with your present
>problem. However, I would use cfg.freq = 2:2:30 in combination with a
>time-window of 0.5 s
>
>Yours,
>
>Jan-Mathijs
>
>-----Original Message-----
>From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
>Of Muthuraman Muthuraman
>Sent: Thursday, June 15, 2006 4:00 PM
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence analysis
>
>Hello
>
>Thankyou for the previous help it works now
>i am able to proceed further to calculate the coherence
>
>The problem now the coherence obtained using the mtmwelch
>when i plot the coherence figures for the channels
>all the coherence figures for the different channel looks the same
>is there is a bug in how i am calculating the coherence
>
>These are the steps i carried out in calculating the coherence
>
>headerfile='pd_mof_tr0_c_0306.cnt';
>hdr = read_fcdc_header(headerfile);
>cfg.trl = [];
>for i=1:floor(hdr.nSamples/hdr.Fs)
>   cfg.trl(i,1) = (i-1)*hdr.Fs + 1;
>   cfg.trl(i,2) = (i  )*hdr.Fs;
>   cfg.trl(i,3) = 0;
>end
>
>cfg.headerfile=headerfile;
> >>cfg.datafile=headerfile;
> >>[data] = preprocessing(cfg);
>
>-and after the data is preprocessed i change the channel labels from actual
>cz to eeg26 and so on
>
>
>
>cfg=[];
>cfg.output='powandcsd';
>cfg.method='mtmwelch';
>cfg.foi=1:2:30;
>numfoi = length(cfg.foi);
>cfg.taper='hanning';
>cfg.t_ftimwin=zeros(1,numfoi);
>cfg.t_ftimwin(:)=0.5;
>cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
>cfg.channelcmb={'EEG' 'EMG2'};
>freq=freqanalysis(cfg,data);
>
>
>-when i calculate using freqanalysis i get these warnings
>
>1.000 Hz : WARNING - using only one taper for specified smoothing
>Warning: Size vector should be a row vector with integer elements.
> >In freqanalysis_mtmconvol at 360
>   In freqanalysis at 182
>   In freqanalysis_mtmwelch at 67
>   In freqanalysis at 182
>and so on till 30.000 hz
>
>-and while processing
>
>processing trial 2: 1000 samples
>Warning: Size vector should be a row vector with integer elements.
> >In freqanalysis_mtmconvol at 398
>   In freqanalysis at 182
>   In freqanalysis_mtmwelch at 67
>   In freqanalysis at 182
>
>
>
>fd=freqdescriptives([],freq);
>
>
>cfg=[];
>cfg.xparam='freq';
>cfg.yparam='cohspctrm';
>cfg.xlim=[3 30];
>cfg.cohrefchannel='EMG2';
>cfg.box='yes';
>cfg.showlabels='yes';
>
>cfg.channelname='EEG27';
>singleplotER(cfg,fd);
>-when i try to plot i get this error
>??? Error using ==> char
>Cell elements must be character arrays.
>
>Error in ==> singleplotER at 326
>   t=[char(cfg.channelname) ' / ' num2str(cfg.channelindex) ];
>
>
>please , look at it and help me in this regard
>
>thanking you
>with regards
>muthuraman

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From Jan.Schoffelen at FCDONDERS.RU.NL  Wed Jun 21 11:31:07 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Wed, 21 Jun 2006 11:31:07 +0200
Subject: query on coherence analysis
In-Reply-To: <BAY121-F3382C80D92ABF19D39C798CE840@phx.gbl>
Message-ID: <WED.21.JUN.2006.113107.0200.FIELDTRIP@NIC.SURFNET.NL>

>the other question i have asked in the previous mail
>i would like to do the source analysis
>and the values specified in for ex:elec1010
>it has four values and the channel label
>the first three values are x,y,z position values
>what is the fourth value?

Dear Muthuraman,

Please have a look at the FAQ-section of the fieldtrip-website. It is
explained what is specified in the layout-files.

Yours,

Jan-M


From Jan.Schoffelen at FCDONDERS.RU.NL  Wed Jun 21 12:32:15 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Wed, 21 Jun 2006 12:32:15 +0200
Subject: query on coherence analysis
In-Reply-To: <BAY121-F3382C80D92ABF19D39C798CE840@phx.gbl>
Message-ID: <WED.21.JUN.2006.123215.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Muthuraman,

Please find attached a script and a figure.
I compared the 'mtmfft' with 'mtmwelch', and the results look very similar.
I did not test the 'mtmconvol' method, since this function is called when
you specify 'mtmwelch'. I guess you have to check your configuration in that
respect. I would say that the code is doing what it should do.
Please make sure that you use the latest fieldtrip-version.

Yours,

Jan-Mathijs

-----Original Message-----
From: Muthuraman Muthuraman [mailto:muthuraman10 at hotmail.com]
Sent: Wednesday, June 21, 2006 11:05 AM
To: Jan.Schoffelen at fcdonders.ru.nl
Subject: RE: [FIELDTRIP] query on coherence analysis

Hello Jan

Thanks for the suggestions

I have tried 'mtmconvol' and also plotting using singleplotTFR
the figure looks totally blue
i have attached the figure with this mail for the same channel combination
Figure-mtmconvol

and also i have uploaded two files
one is the CNT file of a patient
and the other file is data structure after preprocessing and changing the
channel label

If u have any different results from the data
please let me know
my aim is to do the coherence analysis followed by the source analysis using

'DICS'


the other question i have asked in the previous mail
i would like to do the source analysis
and the values specified in for ex:elec1010
it has four values and the channel label
the first three values are x,y,z position values
what is the fourth value?


thanking you
with regards
muthu
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From srampp at TISCALI.DE  Wed Jun 21 23:07:50 2006
From: srampp at TISCALI.DE (Stefan Rampp)
Date: Wed, 21 Jun 2006 23:07:50 +0200
Subject: Missing minimumnormestimate etc
Message-ID: <WED.21.JUN.2006.230750.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi everyone,

I was just trying to do source localization of epilepsy MEG data using mne, however, it appears that some functions are missing: minimumnormestimate, music, loreta and rv are used in sourceanalysis.m, but I can't find the implementations (and neither can matlab). Do I need to download additional libraries/toolboxes?

Thank you,
Stefan Rampp.
Epilepsycenter Erlangen
Germany
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From t.montez at VUMC.NL  Thu Jun 22 01:27:29 2006
From: t.montez at VUMC.NL (Montez, T.)
Date: Thu, 22 Jun 2006 01:27:29 +0200
Subject: channel location file to import planar to EEGLAB
Message-ID: <THU.22.JUN.2006.012729.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtripers,

I am using EEGLAB to compute ICA of CTF 151 channels data.

I used to read the data in EEGLAB directly from the CTF format, 
but some components are affected by the bad channels. 

Since removing the bad channels will reduce the number of components
and will give problems later at the planar transformation;
I tried using megrepair first and then importing the matlab array
of data.trial{1}. I use the channel locations of a previous 
dataset opened from the CTF format.

- I still get some components reflecting the bad channels, 
should I increase the cfg.neighbourdist?  
(I was using the default of 4 cm).

- To import the data after the planar transformation I need 
a channel location file for the dH and dV pairs, 
can you help me with that? 

Thanks in advance,
Teresa Montez

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From srampp at TISCALI.DE  Thu Jun 22 01:51:25 2006
From: srampp at TISCALI.DE (Stefan Rampp)
Date: Thu, 22 Jun 2006 01:51:25 +0200
Subject: channel location file to import planar to EEGLAB
Message-ID: <THU.22.JUN.2006.015125.0200.FIELDTRIP@NIC.SURFNET.NL>

channel location file to import planar to EEGLABDear Teresa,

I can't really provide much info regarding your first question, however, I might be able to help you with the second: 
Have you applied 'combineplanar' after the planar transformation? This will combine the dH and dV pairs into one channel per pair, e.g.

cfg = [];
combplan = combineplanar(cfg, plan);

were plan is the planar transformed data set. combineplanar allows to choose the method for combination of the pairs. For further details, you might want to have a look at the tutorial about event related averaging:
http://www2.ru.nl/fcdonders/fieldtrip/doku.php?id=fieldtrip:documentation:tutorial:eventrelatedaveraging

Sincerely,
Stefan Rampp
Epilepsycenter Erlangen
Germany.
  ----- Original Message ----- 
  From: Montez, T. 
  To: FIELDTRIP at NIC.SURFNET.NL 
  Sent: Thursday, June 22, 2006 1:27 AM
  Subject: [FIELDTRIP] channel location file to import planar to EEGLAB


  Dear Fieldtripers,

  I am using EEGLAB to compute ICA of CTF 151 channels data.

  I used to read the data in EEGLAB directly from the CTF format,
  but some components are affected by the bad channels.

  Since removing the bad channels will reduce the number of components
  and will give problems later at the planar transformation;
  I tried using megrepair first and then importing the matlab array
  of data.trial{1}. I use the channel locations of a previous
  dataset opened from the CTF format.

  - I still get some components reflecting the bad channels,
  should I increase the cfg.neighbourdist? 
  (I was using the default of 4 cm).

  - To import the data after the planar transformation I need
  a channel location file for the dH and dV pairs,
  can you help me with that?

  Thanks in advance,
  Teresa Montez


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From r.oostenveld at FCDONDERS.RU.NL  Thu Jun 22 09:25:56 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 22 Jun 2006 09:25:56 +0200
Subject: Statistics for coherence in a within-subject experiment
In-Reply-To: <000901c693b5$79d47c10$0200a8c0@laptop>
Message-ID: <THU.22.JUN.2006.092556.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Jurij

The parametric tests that you suggest are not implemented in  
FieldTrip. In the clusterrandanalysis function we use a randomization  
approach for statistical testing. It is a non-parametrical approach,  
and the test statistic consists of a parametrtical statistic per time- 
frequency-channel, which is clustered and summed over neighbouring  
timepoints/frequencies/channels. Not the single-sample statistic, but  
the clustersum is used for the statistical test, thereby increasing  
sensitivity and controlling for  multiple comparisons. The single  
sample (time-frequency-channel) statistic has to be chosen to match  
with the experimental design (e.g. F or F) and the randomization/ 
permutation of the data between the subjects and conditions has to be  
adequate (in your case you want to shuffle data between conditions  
but only within each subject). That determines the statistic to use.  
I suggest that you go over the clusterrandanalysis tutorial at
http://www2.ru.nl/fcdonders/fieldtrip/doku.php? 
id=fieldtrip:documentation:tutorial:clusterrandanalysis

best regards,
Robert


On 19 Jun 2006, at 17:31, Jurij Dreo wrote:

> Hello!
>
> Thank you for your answers. Here are my replies to them:
>
> To avoid any misunderstandings here is again a summary of my study  
> design
> - I have 11 subjects.
> - Each of them performed 6 tasks related to working memory.
> - Each subject performed anywehere from 25 to 60 repeats (trial) of  
> each condition (the standard number of trials per task was 30 - but  
> some subjects performed the entire experiment twice (ergo 60  
> potential trials) .... and in some some of their trials are  
> unusable - artifacts ... ergo 25 min number of possible trials)
>
> Given my study design I thought something like a one-way ANOVA for  
> correlated samples would be in order.
> (as I am comparing 6 conditions within-subjects as every subject  
> performed all sets)
>
>
> -----------------
> > In your case you have observed a "value" in 11 subjects, over 6
> > conditions. That value happens to be coherence, but could as well
> > have been something else. Since you have manipulated the conditions
> > with each subject, you can use a dependent-samples test: the  
> observed
> > values depend on the subject (an example of a dependent-samples test
> > is a paired-t test).
> -------------------
>
> I´m not sure what you are saying here.... I agree with the  
> dependent samples idea... but I cannot preform a t-test ... ie.  
> more of them as that would inflate my p-rate overall.
>
> I thought that I would first do an ANOVA and then something like  
> the Tukey HSD Test to cimpare individual conditions
>
> --------------------
> > If the number of trials varies between subjects and/or sessions, it
> > will be preferable to transform your coherence values to z-scores
> > manually prior to submitting the values to clusterrandanalysis.
> --------------------
> Yes I agree that would need to be done manually.
>
> -----------
> > Now about the 6 conditions, am I right that you have a 1x6 factorial
> > design, or is there more strucure in the design? Do you have a
> > specific hypothesis about the different conditions? If you only want
> > to reject the null-hypothesis "the observed value (coherence) is the
> > same (more accurately: stems from the same distribution) in all my 6
> > conditions", you would use an omnibus F-statistic, i.e.
> > 'depsamplesF'. It might be that your hypothesis is more specific, or
> > also in case you find an omnibus effect, then you would probably  
> want
> > to perform explicit tests between two subsets of your 6 conditions
> > using a 'depsamplesT' test.
> >
> ----------
>
> I want to contrast all conditions at once (f -test anova) AND also  
> each combination of conditions (say a post- ANOVA Q-test)
>
> But Im still not sure which statistic to use and even if the one I  
> use will be able to deal with the fact that I have a different  
> number of conditions per condition per subject
>
> As far as I understand it... we must use some kind of ANOVA here...  
> A simple "paired" t-test will not do... as we are comparing more  
> than 2 conditions at once and I do not want to inflate my p-rate.
>
> Thank you for your help!
>
> Regards,
> Jurij Dreo
>


From r.oostenveld at FCDONDERS.RU.NL  Thu Jun 22 09:31:10 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 22 Jun 2006 09:31:10 +0200
Subject: Missing minimumnormestimate etc
In-Reply-To: <006c01c69576$c1d13270$14b2a8c0@mirandola>
Message-ID: <THU.22.JUN.2006.093110.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Stefan,

The SOURCEANALYSIS function is used as wrapper for various
distributed or scanning inverse approaches, and DIPOLEFITTING is used
for underdetermined model fitting to the data. The only underlying
functions for SOURCEANALYSIS that are released on the ftp server are
the lcmv and the dics beamformer methods. The functions that you
refer to are implemented in our in-house version of FieldTrip but
have not been tested thouroughly. I can give you a pre-release if you
are willing to aid in the testing of those functions.

best regards,
Robert


On 21 Jun 2006, at 23:07, Stefan Rampp wrote:

> Hi everyone,
>
> I was just trying to do source localization of epilepsy MEG data
> using mne, however, it appears that some functions are missing:
> minimumnormestimate, music, loreta and rv are used in
> sourceanalysis.m, but I can't find the implementations (and neither
> can matlab). Do I need to download additional libraries/toolboxes?
>
> Thank you,
> Stefan Rampp.
> Epilepsycenter Erlangen
> Germany
>


From r.oostenveld at FCDONDERS.RU.NL  Thu Jun 22 09:40:31 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 22 Jun 2006 09:40:31 +0200
Subject: channel location file to import planar to EEGLAB
In-Reply-To: <28FF6B8D22C94B44A55E4E1325A94AF2348059@vumc-mb02.vumc.nl>
Message-ID: <THU.22.JUN.2006.094031.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Theresa

On 22 Jun 2006, at 1:27, Montez, T. wrote:
> I am using EEGLAB to compute ICA of CTF 151 channels data.
>
> I used to read the data in EEGLAB directly from the CTF format,
> but some components are affected by the bad channels.
The bad channels do not reflect a linear mixture of underlying
sources, therefore you should remove them prior to ICA. You should
also remove all trials containing anomalous artifacts.
> Since removing the bad channels will reduce the number of components
> and will give problems later at the planar transformation;
> I tried using megrepair first and then importing the matlab array
> of data.trial{1}. I use the channel locations of a previous
> dataset opened from the CTF format.
MEGREPAIR uses a nearest-neighbour approach for fixing the missing
channels. The "repaired" channels are linear combinations (i.e. a
linear mixture) of the neighbours and hence do not add any
information (i.e. components) to the data, doing ICA on the repaired
dataset does not give you all 151 components.
> - I still get some components reflecting the bad channels,
> should I increase the cfg.neighbourdist?
> (I was using the default of 4 cm).
>
> - To import the data after the planar transformation I need
> a channel location file for the dH and dV pairs,
> can you help me with that?
The planar transformation in MEGPLANAR also results in a linear
estimation of the horizontal and vertical gradients, i.e. if you
start with 151 axial channels and you do MEGPLANAR, you will have 302
planar channels, but the dimensionality of that data will still be
151. That means that ICA on the 302-channel planar data will result
in a maximum of 151 components.

I suggest to do the ICA on the axial data with the bad channels
removed. Subsequently you can switch from EEGLAB to FieldTrip and
compute the planar representation of the ICA components using the
MEGPLANAR function (I am not sure whether megplanar knows how to deal
with ICA data, but it is easy to convert the ICA data into something
that resembles an average ERF or alternatively to add support for the
ICA data in megplanar).

best regards,
Robert


From srampp at TISCALI.DE  Thu Jun 22 10:43:01 2006
From: srampp at TISCALI.DE (Stefan Rampp)
Date: Thu, 22 Jun 2006 10:43:01 +0200
Subject: Missing minimumnormestimate etc
Message-ID: <THU.22.JUN.2006.104301.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Robert,

Thank you for the fast answer. Since I'm interested in comparing various
methods, I'd greatly appreciate a pre-release version. And of course I could
contribute to Fieldtrip as a betatester for these functions like that.

Sincerely,
Stefan Rampp
Epilepsycenter Erlangen
Germany


----- Original Message -----
From: "Robert Oostenveld" <r.oostenveld at FCDONDERS.RU.NL>
To: <FIELDTRIP at NIC.SURFNET.NL>
Sent: Thursday, June 22, 2006 9:31 AM
Subject: Re: [FIELDTRIP] Missing minimumnormestimate etc


> Dear Stefan,
>
> The SOURCEANALYSIS function is used as wrapper for various  distributed or
> scanning inverse approaches, and DIPOLEFITTING is used  for
> underdetermined model fitting to the data. The only underlying  functions
> for SOURCEANALYSIS that are released on the ftp server are  the lcmv and
> the dics beamformer methods. The functions that you  refer to are
> implemented in our in-house version of FieldTrip but  have not been tested
> thouroughly. I can give you a pre-release if you  are willing to aid in
> the testing of those functions.
>
> best regards,
> Robert
>
>
> On 21 Jun 2006, at 23:07, Stefan Rampp wrote:
>
>> Hi everyone,
>>
>> I was just trying to do source localization of epilepsy MEG data  using
>> mne, however, it appears that some functions are missing:
>> minimumnormestimate, music, loreta and rv are used in  sourceanalysis.m,
>> but I can't find the implementations (and neither  can matlab). Do I need
>> to download additional libraries/toolboxes?
>>
>> Thank you,
>> Stefan Rampp.
>> Epilepsycenter Erlangen
>> Germany
>>


From MZvyagintsev at UKAACHEN.DE  Thu Jun 22 18:08:43 2006
From: MZvyagintsev at UKAACHEN.DE (Mikhail Zvyagintsev)
Date: Thu, 22 Jun 2006 18:08:43 +0200
Subject: Missing minimumnormestimate etc
In-Reply-To: <21EE19CF-BE60-4719-BC9E-C1F3737F26B5@fcdonders.ru.nl>
Message-ID: <THU.22.JUN.2006.180843.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Robert,

Would be also nice to have an implementaion of LORETA approach for
source analysis from your in-house software. I would appreciate if you
could send it to me as well.

Best regards,

Mikhail Zvyagintsev

MZvyagintsev at UKAachen.de



Robert Oostenveld wrote:

> Dear Stefan,
>
> The SOURCEANALYSIS function is used as wrapper for various
> distributed or scanning inverse approaches, and DIPOLEFITTING is used
> for underdetermined model fitting to the data. The only underlying
> functions for SOURCEANALYSIS that are released on the ftp server are
> the lcmv and the dics beamformer methods. The functions that you
> refer to are implemented in our in-house version of FieldTrip but
> have not been tested thouroughly. I can give you a pre-release if you
> are willing to aid in the testing of those functions.
>
> best regards,
> Robert


From muthuraman10 at HOTMAIL.COM  Fri Jun 23 12:54:57 2006
From: muthuraman10 at HOTMAIL.COM (Muthuraman Muthuraman)
Date: Fri, 23 Jun 2006 10:54:57 +0000
Subject: query on CTF software!!!
Message-ID: <FRI.23.JUN.2006.105457.0000.FIELDTRIP@NIC.SURFNET.NL>

Hello

For the Beamformer source analysis, do we need the CTF software
because when i am trying out the tutorial in beamforming

Matlab
>>freq=19.0;
>>Ncycles=10;
>>dTimeWin=Ncycles/freq;
>>cfg=[];
>>cfg.dataset='Subject01.ds';
>>cfg.channel={'MEG' 'STIM'};
>>cfg.trialdef.excludeConditions={'BAD'};
>>cfg.trialdef.includeTrigger=3;
>>cfg.trialdef.prestim=0.1+dTimeWin;
>>cfg.trialdef.poststim=-0.1;
>>datapre=preprocessing(cfg);

CTF_READ_RES4 [v  1.12]
....done (  0.67 sec)

i get the error

??? Error using ==> read_fcdc_header
could not read CTF res4 header file

Error in ==> preprocessing at 263
hdr = read_fcdc_header(cfg.headerfile);


with regards
muthu


From r.oostenveld at FCDONDERS.RU.NL  Fri Jun 23 15:23:22 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 23 Jun 2006 15:23:22 +0200
Subject: query on CTF software!!!
In-Reply-To: <BAY121-F290E321E30CF71939F2A00CE7A0@phx.gbl>
Message-ID: <FRI.23.JUN.2006.152322.0200.FIELDTRIP@NIC.SURFNET.NL>

dear Muthuraman

On 23 Jun 2006, at 12:54, Muthuraman Muthuraman wrote:
> For the Beamformer source analysis, do we need the CTF software
> because when i am trying out the tutorial in beamforming

You do not need the ctf software to follow the tutorial. The tutorial
is based however on a ctf MEG dataset.

> CTF_READ_RES4 [v  1.12]
> ....done (  0.67 sec)
>
> i get the error
>
> ??? Error using ==> read_fcdc_header
> could not read CTF res4 header file
>
> Error in ==> preprocessing at 263
> hdr = read_fcdc_header(cfg.headerfile);

Based on your error I suspect that matlab/fieldtrip cannot find the
dataset that you are trying to analyze, or that you matlab path is
incorrect. The function "CTF_READ_RES4" is not supposed to be called
(it is part of the NIH ctf import routines, e.g. used in EEGLAB),
since the default private/read_ctf_res4.m function can deal with the
tutorial dataset just fine. Please look into the code of
read_fcdc_header (using the matlab debugger) to figure out what your
exact problem is.

best
Robert


From r.oostenveld at FCDONDERS.RU.NL  Fri Jun 23 15:28:03 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 23 Jun 2006 15:28:03 +0200
Subject: Missing minimumnormestimate etc
In-Reply-To: <449AC08B.4080202@UKAachen.de>
Message-ID: <FRI.23.JUN.2006.152803.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Mikhail

My loreta implementation still has some problems and is not 100%
correct. I first want to fix it before I release it. If you know how
to work with KEY-LORETA (the software from Pasqual Marqui) and could
compare the two implementations, you could get a pre-release version
and help fix the bugs.

Robert


On 22 Jun 2006, at 18:08, Mikhail Zvyagintsev wrote:

> Dear Robert,
>
> Would be also nice to have an implementaion of LORETA approach for
> source analysis from your in-house software. I would appreciate if
> you could send it to me as well.
>
> Best regards,
>
> Mikhail Zvyagintsev
>
> MZvyagintsev at UKAachen.de


From MZvyagintsev at UKAACHEN.DE  Mon Jun 26 13:15:34 2006
From: MZvyagintsev at UKAACHEN.DE (Mikhail Zvyagintsev)
Date: Mon, 26 Jun 2006 13:15:34 +0200
Subject: Missing minimumnormestimate etc
In-Reply-To: <29758FB9-8B0E-4C41-8067-BF39410560A0@fcdonders.ru.nl>
Message-ID: <MON.26.JUN.2006.131534.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Robert,
Thank you for this encouragement. I was working with LORETA from Pasqual
Marqui only with EEG data. I hope it will help me to be useful with
fixing bugs.
Kindly,
Mikhail.

MZvyagintsev at UKAachen.de

Robert Oostenveld wrote:

> Dear Mikhail
>
> My loreta implementation still has some problems and is not 100%
> correct. I first want to fix it before I release it. If you know how
> to work with KEY-LORETA (the software from Pasqual Marqui) and could
> compare the two implementations, you could get a pre-release version
> and help fix the bugs.
>
> Robert


From esther.meeuwissen at FCDONDERS.RU.NL  Mon Jun 26 15:04:27 2006
From: esther.meeuwissen at FCDONDERS.RU.NL (Esther Meeuwissen)
Date: Mon, 26 Jun 2006 15:04:27 +0200
Subject: artifact rejection
Message-ID: <MON.26.JUN.2006.150427.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi all,

A few weeks ago I started to work with Fieldtrip. I would like use it to 
analyze EEG data.

I have a question concerning preprocessing of EEG data. I would like to do 
a artifact rejection during preprocessing partly using the functions in 
fieldtrip (detection and rejection of  muscle artifacts) and partly 
reading in artifact markers that are exported out of brain vision analyser 
(I used the raw data inspector to detect eye blinks).

I used the following script:

EEGchans = 
{'Fp2', 'F7', 'F3', 'Fz', 'F4', 'F8', 'FC5', 'FC1', 'FCz', 'FC2', 'FC6', 'T
7', 'C3', 'Cz', 'C4', 'T8', 'CP5', 'CP1', 'CP2', 'CP6', 'TP10', 'P7', 'P3',
 'Pz', 'P4', 'P8', 'O1', 'O2'};
EOGchans = {'VB','HL', 'HR', 'VO'};

files = {'GOS10B'...
    'GOS11C'};
for subject=1:2,
   
% Parameters
cfg = [];
cfg.datafile            = strcat('',files{subject},'.eeg');
cfg.headerfile          = strcat('',files{subject},'.vhdr');
cfg.trialdef.trgfile    = strcat('',files{subject},'.vmrk');
cfg.rejectfile          = strcat('',files{subject},'_Reject.Marker');
cfg.icaresultfile       = strcat('',files{subject},'.ica');
cfg.outdatafile         = strcat('',files{subject},'.mat');

cfg.channel    = {'all'};
cfg.padding    = 1.5;
cfg.bpfilter   = 'yes';
cfg.bpfreq     = [0.3 30];
cfg.blc        = 'yes';
cfg.blcwindow  = [-0.1 0.0];

% EEG options
cfg.reref      = 'no';
cfg.implicitref = [];
cfg.refchannel  = {};

% Trial definition
cfg.trialdef.stim = [1 2 3 4];   
cfg.trialdef.prestim    = 0.200;
cfg.trialdef.poststim   = 1.000;

% Artifact options (preprocessing)
cfg.artfctdef.reject            = 'complete';
cfg.artfctdef.muscle.sgn        = EEGchans;
cfg.artfctdef.muscle.feedback   = 'no';
cfg.artfctdef.muscle.cutoff     = 15;

% Do preprocessing
cfg = definetrial(cfg);
cfg = artifact_muscle(cfg)
cfg = rejectartifact(cfg);
data = preprocessing(cfg);

%Save intermediate result
save(cfg.outdatafile,'data');
clear data;
pack;
end;

and get the following error message:

 Error using ==> horzcat
CAT arguments dimensions are not consistent.

Error in ==> rejectartifact at 182
    cfg.artfctdef.type = [{'file'} cfg.artfctdef.type];

Error in ==> preprocessing at 317
[cfg] = rejectartifact(cfg);

Error in ==> preproesther1 at 45
data = preprocessing(cfg);

By trying to make it work I figured out that it is possible to do both the 
artifact rejection parts separately using (parts of) the script above but  
(Fieldtrip wants to combine two matrices to 1 matrix and that is what goes 
wrong). Does anyone know how (/whether) it is possible to do a artifact 
detection/rejection in Fieldtrip partly using functions of Fieldtrip 
itself and partly read markers of EEG parts containing a artifact (the 
file made by brain vision analyzer)?

Thanks in advance for the answer(s)!
Esther Meeuwissen


From r.oostenveld at FCDONDERS.RU.NL  Mon Jun 26 17:17:49 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Mon, 26 Jun 2006 17:17:49 +0200
Subject: artifact rejection
In-Reply-To: <LISTSERV%200606261504275190.1F7B@NIC.SURFNET.NL>
Message-ID: <MON.26.JUN.2006.171749.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Esther,

On 26 Jun 2006, at 15:04, Esther Meeuwissen wrote:
> and get the following error message:
>
>  Error using ==> horzcat
> CAT arguments dimensions are not consistent.
>
> Error in ==> rejectartifact at 182
>     cfg.artfctdef.type = [{'file'} cfg.artfctdef.type];

I suspect here that cfg.artfctdef.type is a cell-array with strings
represented as a vertical cell-vector, and that line 182 tries to
combine it with something that Matlab treats as horizontal cell-
vector. It is unclear to me why it does that, since the
cfg.artfctdef.type is built up internally (you did not explicitely
specify it).

> Error in ==> preprocessing at 317
> [cfg] = rejectartifact(cfg);
>
> Error in ==> preproesther1 at 45
> data = preprocessing(cfg);
>
> By trying to make it work I figured out that it is possible to do
> both the
> artifact rejection parts separately using (parts of) the script
> above but
> (Fieldtrip wants to combine two matrices to 1 matrix and that is
> what goes
> wrong). Does anyone know how (/whether) it is possible to do a
> artifact
> detection/rejection in Fieldtrip partly using functions of Fieldtrip
> itself and partly read markers of EEG parts containing a artifact (the
> file made by brain vision analyzer)?

I have tried replicating your problem (with the data that I found on /
home/electromag/estmee/GOs/analyses/datagoed), but did not encounter
any problems up to the definetrial, artifatc_muscle and
rejectartifact. However, the problem comes only in when preprocessing
is called. For backward compatibility with other peoples old scripts,
preprocessing is also calling definetrial and rejhectartifact, and
rejectartifact seems confused by being called twice.

I made a small change to rejectartifact that hopefully fixes the
problem. The updated version is on home/common now and will be on the
ftp this evening.

best regards,
Robert


From Esther.Meeuwissen at FCDONDERS.RU.NL  Tue Jun 27 09:05:21 2006
From: Esther.Meeuwissen at FCDONDERS.RU.NL (Esther Meeuwissen)
Date: Tue, 27 Jun 2006 09:05:21 +0200
Subject: artifact rejection
In-Reply-To: <442FC113-07E9-4479-9237-6D20F1D026C8@fcdonders.ru.nl>
Message-ID: <TUE.27.JUN.2006.090521.0200.FIELDTRIP@NIC.SURFNET.NL>

Robert Oostenveld wrote:
> Hi Esther,
>
> On 26 Jun 2006, at 15:04, Esther Meeuwissen wrote:
>> and get the following error message:
>>
>>  Error using ==> horzcat
>> CAT arguments dimensions are not consistent.
>>
>> Error in ==> rejectartifact at 182
>>     cfg.artfctdef.type = [{'file'} cfg.artfctdef.type];
>
> I suspect here that cfg.artfctdef.type is a cell-array with strings
> represented as a vertical cell-vector, and that line 182 tries to
> combine it with something that Matlab treats as horizontal
> cell-vector. It is unclear to me why it does that, since the
> cfg.artfctdef.type is built up internally (you did not explicitely
> specify it).
>
>> Error in ==> preprocessing at 317
>> [cfg] = rejectartifact(cfg);
>>
>> Error in ==> preproesther1 at 45
>> data = preprocessing(cfg);
>>
>> By trying to make it work I figured out that it is possible to do
>> both the
>> artifact rejection parts separately using (parts of) the script above
>> but
>> (Fieldtrip wants to combine two matrices to 1 matrix and that is what
>> goes
>> wrong). Does anyone know how (/whether) it is possible to do a artifact
>> detection/rejection in Fieldtrip partly using functions of Fieldtrip
>> itself and partly read markers of EEG parts containing a artifact (the
>> file made by brain vision analyzer)?
>
> I have tried replicating your problem (with the data that I found on
> /home/electromag/estmee/GOs/analyses/datagoed), but did not encounter
> any problems up to the definetrial, artifatc_muscle and
> rejectartifact. However, the problem comes only in when preprocessing
> is called. For backward compatibility with other peoples old scripts,
> preprocessing is also calling definetrial and rejhectartifact, and
> rejectartifact seems confused by being called twice.
>
> I made a small change to rejectartifact that hopefully fixes the
> problem. The updated version is on home/common now and will be on the
> ftp this evening.
>
> best regards,
> Robert
>



From cgra05 at HST.AUC.DK  Thu Jun  1 12:34:31 2006
From: cgra05 at HST.AUC.DK (Carina Graversen)
Date: Thu, 1 Jun 2006 12:34:31 +0200
Subject: SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG
 data ???
In-Reply-To: <003e01c68493$c1b918f0$642dae83@fcdonders.nl>
Message-ID: <THU.1.JUN.2006.123431.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Ingrid,

OH - sorry, I didn't notice the question had already been asked on the
webpage.

However, I still couldn't find the answer on how to create the values for
column 2 and 3, since it says at the webpage "The 2nd and 3rd are the
X-position and Y-position". However, when I generate the layout file from
Neuroscan I get some values for the X and Y coordinates, that are very
different from yours, and the plot ends up in a big mess (see the attached
file).

So I was wondering if you have any idea of how to generate the X- and
Y-positions from Neuroscan ???
(I have attached the generated layout-file from Neuroscan, in case that
helps you. This one is named test128_neuroscan.lay)

We were also wondering about the figure you e-mailed from our data, all
channels appeared to be blue with a green cone (and then some frequency
contributions in some channels). Is it because of some settings not edited
correct, because we would have expected something like in the
documentation - like figure 2 at the "Time-frequency Analysis Using
Multitapers and Wavelets" page.

>>From the test128_neuroscan.lay I tried to create the layout file
test128_fieldtrip.lay, and got the plot shown in figure
test128_fieldtrip.png



Best regards,
Carina Graversen





-----Oprindelig meddelelse-----
Fra: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]Pa vegne
af Ingrid Nieuwenhuis
Sendt: 31. maj 2006 10:23
Til: FIELDTRIP at NIC.SURFNET.NL
Emne: Re: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel
Neuroscan EEG data ???


Hi Carina,

If you look at the FieldTrip page -> documentation -> frequently asked
questions you can find the question (and answer):

What is the format of the layout file, which is used for plotting?

...The 4th and 5th column specify the with and height of the subplot that
will be made in multiplotER and multiplotTFR....

So the two columns with the same value for all channels are those columns.

Bests,
Ingrid

-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Carina Graversen
Sent: Wednesday, May 31, 2006 10:58 AM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan
EEG data ???

Hi Ingrid.

Thanks a lot.

I have tried to generate my own layout file in Neuroscan, but unfortunately
it doesn't work. So I was wondering if you can tell me the format of the
layout-file, because when I look at your file, 2 of the columns contain the
same value for all channels.

I have tried to generate for both cartesian and polor, but none of them
matches. In the generated file I get the format:
<display page><channel number><pos x0><pos y0><pos x1><pos y1>

Can I change my input configuration to either use this format, or how should
I change the format of the layout file ???

Thanks in advance  :o)

/Carina





-----Oprindelig meddelelse-----
Fra: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]Pa vegne
af Ingrid Nieuwenhuis
Sendt: 26. maj 2006 13:29
Til: FIELDTRIP at NIC.SURFNET.NL
Emne: Re: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG data
???


Hi Carina,

Thanks for sending me the data. Indeed the biosemi 128ch layout doesn't
correspond to your layout. You have 128 channels labeled from 1 to 128. If
you open biosemi128.lay in a text-editor you can see that this layout file
has 150 channels labeled from A1 to P7. The labels in your data
(TFRmult.label) and the labels in the layout file don't match, that's why
you got an empty figure (I'll add an error in the plot function, so that
when no labels match you'll get an error message in the future).

So what you have to do now is to make your own layout file that matches the
data; with the correct x and y coordinates of the 128 channels and the same
label names as in your data. Just as an illustration I attached an adapted
version of the biosemi128.lay file, with only the first 128 channels, and
labels 1 to 128, just as in your data. With the following configuration:

cfg8 = [];
cfg8.baseline   = [0 0.1];
cfg8.xlim       = [0 0.3]
cfg8.ylim       = [15 29];
cfg8.zlim       = [-100 100];
cfg8.showlabels = 'yes';
cfg8.layout    = 'testlay128.lay';

I got the attached figure from your data.

Good luck,
Ingrid



-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Robert Oostenveld
Sent: Wednesday, May 24, 2006 8:57 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG data ???

Hi Carina

Are you sure that the biosemi 128ch layout corresponds with your
electrode layout? Open the layout file in a tetx editor and look at
http://www2.ru.nl/fcdonders/fieldtrip/doku.php?
id=fieldtrip:documentation:frequently_asked_questions#what_is_the_format
_of_the_layout_file_which_is_used_for_plotting

I suggest that you try the elec1010.lay or elec1005.lay, or even
better, that you construct your own layout file corresponding with
your own electrode locations.

Robert


On 24 May 2006, at 12:29, Carina Graversen wrote:

> Hi.
>
> I'm trying to use the Fieldtrip program to create a wavelet plot of
> my EEG
> data.
>
> I have used it previously for 64 channel recordings, but now I'm
> working
> with 128 channels of data, which is causing me some problems. The
> only thing
> I have changed is the command:
> cfg8.layout    = 'biosemi128.lay';
>
> But now the figure only outputs a grey page with no Time-Frequency
> distributions at all.
>
> Can anyone tell me what I'm doing wrong - below is a complete list
> of all
> the commands I use  :o).
>
> Best Regards,
> Carina Graversen
>
>
>
>
> %
> **********************************************************************
> ***
> % EVENTRELATEDAVERAGING
> %
> **********************************************************************
> ***
> cfg1 = [];                                                     % empty
> configuration
> cfg1.datafile                      = 'test128.eeg';            %
> 128 channel
> Neuroscan eeg file
> cfg1.headerfile                    = 'test128.eeg';
> cfg1.channel                       = 'all';
>
> dataFIC = preprocessing(cfg1);                                 %
> Preprocess!
>
> cfg2 = [];                                                     % empty
> configuration
>
> avgFIC = timelockanalysis(cfg2, dataFIC);
>
>
> % %
> **********************************************************************
> ***
> % % WAVELET
> % %
> **********************************************************************
> ***
> cfg7 = [];
> cfg7.output     = 'pow';
> cfg7.method     = 'wltconvol'
> cfg7.foi        = 1:2:30;
> cfg7.t_ftimwin  = 5./cfg7.foi;
> cfg7.tapsmofrq  = 0.4 *cfg7.foi;
> cfg7.toi        = 0:0.01:0.5;
>
> TFRmult = freqanalysis(cfg7, avgFIC);
>
> cfg8 = [];
> cfg8.baseline   = [-0.5 0.5];
> cfg8.xlim       = [0 0.5]
> cfg8.zlim       = [-3e-27 0.2];
> cfg8.showlabels = 'yes';
> cfg8.layout    = 'biosemi128.lay';
>
> multiplotTFR(cfg8, TFRmult);
>
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From r.oostenveld at FCDONDERS.RU.NL  Thu Jun  1 12:35:43 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 1 Jun 2006 12:35:43 +0200
Subject: Filtering
In-Reply-To: <000001c683f3$4e30cb30$90514484@dellgx240>
Message-ID: <THU.1.JUN.2006.123543.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Vladimir

On 30 May 2006, at 16:14, Vladimir Litvak wrote:
> As I understand, when I do filtering in preprocessing the filter is
> applied before the data is cut to epochs.

Not completely: a segment of data is read from file that contains the
trial (trl) plus the optional padding. That segment is filtered and
then the padding is thrown away. Eventual filter atrifacts at the
boundaries of the data segment that was read are in the padding and
thus would not affect the data of interest itself. If you apply
padding, the effect is the same as if you would have filtered the
complete data continuously.

> I now want to do some analysis where I want to filter after the
> epochs are cut out (because there are TMS deltas there and I don't
> want them to affect everything around them). Is there a simple way
> to filter epoched data in FT (other than by my own code)?

You can specify cfg.padding=0 in preprocessing and ensure that the
TMS pulse is not inside the trial definition. You can do
preprocessing without any options and then use timelockanalysis (with
keeptrials) on it. Timelockanalysis supports almost all options that
preprocessing has, i.e. all filtering and baselinecorection options,
but of course cannot do the padding. Those additional options are not
documented in timelockanalysis, but look in the code and you will
see  them. Doing it in timelockanalysis has the advantage that it is
easier to play around with filter settings (i.e. it is faster not
having to read the data every time). Also interesting to know perhaps
is that you can also apply timelockanalysis and its filtering to an
average, i.e. timelockanalysis will accept a timelock-structure as
input. So you can average in the first call to timelockanalysis, and
then throw that average into timelockanalysis a second time to see
the effect of the filter. In the latter case only the average is
filtered, i.e. it is very fast.

best
Robert


From ingrid.nieuwenhuis at FCDONDERS.RU.NL  Thu Jun  1 13:21:11 2006
From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis)
Date: Thu, 1 Jun 2006 13:21:11 +0200
Subject: SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG
 data ???
In-Reply-To: <LMELLGAMDIJKNDEFIMFHEECDCHAA.cgra05@hst.auc.dk>
Message-ID: <THU.1.JUN.2006.132111.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Carina,

The problem is that the width and height of the boxes (column 4 and 5) are
too big compared to your x and y coordinates. What multiplotTFR does is that
it plots the TFR boxes at the specified coordinates. The x and y coordinates
are between +/- 0 and 0.7 and the box width/height is 0.18	and 1.14, so
all the plots are plotted on top of each other. That's why it is a mess. So
you could use the x and y coordinates, but the boxes should be smaller, or
you can scale it al up.

What comes out of the plots is just what the data is. Probably depends on
your settings during the TFR analysis. The dark blue at the edges and bottom
are NaN's in the data.

Bests,
Ingrid



-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Carina Graversen
Sent: Thursday, June 01, 2006 12:35 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel
Neuroscan EEG data ???

Hi Ingrid,

OH - sorry, I didn't notice the question had already been asked on the
webpage.

However, I still couldn't find the answer on how to create the values for
column 2 and 3, since it says at the webpage "The 2nd and 3rd are the
X-position and Y-position". However, when I generate the layout file from
Neuroscan I get some values for the X and Y coordinates, that are very
different from yours, and the plot ends up in a big mess (see the attached
file).

So I was wondering if you have any idea of how to generate the X- and
Y-positions from Neuroscan ???
(I have attached the generated layout-file from Neuroscan, in case that
helps you. This one is named test128_neuroscan.lay)

We were also wondering about the figure you e-mailed from our data, all
channels appeared to be blue with a green cone (and then some frequency
contributions in some channels). Is it because of some settings not edited
correct, because we would have expected something like in the
documentation - like figure 2 at the "Time-frequency Analysis Using
Multitapers and Wavelets" page.

>>From the test128_neuroscan.lay I tried to create the layout file
test128_fieldtrip.lay, and got the plot shown in figure
test128_fieldtrip.png



Best regards,
Carina Graversen





-----Oprindelig meddelelse-----
Fra: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]Pa vegne
af Ingrid Nieuwenhuis
Sendt: 31. maj 2006 10:23
Til: FIELDTRIP at NIC.SURFNET.NL
Emne: Re: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel
Neuroscan EEG data ???


Hi Carina,

If you look at the FieldTrip page -> documentation -> frequently asked
questions you can find the question (and answer):

What is the format of the layout file, which is used for plotting?

...The 4th and 5th column specify the with and height of the subplot that
will be made in multiplotER and multiplotTFR....

So the two columns with the same value for all channels are those columns.

Bests,
Ingrid

-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Carina Graversen
Sent: Wednesday, May 31, 2006 10:58 AM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: [FIELDTRIP] SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan
EEG data ???

Hi Ingrid.

Thanks a lot.

I have tried to generate my own layout file in Neuroscan, but unfortunately
it doesn't work. So I was wondering if you can tell me the format of the
layout-file, because when I look at your file, 2 of the columns contain the
same value for all channels.

I have tried to generate for both cartesian and polor, but none of them
matches. In the generated file I get the format:
<display page><channel number><pos x0><pos y0><pos x1><pos y1>

Can I change my input configuration to either use this format, or how should
I change the format of the layout file ???

Thanks in advance  :o)

/Carina





-----Oprindelig meddelelse-----
Fra: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]Pa vegne
af Ingrid Nieuwenhuis
Sendt: 26. maj 2006 13:29
Til: FIELDTRIP at NIC.SURFNET.NL
Emne: Re: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG data
???


Hi Carina,

Thanks for sending me the data. Indeed the biosemi 128ch layout doesn't
correspond to your layout. You have 128 channels labeled from 1 to 128. If
you open biosemi128.lay in a text-editor you can see that this layout file
has 150 channels labeled from A1 to P7. The labels in your data
(TFRmult.label) and the labels in the layout file don't match, that's why
you got an empty figure (I'll add an error in the plot function, so that
when no labels match you'll get an error message in the future).

So what you have to do now is to make your own layout file that matches the
data; with the correct x and y coordinates of the 128 channels and the same
label names as in your data. Just as an illustration I attached an adapted
version of the biosemi128.lay file, with only the first 128 channels, and
labels 1 to 128, just as in your data. With the following configuration:

cfg8 = [];
cfg8.baseline   = [0 0.1];
cfg8.xlim       = [0 0.3]
cfg8.ylim       = [15 29];
cfg8.zlim       = [-100 100];
cfg8.showlabels = 'yes';
cfg8.layout    = 'testlay128.lay';

I got the attached figure from your data.

Good luck,
Ingrid



-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Robert Oostenveld
Sent: Wednesday, May 24, 2006 8:57 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG data ???

Hi Carina

Are you sure that the biosemi 128ch layout corresponds with your
electrode layout? Open the layout file in a tetx editor and look at
http://www2.ru.nl/fcdonders/fieldtrip/doku.php?
id=fieldtrip:documentation:frequently_asked_questions#what_is_the_format
_of_the_layout_file_which_is_used_for_plotting

I suggest that you try the elec1010.lay or elec1005.lay, or even
better, that you construct your own layout file corresponding with
your own electrode locations.

Robert


On 24 May 2006, at 12:29, Carina Graversen wrote:

> Hi.
>
> I'm trying to use the Fieldtrip program to create a wavelet plot of
> my EEG
> data.
>
> I have used it previously for 64 channel recordings, but now I'm
> working
> with 128 channels of data, which is causing me some problems. The
> only thing
> I have changed is the command:
> cfg8.layout    = 'biosemi128.lay';
>
> But now the figure only outputs a grey page with no Time-Frequency
> distributions at all.
>
> Can anyone tell me what I'm doing wrong - below is a complete list
> of all
> the commands I use  :o).
>
> Best Regards,
> Carina Graversen
>
>
>
>
> %
> **********************************************************************
> ***
> % EVENTRELATEDAVERAGING
> %
> **********************************************************************
> ***
> cfg1 = [];                                                     % empty
> configuration
> cfg1.datafile                      = 'test128.eeg';            %
> 128 channel
> Neuroscan eeg file
> cfg1.headerfile                    = 'test128.eeg';
> cfg1.channel                       = 'all';
>
> dataFIC = preprocessing(cfg1);                                 %
> Preprocess!
>
> cfg2 = [];                                                     % empty
> configuration
>
> avgFIC = timelockanalysis(cfg2, dataFIC);
>
>
> % %
> **********************************************************************
> ***
> % % WAVELET
> % %
> **********************************************************************
> ***
> cfg7 = [];
> cfg7.output     = 'pow';
> cfg7.method     = 'wltconvol'
> cfg7.foi        = 1:2:30;
> cfg7.t_ftimwin  = 5./cfg7.foi;
> cfg7.tapsmofrq  = 0.4 *cfg7.foi;
> cfg7.toi        = 0:0.01:0.5;
>
> TFRmult = freqanalysis(cfg7, avgFIC);
>
> cfg8 = [];
> cfg8.baseline   = [-0.5 0.5];
> cfg8.xlim       = [0 0.5]
> cfg8.zlim       = [-3e-27 0.2];
> cfg8.showlabels = 'yes';
> cfg8.layout    = 'biosemi128.lay';
>
> multiplotTFR(cfg8, TFRmult);
>


From r.oostenveld at FCDONDERS.RU.NL  Thu Jun  1 13:51:02 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 1 Jun 2006 13:51:02 +0200
Subject: SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG
 data ???
In-Reply-To: <LMELLGAMDIJKNDEFIMFHEECDCHAA.cgra05@hst.auc.dk>
Message-ID: <THU.1.JUN.2006.135102.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Carina,

Please take attached "layoutplot" function and copy it into the
fieldtrip directory. Then do

 >> cfg.layout = 'CTF151.lay'
cfg =
     layout: 'CTF151.lay'

 >> layoutplot(cfg)
reading layout from file CTF151.lay

and you will get the attached figure for the 151 channel CTF system.
Then try plotting the other layouts (the *.lay files) and your own
layout, and modify the values in your own layout file (in a text
editor) untill you like what you see.

Robert

PS when I was looking at the other layouts, I noticed that the
elec1020, elec1010 and elec1005 layouts supplied with fieldtrip are
not optimal, since they also have overlapping boxes.

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From r.oostenveld at FCDONDERS.RU.NL  Thu Jun  1 13:58:48 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 1 Jun 2006 13:58:48 +0200
Subject: query on coherence source analysis
In-Reply-To: <BAY12-F10440EA05E5791B6BF0425CE9D0@phx.gbl>
Message-ID: <THU.1.JUN.2006.135848.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Muthuraman

I have not been able to reproduce your error. I suggest that you get
the latest version of FieldTrip from our FTP server and try again.

best egards,
Robert

PS this is the test script I used. It uses some simulated data, which
again uses a MEG gradiometer definition and a head model from the
tutorial data.


-----------------
% read some data that is required to simulate MEG data, i.e. volume
model,
% sensor positions and MRI (optional, only for plotting)
vol  = read_ctf_hdm('Subject01.hdm');
hdr  = read_fcdc_header('Subject01.ds/Subject01.res4');
grad = hdr.grad;

% construct the simulated MEG data for condition A ("active")
cfg               = [];
cfg.vol           = vol;
cfg.grad          = grad;
cfg.fsample       = 300;
cfg.ntrials       = 2;
cfg.triallength   = 1;
cfg.dip.pos       = [0 7 8];
cfg.dip.mom       = [1 0 0];
cfg.dip.signal    = sin(2*pi*10*(1:cfg.fsample)./cfg.fsample);
cfg.absnoise      = 1e-8;
data = dipolesimulation(cfg);

% add the source signal as fake EMG channel
for i=1:cfg.ntrials
   data.trial{i}(end+1,:) = cfg.dip.signal + randn(size
(cfg.dip.signal));
end
data.label{end+1} = 'EMG';

cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'MEG' 'EMG'},data.label);
cfg.channelcmb={'MEG' 'EMG'};
freq=freqanalysis(cfg,data);





From olga at GRAPHICMIND.INFO  Sat Jun  3 12:45:41 2006
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Sat, 3 Jun 2006 14:45:41 +0400
Subject: deleting two EOG channale from data-stucture
Message-ID: <SAT.3.JUN.2006.144541.0400.FIELDTRIP@NIC.SURFNET.NL>

Dear list members,
I would like to delete two channels from my data. How is it better to do this?
Best Regards,
Olga
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From olga at GRAPHICMIND.INFO  Sat Jun  3 14:16:57 2006
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Sat, 3 Jun 2006 16:16:57 +0400
Subject: and clusterrandomization
Message-ID: <SAT.3.JUN.2006.161657.0400.FIELDTRIP@NIC.SURFNET.NL>

Thank you very much, Eric!
That was an inconsistency in the loci of EOG channels between subjects. Now
I corrected it: HEOG and VEOG data are still presented in the data
structure, but do not have the location (pnt 0 0 0). Is it OK? The results
looks as what I excpected.
Best Regards,
Olga.

----- Original Message -----
From: "Eric Maris" <maris at NICI.RU.NL>
To: <FIELDTRIP at NIC.SURFNET.NL>
Sent: Friday, May 26, 2006 5:35 PM
Subject: Re: [FIELDTRIP] and clusterrandomization


> Dear Olga,
>
>
> But the problems is still in my clusterrandomization.
> Could the fact that the order of the channel in the file (C_vc11.label) is
> not the same as in the C_vc11.elec.label influences the result of
> clusterrandomization (I do not have my neigbouring channel file)?
>
>
> That should not matter. However, the labels in your data structure (.label
> in the output of timelockgrandaverage) should exactly match the labels in
> the elec-structure. If that is OK, then something might have gone wrong
> with the combination of the data of the different subjects. Do they all
> have the same elec-structure? If the same physical channel has different
> labels for different subjects, then this may create inconsistencies
> between EEGlab and Fieldtrip. For Fieldtrip, channels that have the same
> label are assumed to be physically identical, even if they are in
> different positions in the data structure. This is only a guess, of
> course.
>
>
> kind regards,
>
> Eric Maris
>
>
>
>
>
>
>
>
>
> Best Regards,
> Olga.
>  ----- Original Message -----
>  From: Ingrid Nieuwenhuis
>  To: FIELDTRIP at NIC.SURFNET.NL
>  Sent: Wednesday, May 24, 2006 8:45 PM
>  Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>
>
>  Hi Olga,
>
>
>
>  About the z-param:
>
>  This is the field that contains the data to be plotted; for instance
> 'avg', 'powspctrm' or 'cohspctrm'. Normally the function looks in your
> data.dimord to find out which z-param to use. To make the function work
> you could give cfg.zparam = 'avg' (for instance if you want to plot an
> ERF/ERP). But if you could send me what the dimord field of the data that
> you want to plot is, I could look why the plot functions don't extract the
> correct zparam themselves.
>
>
>
>  About the timelockgranaveraging: I also think it should be the same. I
> have no idea what it could be.
>
>
>
>  Good luck,
>
>  Ingrid Nieuwenhuis
>
>
>
>
> ------------------------------------------------------------------------------
>
>  From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf Of Olga Sysoeva
>  Sent: Wednesday, May 24, 2006 5:44 PM
>  To: FIELDTRIP at NIC.SURFNET.NL
>  Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>
>
>
>  Dear List member,
>
>
>
>  Sorry for such dull questions but,
>
>  I am again facing the new problems with Fieldtrip, although did not solve
> some previous one (still can not singleplot and multiplot anything 'cause
> of "unknown zparam field".
>
>
>
>  OK, about new one :-)
>
>
>
>  It seems that I did not use write the timelockgranaveraging.
>
>
>
>   The problem must be here, when I made grand averaging of all my 11
> subject
>   data
>
>                    cfg =[];
>                     cfg.keepindividual = 'yes'
>                     C_vc11  =
>
> timelockgrandaverage(cfg,vc_c_avg1,vc_c_avg2,vc_c_avg3,vc_c_avg4,vc_c_avg5,
> vc_c_avg6,vc_c_avg7,vc_c_avg8,vc_c_avg9,vc_c_avg10,vc_c_avg11 );
>
>  As I understand the
>
>  vc_c_avg11.avg([9],[43]) should be similar with C_vc11.individual ([11],
> [9], [43])
>  But it is not.
>  What can it be?
>
>  Best Regards,
>
>  Olga.
>
>
>
>
>
>    ----- Original Message -----
>
>    From: Olga Sysoeva
>
>    To: FIELDTRIP at NIC.SURFNET.NL
>
>    Sent: Saturday, May 13, 2006 4:34 PM
>
>    Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>
>
>
>    Thank you very much, Lilla!
>
>    Now I knwo what to do but faced the problem with " unknown zparam
> field" when ploting the results. Unfortunatly cfg.zparam does not
> discribed in help file...
>
>    Best Regards, Olga
>
>      ----- Original Message -----
>
>      From: Lilla Magyari
>
>      To: FIELDTRIP at NIC.SURFNET.NL
>
>      Sent: Saturday, May 13, 2006 3:11 PM
>
>      Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data
> within-subject
>
>
>
>      Dear Olga,
>
>
>
>      I am just studying time-frequency analysis but I have done already on
> my data, so perhaps I can help you.
>
>      First, yes, you have to do freqanalysis on the preprocessed data of
> the individual subjects for all conditions that you want to compare (i.e.
> the input for this function contains all trials from one subject in one
> condition.) And it is also important that the other input for this
> function is the cfg where for example, in the cfg.method you have to
> specify what kind of time-frequency analysis you want to use. (You have to
> write 'wltconvol' for wavelet transformation and 'mltconvol' for
> multitaper analysis.)
>
>      When you use freqanalysis as output you can get TFR for one subject
> in one condition (but it is also possible to keep the information for the
> individual trials of the condition by specifying cfg.keeptrials = 'yes').
> When you have the TFRs for each subject you can grandaverage them with
> freqgrandaverage where the input is the TFRs of all subjects (and before
> averaging you can use also freqbaseline for giving a baseline for your
> TFRs).
>
>
>
>      I hope it helps.
>
>
>
>      Best regards,
>
>      Lilla Magyari
>
>
>
>
>
>
>
>
> --------------------------------------------------------------------------
>
>      From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf Of Olga Sysoeva
>      Sent: Saturday, May 13, 2006 9:28 AM
>      To: FIELDTRIP at NIC.SURFNET.NL
>      Subject: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>
>
>
>      Dear list members,
>
>
>
>      Thank you everybody for your help! I've already got interesting
> results using clusterrandomization on my data! Thanks a lot!
>
>
>
>      Now I have a question about using the clusterrandomization on 3-D
> data (channel-time-frequency) in within-subject analysis.
>
>      As I understand it is possible with Fieldtrip, but I really newby in
> time-frequency anlysis, therefore wanted your comments,
>
>      as far as I didn't find the example of the application of
> clusteranalysis on this set of the data in tuturial.
>
>
>
>      I successfully conduct the within-subject clusterrandomization on my
> grand-average data, which does not have the third, frequency demintion.
>
>      Now I want to add it. But I could not apply freqanalyisis on
> grandavarage data, could I? Should I made the TFR of individual data and
> than grand-avarage the result?
>
>      Which function should I use?
>
>
>
>      Best Regards,
>
>      Olga.


From olga at GRAPHICMIND.INFO  Sat Jun  3 14:26:35 2006
From: olga at GRAPHICMIND.INFO (Olga Sysoeva)
Date: Sat, 3 Jun 2006 16:26:35 +0400
Subject: clusrand: 19 channels 0 minnbchan
Message-ID: <SAT.3.JUN.2006.162635.0400.FIELDTRIP@NIC.SURFNET.NL>

Dear experts,

Does it make sense to make clusterrandomization if I put "0" in the min number of neibouring channels if I have only 19 of them (10-20 system)?
As I understand in this case just the time is considered when clustering. How many consequent time point is requiered to build a cluster? 

Best Regards,
Olga.
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From maris at NICI.RU.NL  Sat Jun  3 18:47:21 2006
From: maris at NICI.RU.NL (Eric Maris)
Date: Sat, 3 Jun 2006 18:47:21 +0200
Subject: deleting two EOG channale from data-stucture
Message-ID: <SAT.3.JUN.2006.184721.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Olga,


I would like to delete two channels from my data. How is it better to do
this?


Type "help channelselection" at the Matlab command line. This will give you
information on how the Fieldtrip functions perform channelselection on the
basis of the input in cfg.channel. I don't have Matlab running now, but I
think that '-EOG' in cfg.channel will do the job you request.


greetings,

Eric


From maris at NICI.RU.NL  Sat Jun  3 18:50:06 2006
From: maris at NICI.RU.NL (Eric Maris)
Date: Sat, 3 Jun 2006 18:50:06 +0200
Subject: and clusterrandomization
Message-ID: <SAT.3.JUN.2006.185006.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Olga,

> That was an inconsistency in the loci of EOG channels between subjects.
> Now I corrected it: HEOG and VEOG data are still presented in the data
> structure, but do not have the location (pnt 0 0 0). Is it OK? The results
> looks as what I excpected.

Because you never will include the EOG-channels in an analysis of the
EEG-channels, the location of the EOG is not required by
clusterrandanalysis.

greetings,

Eric Maris



> Best Regards,
> Olga.
>
> ----- Original Message -----
> From: "Eric Maris" <maris at NICI.RU.NL>
> To: <FIELDTRIP at NIC.SURFNET.NL>
> Sent: Friday, May 26, 2006 5:35 PM
> Subject: Re: [FIELDTRIP] and clusterrandomization
>
>
>> Dear Olga,
>>
>>
>> But the problems is still in my clusterrandomization.
>> Could the fact that the order of the channel in the file (C_vc11.label)
>> is not the same as in the C_vc11.elec.label influences the result of
>> clusterrandomization (I do not have my neigbouring channel file)?
>>
>>
>> That should not matter. However, the labels in your data structure
>> (.label in the output of timelockgrandaverage) should exactly match the
>> labels in the elec-structure. If that is OK, then something might have
>> gone wrong with the combination of the data of the different subjects. Do
>> they all have the same elec-structure? If the same physical channel has
>> different labels for different subjects, then this may create
>> inconsistencies between EEGlab and Fieldtrip. For Fieldtrip, channels
>> that have the same label are assumed to be physically identical, even if
>> they are in different positions in the data structure. This is only a
>> guess, of course.
>>
>>
>> kind regards,
>>
>> Eric Maris
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Best Regards,
>> Olga.
>>  ----- Original Message -----
>>  From: Ingrid Nieuwenhuis
>>  To: FIELDTRIP at NIC.SURFNET.NL
>>  Sent: Wednesday, May 24, 2006 8:45 PM
>>  Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>>
>>
>>  Hi Olga,
>>
>>
>>
>>  About the z-param:
>>
>>  This is the field that contains the data to be plotted; for instance
>> 'avg', 'powspctrm' or 'cohspctrm'. Normally the function looks in your
>> data.dimord to find out which z-param to use. To make the function work
>> you could give cfg.zparam = 'avg' (for instance if you want to plot an
>> ERF/ERP). But if you could send me what the dimord field of the data that
>> you want to plot is, I could look why the plot functions don't extract
>> the correct zparam themselves.
>>
>>
>>
>>  About the timelockgranaveraging: I also think it should be the same. I
>> have no idea what it could be.
>>
>>
>>
>>  Good luck,
>>
>>  Ingrid Nieuwenhuis
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>>  From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
>> Behalf Of Olga Sysoeva
>>  Sent: Wednesday, May 24, 2006 5:44 PM
>>  To: FIELDTRIP at NIC.SURFNET.NL
>>  Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>>
>>
>>
>>  Dear List member,
>>
>>
>>
>>  Sorry for such dull questions but,
>>
>>  I am again facing the new problems with Fieldtrip, although did not
>> solve some previous one (still can not singleplot and multiplot anything
>> 'cause of "unknown zparam field".
>>
>>
>>
>>  OK, about new one :-)
>>
>>
>>
>>  It seems that I did not use write the timelockgranaveraging.
>>
>>
>>
>>   The problem must be here, when I made grand averaging of all my 11
>> subject
>>   data
>>
>>                    cfg =[];
>>                     cfg.keepindividual = 'yes'
>>                     C_vc11  =
>>
>> timelockgrandaverage(cfg,vc_c_avg1,vc_c_avg2,vc_c_avg3,vc_c_avg4,vc_c_avg5,
>> vc_c_avg6,vc_c_avg7,vc_c_avg8,vc_c_avg9,vc_c_avg10,vc_c_avg11 );
>>
>>  As I understand the
>>
>>  vc_c_avg11.avg([9],[43]) should be similar with C_vc11.individual ([11],
>> [9], [43])
>>  But it is not.
>>  What can it be?
>>
>>  Best Regards,
>>
>>  Olga.
>>
>>
>>
>>
>>
>>    ----- Original Message -----
>>
>>    From: Olga Sysoeva
>>
>>    To: FIELDTRIP at NIC.SURFNET.NL
>>
>>    Sent: Saturday, May 13, 2006 4:34 PM
>>
>>    Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data
>> within-subject
>>
>>
>>
>>    Thank you very much, Lilla!
>>
>>    Now I knwo what to do but faced the problem with " unknown zparam
>> field" when ploting the results. Unfortunatly cfg.zparam does not
>> discribed in help file...
>>
>>    Best Regards, Olga
>>
>>      ----- Original Message -----
>>
>>      From: Lilla Magyari
>>
>>      To: FIELDTRIP at NIC.SURFNET.NL
>>
>>      Sent: Saturday, May 13, 2006 3:11 PM
>>
>>      Subject: Re: [FIELDTRIP] clusterrandomization on 3D-data
>> within-subject
>>
>>
>>
>>      Dear Olga,
>>
>>
>>
>>      I am just studying time-frequency analysis but I have done already
>> on my data, so perhaps I can help you.
>>
>>      First, yes, you have to do freqanalysis on the preprocessed data of
>> the individual subjects for all conditions that you want to compare (i.e.
>> the input for this function contains all trials from one subject in one
>> condition.) And it is also important that the other input for this
>> function is the cfg where for example, in the cfg.method you have to
>> specify what kind of time-frequency analysis you want to use. (You have
>> to write 'wltconvol' for wavelet transformation and 'mltconvol' for
>> multitaper analysis.)
>>
>>      When you use freqanalysis as output you can get TFR for one subject
>> in one condition (but it is also possible to keep the information for the
>> individual trials of the condition by specifying cfg.keeptrials = 'yes').
>> When you have the TFRs for each subject you can grandaverage them with
>> freqgrandaverage where the input is the TFRs of all subjects (and before
>> averaging you can use also freqbaseline for giving a baseline for your
>> TFRs).
>>
>>
>>
>>      I hope it helps.
>>
>>
>>
>>      Best regards,
>>
>>      Lilla Magyari
>>
>>
>>
>>
>>
>>
>>
>>
>> --------------------------------------------------------------------------
>>
>>      From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
>> Behalf Of Olga Sysoeva
>>      Sent: Saturday, May 13, 2006 9:28 AM
>>      To: FIELDTRIP at NIC.SURFNET.NL
>>      Subject: [FIELDTRIP] clusterrandomization on 3D-data within-subject
>>
>>
>>
>>      Dear list members,
>>
>>
>>
>>      Thank you everybody for your help! I've already got interesting
>> results using clusterrandomization on my data! Thanks a lot!
>>
>>
>>
>>      Now I have a question about using the clusterrandomization on 3-D
>> data (channel-time-frequency) in within-subject analysis.
>>
>>      As I understand it is possible with Fieldtrip, but I really newby in
>> time-frequency anlysis, therefore wanted your comments,
>>
>>      as far as I didn't find the example of the application of
>> clusteranalysis on this set of the data in tuturial.
>>
>>
>>
>>      I successfully conduct the within-subject clusterrandomization on my
>> grand-average data, which does not have the third, frequency demintion.
>>
>>      Now I want to add it. But I could not apply freqanalyisis on
>> grandavarage data, could I? Should I made the TFR of individual data and
>> than grand-avarage the result?
>>
>>      Which function should I use?
>>
>>
>>
>>      Best Regards,
>>
>>      Olga.


From maris at NICI.RU.NL  Sat Jun  3 18:53:19 2006
From: maris at NICI.RU.NL (Eric Maris)
Date: Sat, 3 Jun 2006 18:53:19 +0200
Subject: clusrand: 19 channels 0 minnbchan
Message-ID: <SAT.3.JUN.2006.185319.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Olga,


Does it make sense to make clusterrandomization if I put "0" in the min
number of neibouring channels if I have only 19 of them (10-20 system)?
As I understand in this case just the time is considered when clustering.
How many consequent time point is requiered to build a cluster?


Yes, it makes sense. The cfg.minnbchan-field is a way to suppress the
tendency of the cluster-growing algorithm to connect everything with
everything, even on the basis of noise. The FA-rate is not affect by the
value of cfg.minnbchan.


greetings,

Eric Maris


From pchris at UNC.EDU  Mon Jun  5 19:05:30 2006
From: pchris at UNC.EDU (Punita Christopher)
Date: Mon, 5 Jun 2006 19:05:30 +0200
Subject: dipole model
Message-ID: <MON.5.JUN.2006.190530.0200.FIELDTRIP@NIC.SURFNET.NL>

Has anyone seen any literature that deals with a spherical multiple layer 
head model in which the dipole spans across layers i.e. the source and 
sink of the dipole are in separate layers.  
Thanks,
Punita


From r.oostenveld at FCDONDERS.RU.NL  Tue Jun  6 10:50:02 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Tue, 6 Jun 2006 10:50:02 +0200
Subject: dipole model
In-Reply-To: <LISTSERV%200606051905308600.5C84@NIC.SURFNET.NL>
Message-ID: <TUE.6.JUN.2006.105002.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Punita,

On 5 Jun 2006, at 19:05, Punita Christopher wrote:
> Has anyone seen any literature that deals with a spherical multiple
> layer
> head model in which the dipole spans across layers i.e. the source and
> sink of the dipole are in separate layers.

In the dipole model the source and sink are infintely close together.
The difference on the scalp between a dipole and a source+sink model
with only a few mm in between will be negligible. A source+sink model
with more distance between them can be modelled as such, it requires
the solution of the monopole in a sphere (i.e. the desired source
+sink consists of the superposition of two monopoles). I am not sure
whether an analytical solution for that exsists in a 3- or 4-shell
model, but I would would guess that it does (*). For a BEM model it
is trivial to replace the dipole infinite medium potential with a
monopole infinite medium potential, i.e the BEM formulation
(separation of source and volume conduction) allows the specification
of arbitrary sources.

best
Robert

*) I don't know literature for a monopole in a multi-shell sphere,
but I would expect it to be in either textbooks as a didactical
example or in older articles (70s or 80s). You may want to search for
multipole expansions, which are described in more recent literature,
the monopole is the first term (0th order) of that, the dipole the
second term. Perhaps "Phys Med Biol. 2001 Aug;46(8):2255-66. A study
of equivalent source techniques for high-resolution EEG imaging. Yao
D, Zhou Y, Zeng M, Fan S, Lian J, Wu D, Ao X, Chen L, He B." could
provide more insight.


From muthuraman10 at HOTMAIL.COM  Tue Jun  6 11:19:56 2006
From: muthuraman10 at HOTMAIL.COM (Muthuraman Muthuraman)
Date: Tue, 6 Jun 2006 09:19:56 +0000
Subject: query on coherence analysis
In-Reply-To: <FA431909-950B-4EC2-9598-1C6C49250100@fcdonders.ru.nl>
Message-ID: <TUE.6.JUN.2006.091956.0000.FIELDTRIP@NIC.SURFNET.NL>

Hello

Thanks for the comments, i have downloaded the latest version
and now i am able to calculate using mtmwelch

but i get a error when i am plotting
i will included the matlab commands

>>cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
cfg.channelcmb={'EEG' 'EMG2'};
freq=freqanalysis(cfg,data);

>>fd=freqdescriptives([],freq);

cfg=[];
cfg.xparam='foi';
cfg.yparam='cohspctrm';
cfg.xlim=[0 30];
cfg.cohrefchannel='EMG2';
cfg.box='yes';
cfg.showlabels='yes';
cfg.channelname='EEG26';
singleplotER(cfg,fd);

??? Reference to non-existent field 'foi'.

Error in ==> singleplotER at 272
  plot(varargin{k-1}.(cfg.xparam), P, style);

with regards
muthu


>From: Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>
>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence source analysis
>Date: Thu, 1 Jun 2006 13:58:48 +0200
>
>Dear Muthuraman
>
>I have not been able to reproduce your error. I suggest that you get  the
>latest version of FieldTrip from our FTP server and try again.
>
>best egards,
>Robert
>
>PS this is the test script I used. It uses some simulated data, which
>again uses a MEG gradiometer definition and a head model from the  tutorial
>data.
>
>
>-----------------
>% read some data that is required to simulate MEG data, i.e. volume  model,
>% sensor positions and MRI (optional, only for plotting)
>vol  = read_ctf_hdm('Subject01.hdm');
>hdr  = read_fcdc_header('Subject01.ds/Subject01.res4');
>grad = hdr.grad;
>
>% construct the simulated MEG data for condition A ("active")
>cfg               = [];
>cfg.vol           = vol;
>cfg.grad          = grad;
>cfg.fsample       = 300;
>cfg.ntrials       = 2;
>cfg.triallength   = 1;
>cfg.dip.pos       = [0 7 8];
>cfg.dip.mom       = [1 0 0];
>cfg.dip.signal    = sin(2*pi*10*(1:cfg.fsample)./cfg.fsample);
>cfg.absnoise      = 1e-8;
>data = dipolesimulation(cfg);
>
>% add the source signal as fake EMG channel
>for i=1:cfg.ntrials
>   data.trial{i}(end+1,:) = cfg.dip.signal + randn(size (cfg.dip.signal));
>end
>data.label{end+1} = 'EMG';
>
>cfg=[];
>cfg.output='powandcsd';
>cfg.method='mtmwelch';
>cfg.foi=1:2:30;
>numfoi = length(cfg.foi);
>cfg.taper='hanning';
>cfg.t_ftimwin=zeros(1,numfoi);
>cfg.t_ftimwin(:)=0.5;
>cfg.channel=channelselection({'MEG' 'EMG'},data.label);
>cfg.channelcmb={'MEG' 'EMG'};
>freq=freqanalysis(cfg,data);
>
>
>


From ingrid.nieuwenhuis at FCDONDERS.RU.NL  Tue Jun  6 13:33:28 2006
From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis)
Date: Tue, 6 Jun 2006 13:33:28 +0200
Subject: query on coherence analysis
In-Reply-To: <BAY121-F232E75D5ACD864CFE8389CCE950@phx.gbl>
Message-ID: <TUE.6.JUN.2006.133328.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Muthuraman,

cfg.xparam should not be 'foi', but 'freq' (see help singleplotER)

Bests,
Ingrid


-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Muthuraman Muthuraman
Sent: Tuesday, June 06, 2006 11:20 AM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] query on coherence analysis

Hello

Thanks for the comments, i have downloaded the latest version
and now i am able to calculate using mtmwelch

but i get a error when i am plotting
i will included the matlab commands

>>cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
cfg.channelcmb={'EEG' 'EMG2'};
freq=freqanalysis(cfg,data);

>>fd=freqdescriptives([],freq);

cfg=[];
cfg.xparam='foi';
cfg.yparam='cohspctrm';
cfg.xlim=[0 30];
cfg.cohrefchannel='EMG2';
cfg.box='yes';
cfg.showlabels='yes';
cfg.channelname='EEG26';
singleplotER(cfg,fd);

??? Reference to non-existent field 'foi'.

Error in ==> singleplotER at 272
  plot(varargin{k-1}.(cfg.xparam), P, style);

with regards
muthu


>From: Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>
>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence source analysis
>Date: Thu, 1 Jun 2006 13:58:48 +0200
>
>Dear Muthuraman
>
>I have not been able to reproduce your error. I suggest that you get  the
>latest version of FieldTrip from our FTP server and try again.
>
>best egards,
>Robert
>
>PS this is the test script I used. It uses some simulated data, which
>again uses a MEG gradiometer definition and a head model from the  tutorial

>data.
>
>
>-----------------
>% read some data that is required to simulate MEG data, i.e. volume  model,
>% sensor positions and MRI (optional, only for plotting)
>vol  = read_ctf_hdm('Subject01.hdm');
>hdr  = read_fcdc_header('Subject01.ds/Subject01.res4');
>grad = hdr.grad;
>
>% construct the simulated MEG data for condition A ("active")
>cfg               = [];
>cfg.vol           = vol;
>cfg.grad          = grad;
>cfg.fsample       = 300;
>cfg.ntrials       = 2;
>cfg.triallength   = 1;
>cfg.dip.pos       = [0 7 8];
>cfg.dip.mom       = [1 0 0];
>cfg.dip.signal    = sin(2*pi*10*(1:cfg.fsample)./cfg.fsample);
>cfg.absnoise      = 1e-8;
>data = dipolesimulation(cfg);
>
>% add the source signal as fake EMG channel
>for i=1:cfg.ntrials
>   data.trial{i}(end+1,:) = cfg.dip.signal + randn(size (cfg.dip.signal));
>end
>data.label{end+1} = 'EMG';
>
>cfg=[];
>cfg.output='powandcsd';
>cfg.method='mtmwelch';
>cfg.foi=1:2:30;
>numfoi = length(cfg.foi);
>cfg.taper='hanning';
>cfg.t_ftimwin=zeros(1,numfoi);
>cfg.t_ftimwin(:)=0.5;
>cfg.channel=channelselection({'MEG' 'EMG'},data.label);
>cfg.channelcmb={'MEG' 'EMG'};
>freq=freqanalysis(cfg,data);
>
>
>


From ingrid.nieuwenhuis at FCDONDERS.RU.NL  Wed Jun 14 11:55:53 2006
From: ingrid.nieuwenhuis at FCDONDERS.RU.NL (Ingrid Nieuwenhuis)
Date: Wed, 14 Jun 2006 11:55:53 +0200
Subject: missing cumtapcnt field
Message-ID: <WED.14.JUN.2006.115553.0200.FIELDTRIP@NIC.SURFNET.NL>

I'm (trying to) beamform, but I get the following error:

reference to non-existent field 'cumtapcnt' 
In prepare_freq_matrices line 124.
Ntrials = length(freq.cumtapcnt)

I used freqanalysis method 'mtmconvol' to do make the freq, and it indeed 
doesn't contain a 'cumtapcnt'

      cfg = [];
      cfg.method = 'mtmconvol';
      cfg.output = 'powandcsd';
      cfg.foi             = 90;
      cfg.t_ftimwin       = 0.5;
      cfg.tapsmofrq       = 30;
      cfg.pad             = 'maxperlen';
      cfg.taper           = 'dpss';
      cfg.keeptrials      = 'yes';
      cfg.keeptapers      = 'no';
      cfg.toi             = 0.75 
        
      freq_BF = freqanalysis(cfg, data);

So my questions: 
- Why doesn't my freq contain a cumtapcnt field. Should I have kept my 
tapers (cfg.keeptapers = 'yes')?
- Can I solve this without having to freqanalysis my data all over again, I 
can see in my freq.crsspctrm = [76 x 11476 double] that I have 76 trials. 
Can I for instance just make a vector of ones with length 76 and put that 
in my freq, or will that create problems?

Thanks a lot,
Ingrid 


From Jan.Schoffelen at FCDONDERS.RU.NL  Wed Jun 14 12:42:08 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Wed, 14 Jun 2006 12:42:08 +0200
Subject: missing cumtapcnt field
In-Reply-To: <LISTSERV%200606141155536310.74A7@NIC.SURFNET.NL>
Message-ID: <WED.14.JUN.2006.124208.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Ingrid,


>Can I for instance just make a vector of ones with length 76 and put that
>in my freq, or will that create problems?

The answer to this question is yes. Indeed, no cumtapcnt is passed back when
using freqanalysis_mtmconvol. Should be fixed, though.
In your case I think it is sufficient just to provide a vector which has a
dimensionality of Nx1, N being the number of epoch. The content of this
vector will not be used later on in this case.
On the other hand, the cumtapcnt-vector, as outputted by for example
freqanalysis_mtmfft contains for each epoch the number of tapers which have
been used for the estimation of the spectra for that particular epoch.
Please note that if you set the option cfg.keeptapers = 'yes', the vector
consists only of ones (or if you use e.g. a single hanning-taper, or such a
low amount of smoothing, that you only need one 'dpss'-taper, in which case
by the way it does not make sense to use the 'dpss'). In any other case, the
cumtapcnt-vector contains a number, which can be different for each epoch
(when you have trials of different lengths). You can easily compute the
number of tapers, this will be: 2xNxK-1, with N being the length of your
data segment (in seconds), and K being the taper-smoothing you specified in
cfg.tapsmofrq.

Yours,

JM


From nathanweisz at MAC.COM  Thu Jun 15 11:42:43 2006
From: nathanweisz at MAC.COM (Nathan Weisz)
Date: Thu, 15 Jun 2006 11:42:43 +0200
Subject: source positions - brain regions
Message-ID: <THU.15.JUN.2006.114243.0200.FIELDTRIP@NIC.SURFNET.NL>

dear help-list,

sorry for what appears to be a very basic question.
i'm just starting to explore the source analysis possibilities that
fieldtrip offers. for this i downloaded a EEG tutorial dataset from
eeglab, did eeglab2fieldtrip, and the timelockanalysis. now i wanted
to estimate the source waveforms of the erp.

%this is my input:
vol   = [];
vol.r = 12 * [0.88 0.92 1.00]; % radii of spheres, the head radius is
12 cm
vol.c = [1 1/80 1];            % conductivity
vol.o = [0 0 0];

tmp=data.elec;
tmp.pnt=tmp.pnt*12;


cfg=[];
cfg.method='lcmv';
cfg.vol=vol;
cfg.elec=tmp;
cfg.resolution=1;

datamn=sourceanalysis(cfg,dataav);

%this is the output
datamn =

       xgrid: [-10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10]
       ygrid: [-10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10]
       zgrid: [-8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7 8 9 10]
         dim: [21 21 19]
         vol: [1x1 struct]
        time: [1x256 double]
         pos: [8379x3 double]
      inside: [1x4811 double]
     outside: [1x3568 double]
      method: 'average'
         avg: [1x1 struct]
         cfg: [1x1 struct]

there were no error or warning messages, so from the basic structure
things seem to be ok.
the time courses of my source activity appears to be saved in
datamn.avg.mom.

 >> size(datamn.avg.mom{datamn.inside(1)})

ans =

      3   256


however now i'm a little bit stuck. from here, what is the best
method of finding out which dipoles correspond (very roughly) to
which brain regions, so i can extract specifically those to look at
the sourcewaveforms? unfortunatley no mri.
I am aware of the sourceplot function, but was uncapable of producing
a meaningful output.

thanks in advance for any hints & best wishes,
nathan



--------------------------------
Dr. Nathan Weisz
Dept. of Psychology
University of Konstanz
P.O. Box D25
78457 Konstanz, Germany

Tel: ++49-7531-884612
Email & Chat-AV: nathanweisz at mac.com
Homepage: http://homepage.mac.com/nathanweisz/start/research.html


From muthuraman10 at HOTMAIL.COM  Thu Jun 15 15:59:54 2006
From: muthuraman10 at HOTMAIL.COM (Muthuraman Muthuraman)
Date: Thu, 15 Jun 2006 13:59:54 +0000
Subject: query on coherence analysis
In-Reply-To: <002201c6895d$07c0d680$642dae83@fcdonders.nl>
Message-ID: <THU.15.JUN.2006.135954.0000.FIELDTRIP@NIC.SURFNET.NL>

Hello

Thankyou for the previous help it works now
i am able to proceed further to calculate the coherence

The problem now the coherence obtained using the mtmwelch
when i plot the coherence figures for the channels
all the coherence figures for the different channel looks the same
is there is a bug in how i am calculating the coherence

These are the steps i carried out in calculating the coherence

headerfile='pd_mof_tr0_c_0306.cnt';
hdr = read_fcdc_header(headerfile);
cfg.trl = [];
for i=1:floor(hdr.nSamples/hdr.Fs)
  cfg.trl(i,1) = (i-1)*hdr.Fs + 1;
  cfg.trl(i,2) = (i  )*hdr.Fs;
  cfg.trl(i,3) = 0;
end

cfg.headerfile=headerfile;
>>cfg.datafile=headerfile;
>>[data] = preprocessing(cfg);

-and after the data is preprocessed i change the channel labels from actual
cz to eeg26 and so on



cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
cfg.channelcmb={'EEG' 'EMG2'};
freq=freqanalysis(cfg,data);


-when i calculate using freqanalysis i get these warnings

1.000 Hz : WARNING - using only one taper for specified smoothing
Warning: Size vector should be a row vector with integer elements.
>In freqanalysis_mtmconvol at 360
  In freqanalysis at 182
  In freqanalysis_mtmwelch at 67
  In freqanalysis at 182
and so on till 30.000 hz

-and while processing

processing trial 2: 1000 samples
Warning: Size vector should be a row vector with integer elements.
>In freqanalysis_mtmconvol at 398
  In freqanalysis at 182
  In freqanalysis_mtmwelch at 67
  In freqanalysis at 182



fd=freqdescriptives([],freq);


cfg=[];
cfg.xparam='freq';
cfg.yparam='cohspctrm';
cfg.xlim=[3 30];
cfg.cohrefchannel='EMG2';
cfg.box='yes';
cfg.showlabels='yes';

cfg.channelname='EEG27';
singleplotER(cfg,fd);
-when i try to plot i get this error
??? Error using ==> char
Cell elements must be character arrays.

Error in ==> singleplotER at 326
  t=[char(cfg.channelname) ' / ' num2str(cfg.channelindex) ];


please , look at it and help me in this regard

thanking you
with regards
muthuraman

>From: Ingrid Nieuwenhuis <ingrid.nieuwenhuis at FCDONDERS.RU.NL>
>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence analysis
>Date: Tue, 6 Jun 2006 13:33:28 +0200
>
>Dear Muthuraman,
>
>cfg.xparam should not be 'foi', but 'freq' (see help singleplotER)
>
>Bests,
>Ingrid
>
>
>-----Original Message-----
>From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
>Of Muthuraman Muthuraman
>Sent: Tuesday, June 06, 2006 11:20 AM
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence analysis
>
>Hello
>
>Thanks for the comments, i have downloaded the latest version
>and now i am able to calculate using mtmwelch
>
>but i get a error when i am plotting
>i will included the matlab commands
>
> >>cfg=[];
>cfg.output='powandcsd';
>cfg.method='mtmwelch';
>cfg.foi=1:2:30;
>numfoi = length(cfg.foi);
>cfg.taper='hanning';
>cfg.t_ftimwin=zeros(1,numfoi);
>cfg.t_ftimwin(:)=0.5;
>cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
>cfg.channelcmb={'EEG' 'EMG2'};
>freq=freqanalysis(cfg,data);
>
> >>fd=freqdescriptives([],freq);
>
>cfg=[];
>cfg.xparam='foi';
>cfg.yparam='cohspctrm';
>cfg.xlim=[0 30];
>cfg.cohrefchannel='EMG2';
>cfg.box='yes';
>cfg.showlabels='yes';
>cfg.channelname='EEG26';
>singleplotER(cfg,fd);
>
>??? Reference to non-existent field 'foi'.
>
>Error in ==> singleplotER at 272
>   plot(varargin{k-1}.(cfg.xparam), P, style);
>
>with regards
>muthu
>
>
> >From: Robert Oostenveld <r.oostenveld at FCDONDERS.RU.NL>
> >Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
> >To: FIELDTRIP at NIC.SURFNET.NL
> >Subject: Re: [FIELDTRIP] query on coherence source analysis
> >Date: Thu, 1 Jun 2006 13:58:48 +0200
> >
> >Dear Muthuraman
> >
> >I have not been able to reproduce your error. I suggest that you get  the
> >latest version of FieldTrip from our FTP server and try again.
> >
> >best egards,
> >Robert
> >
> >PS this is the test script I used. It uses some simulated data, which
> >again uses a MEG gradiometer definition and a head model from the
>tutorial
>
> >data.
> >
> >
> >-----------------
> >% read some data that is required to simulate MEG data, i.e. volume
>model,
> >% sensor positions and MRI (optional, only for plotting)
> >vol  = read_ctf_hdm('Subject01.hdm');
> >hdr  = read_fcdc_header('Subject01.ds/Subject01.res4');
> >grad = hdr.grad;
> >
> >% construct the simulated MEG data for condition A ("active")
> >cfg               = [];
> >cfg.vol           = vol;
> >cfg.grad          = grad;
> >cfg.fsample       = 300;
> >cfg.ntrials       = 2;
> >cfg.triallength   = 1;
> >cfg.dip.pos       = [0 7 8];
> >cfg.dip.mom       = [1 0 0];
> >cfg.dip.signal    = sin(2*pi*10*(1:cfg.fsample)./cfg.fsample);
> >cfg.absnoise      = 1e-8;
> >data = dipolesimulation(cfg);
> >
> >% add the source signal as fake EMG channel
> >for i=1:cfg.ntrials
> >   data.trial{i}(end+1,:) = cfg.dip.signal + randn(size
>(cfg.dip.signal));
> >end
> >data.label{end+1} = 'EMG';
> >
> >cfg=[];
> >cfg.output='powandcsd';
> >cfg.method='mtmwelch';
> >cfg.foi=1:2:30;
> >numfoi = length(cfg.foi);
> >cfg.taper='hanning';
> >cfg.t_ftimwin=zeros(1,numfoi);
> >cfg.t_ftimwin(:)=0.5;
> >cfg.channel=channelselection({'MEG' 'EMG'},data.label);
> >cfg.channelcmb={'MEG' 'EMG'};
> >freq=freqanalysis(cfg,data);
> >
> >
> >


From linpe at NINDS.NIH.GOV  Thu Jun 15 22:08:19 2006
From: linpe at NINDS.NIH.GOV (Lin, Peter (NIH/NINDS) [E])
Date: Thu, 15 Jun 2006 16:08:19 -0400
Subject: No subject
Message-ID: <THU.15.JUN.2006.160819.0400.FIELDTRIP@NIC.SURFNET.NL>

I am trying to import neuroscan data into fieldtrip for analysis.  I
tried using eeglab to load my epoch's neuroscan file and then used the
eeglab2fieldtrip command on the EEG structure to generate a new data
file.  My question is how to process the data further using the
frequencyanalysis method.  

 

>>[data]=eeglab2fieldtrip(EEG,'preprocessing')

 

data = 

 

      label: {1x64 cell}

    fsample: 1000

       elec: [1x1 struct]

      trial: {1x224 cell}

       time: {1x224 cell}

        cfg: [1x1 struct]

 

I'm wondering if my created data file is not correct.  Any help on how
to proceed would be great.  

 

Thanks,

 

Peter

 

Peter Lin, MD

Clinical Fellow, Human Motor Control Section

Phone: 301-402-0703

email: linpe at ninds.nih.gov

 

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From Jan.Schoffelen at FCDONDERS.RU.NL  Fri Jun 16 09:05:50 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Fri, 16 Jun 2006 09:05:50 +0200
Subject: No subject
In-Reply-To: <C95F8E297215B6489AC8E595CF2239B0053B989F@NIHCESMLBX.nih.gov>
Message-ID: <FRI.16.JUN.2006.090550.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Peter,



As far as I can see, the data looks OK. At least it contains the fields
subsequent analysis steps need to know. However, I cannot judge the content
of these fields, but there's no reason to assume that's not fine.

To proceed, I would first advice you to have a look at the fieldtrip
website. If you follow the link documentation, and then
tutorial-documentation, there's already some stuff regarding frequency
analysis. Moreover, the website also contains the documentation of all
fieldtrip functions, which you can also access from the matlab command line,
by typing help functionname. For example, try help freqanalysis, or help
freqanalysis_mtmconvol. There's already quite some information in there, as
well as all the options you can play with.



Good luck



Jan-mathijs



  _____

From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Lin, Peter (NIH/NINDS) [E]
Sent: Thursday, June 15, 2006 10:08 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: [FIELDTRIP]



I am trying to import neuroscan data into fieldtrip for analysis.  I tried
using eeglab to load my epoch's neuroscan file and then used the
eeglab2fieldtrip command on the EEG structure to generate a new data file.
My question is how to process the data further using the frequencyanalysis
method.



>>[data]=eeglab2fieldtrip(EEG,'preprocessing')



data =



      label: {1x64 cell}

    fsample: 1000

       elec: [1x1 struct]

      trial: {1x224 cell}

       time: {1x224 cell}

        cfg: [1x1 struct]



I'm wondering if my created data file is not correct.  Any help on how to
proceed would be great.



Thanks,



Peter



Peter Lin, MD

Clinical Fellow, Human Motor Control Section

Phone: 301-402-0703

email: linpe at ninds.nih.gov



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From Jan.Schoffelen at FCDONDERS.RU.NL  Fri Jun 16 09:15:15 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Fri, 16 Jun 2006 09:15:15 +0200
Subject: query on coherence analysis
In-Reply-To: <BAY121-F19F3FD6B01B619882BC777CE820@phx.gbl>
Message-ID: <FRI.16.JUN.2006.091515.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Muthuraman,

At first glance I don't have a clue what's going on.
Did you have a look into fd.powspctrm, and fd.cohspctrm?
Does it contain normal numbers, zeros, or nan?
It might be a bug in freqanalysis_mtmwelch.
Did you try out other methods, to be specified in cfg.method?
If yes, did this also give strange results? If no, could you try out
cfg.method = 'mtmconvol' instead of 'mtmwelch'? Please have a look at the
documentation which additional options you have to specify.
What matlab-version do you use? Do you use the latest fieldtrip-version?

One additional thing: please note that you specified the odd frequencies
1:2:29, whereas your time-window is half a second wide. These are not
optimal settings, since the frequency-resolution of your time-window is 2
Hz. This means that your time-window never contains an integer amount of
cycles of the frequency you want to estimate. This might lead to strange
results, though I don't think it has anything to do with your present
problem. However, I would use cfg.freq = 2:2:30 in combination with a
time-window of 0.5 s

Yours,

Jan-Mathijs

-----Original Message-----
From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Muthuraman Muthuraman
Sent: Thursday, June 15, 2006 4:00 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] query on coherence analysis

Hello

Thankyou for the previous help it works now
i am able to proceed further to calculate the coherence

The problem now the coherence obtained using the mtmwelch
when i plot the coherence figures for the channels
all the coherence figures for the different channel looks the same
is there is a bug in how i am calculating the coherence

These are the steps i carried out in calculating the coherence

headerfile='pd_mof_tr0_c_0306.cnt';
hdr = read_fcdc_header(headerfile);
cfg.trl = [];
for i=1:floor(hdr.nSamples/hdr.Fs)
  cfg.trl(i,1) = (i-1)*hdr.Fs + 1;
  cfg.trl(i,2) = (i  )*hdr.Fs;
  cfg.trl(i,3) = 0;
end

cfg.headerfile=headerfile;
>>cfg.datafile=headerfile;
>>[data] = preprocessing(cfg);

-and after the data is preprocessed i change the channel labels from actual
cz to eeg26 and so on



cfg=[];
cfg.output='powandcsd';
cfg.method='mtmwelch';
cfg.foi=1:2:30;
numfoi = length(cfg.foi);
cfg.taper='hanning';
cfg.t_ftimwin=zeros(1,numfoi);
cfg.t_ftimwin(:)=0.5;
cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
cfg.channelcmb={'EEG' 'EMG2'};
freq=freqanalysis(cfg,data);


-when i calculate using freqanalysis i get these warnings

1.000 Hz : WARNING - using only one taper for specified smoothing
Warning: Size vector should be a row vector with integer elements.
>In freqanalysis_mtmconvol at 360
  In freqanalysis at 182
  In freqanalysis_mtmwelch at 67
  In freqanalysis at 182
and so on till 30.000 hz

-and while processing

processing trial 2: 1000 samples
Warning: Size vector should be a row vector with integer elements.
>In freqanalysis_mtmconvol at 398
  In freqanalysis at 182
  In freqanalysis_mtmwelch at 67
  In freqanalysis at 182



fd=freqdescriptives([],freq);


cfg=[];
cfg.xparam='freq';
cfg.yparam='cohspctrm';
cfg.xlim=[3 30];
cfg.cohrefchannel='EMG2';
cfg.box='yes';
cfg.showlabels='yes';

cfg.channelname='EEG27';
singleplotER(cfg,fd);
-when i try to plot i get this error
??? Error using ==> char
Cell elements must be character arrays.

Error in ==> singleplotER at 326
  t=[char(cfg.channelname) ' / ' num2str(cfg.channelindex) ];


please , look at it and help me in this regard

thanking you
with regards
muthuraman


From r.oostenveld at FCDONDERS.RU.NL  Fri Jun 16 10:39:48 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 16 Jun 2006 10:39:48 +0200
Subject: source positions - brain regions
In-Reply-To: <5E221385-C805-4FFA-BE76-F2C0DF9BEE72@mac.com>
Message-ID: <FRI.16.JUN.2006.103948.0200.FIELDTRIP@NIC.SURFNET.NL>

hi Nathan

On 15 Jun 2006, at 11:42, Nathan Weisz wrote:
> however now i'm a little bit stuck. from here, what is the best
> method of finding out which dipoles correspond (very roughly) to
> which brain regions, so i can extract specifically those to look at
> the sourcewaveforms? unfortunatley no mri.
> I am aware of the sourceplot function, but was uncapable of
> producing a meaningful output.

So far it seems ok. The headmodel is in cm, the electrodes as well (I
presume, otherwise it would have given warnings and/or errors), so
the source locations are also expressed in cm, since they are
expresed in the same coordinate system. I suggest that you have a
look at http://www2.ru.nl/fcdonders/fieldtrip/doku.php?
id=fieldtrip:documentation:frequently_asked_questions#how_are_the_differ
ent_head_and_mri_coordinate_systems_defined to get a better
understanding in general.

What we normally do in such a case is to use an indivudual headmodel,
and what we thus subsequently would do is to take an anatomical MRI
of the same subject, in which the MRI is aligned to the same head/
model coordinate system (using the ears and nose fiducials). Since
you do not have a MRI, you could take a standard MRI (i.e. the MNI
template in single_subj_T1 from SPM). Some time ago I (or Arno)
posted a homogenous transformation matrix "besa2spm" on the eeglab
mailing list (*). That homogenous transformation matrix transforms
from besa coordinates for a spherical model to MNI coordinates.

besa2spm = [
     0.0101   -0.9400         0    0.5588
     1.1889    0.0080    0.0530  -18.0041
    -0.0005   -0.0000    1.1268    1.8045
          0         0         0    1.0000 ];

spm2besa = inv(besa2spm);

The transformation matrix is for the "besa" spherical model in
EEGLAB, which has different sphere radii (85mm outer sphere) than you
have used. So you should add a scaling from the besa radii to yours.

your2besa = eye(4);
your2besa(1,1) = 8.5/12;
your2besa(2,2) = 8.5/12;
your2besa(3,3) = 8.5/12;

then

your2spm = besa2spm * your2besa
spm2your = inv(your2spm);

It is most convenient to apply the inverse transformation to the MRI
corodinate system. I.e. do
   mri = read_fcdc_mri('single_subj_T1.mnc')
then mri.transform describes the voxels in SPM/MNI coordinates, so
   mri.transform = spm2your * mri.transform;
changes the anatomical MRI into your headmodel coordinates.

Subsequently you can interpolate the functional values onto the
anaomtical voxel locations with SOURCEINTERPOLATE, and plot the
functional values overlaid over the anatomical with SOURCEPLLOT or
SLICEINTERP.

best regards,
Robert

PS (*) the besa2spm coordinate transformation matrix was constructed
using ELECTORDENORMAMALIZE, which warps electrodes. In this case the
spherical 1020 electrodes were warped to the corresponding electrodes
in the MNI template. The homogenous transformation matrix describes
the warp/deformation and can be used as well for the dipoles inside
the head.


From jurij.dreo at GUEST.ARNES.SI  Sat Jun 17 12:18:26 2006
From: jurij.dreo at GUEST.ARNES.SI (Jurij Dreo)
Date: Sat, 17 Jun 2006 11:18:26 +0100
Subject: Statistics for coherence in a within-subject experiment
Message-ID: <SAT.17.JUN.2006.111826.0100.FIELDTRIP@NIC.SURFNET.NL>

Hello,

I am using BESA to perform coherence and source coherence 
calculations for a multiple-subject/multiple-condition experiment. In 
the experiment I have 11 subjects, 6 conditions and around 30 sets 
per condition per subject.

In BESA the data was preprocessed and the coherence values in the 
Time-Frequency domain were calculated for each person.

As BESA has no capabilities to calculate statistics in a multiple-
subject study, their support personnel directed me towards FieldTrip.

I´ve been looking over the documentation and tutorials on your web 
page and also downloaded the scrip and ran it in matlab.

The tutorial on Cluster-Lever randomization Tests for the Time-
Frequency domain is quite straight-forward. I am however not quite 
sure which statistic to use for the cfg.statistic variable to analyze 
coherence in a within-subject study such as the one I have.

The documentation on the cfg.statistic variable says it can have 
these values:
1. indepsamplesT' (independent samples T-statistic) 
2. 'indepsamplesregrT' (independent samples regression coefficient T-
statistic)
3. 'indepsamplesZcoh' (independent samples Z-statistic for coherence)
4. 'indepsamplesTsqcrs' (independent samples T-square-statistic for 
the cross-spectrum)
5. 'depsamplesT' (dependent samples T-statistic)
6. 'actvsblT' (activation versus baseline T-statistic)
7. 'depsamplesregrT' (dependent samples regression coefficient T-
statistic) 
8. 'indepsamplesF' (independent samples F-statistic)
9. 'depsamplesF' (dependent samples F-statistic)

I am not sure if any of these options are compatible with a within-
subject multiple condition coherence statistical analysis.

option 3. - indepsamplesZcoh is obviously only suitable for a between-
trial, two-condition experiment

and there are no other options that explicitally say they are used 
for coherence. 

So how can one compare 6 conditions for 11 subjects with regards to 
coherence if one imports the Time-Frequency domain data for each 
person into FieldTrip?

Thank you for your help!

Regards,
Jurij Dreo


From r.oostenveld at FCDONDERS.RU.NL  Mon Jun 19 16:18:55 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Mon, 19 Jun 2006 16:18:55 +0200
Subject: Statistics for coherence in a within-subject experiment
In-Reply-To: <20060617_091826_063328.jurij.dreo@guest.arnes.si>
Message-ID: <MON.19.JUN.2006.161855.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Jurij

> option 3. - indepsamplesZcoh is obviously only suitable for a between-
> trial, two-condition experiment

Yes, that is for testing coherence differences between two conditions
within one subject.

> and there are no other options that explicitally say they are used
> for coherence.
>
> So how can one compare 6 conditions for 11 subjects with regards to
> coherence if one imports the Time-Frequency domain data for each
> person into FieldTrip?

In your case you have observed a "value" in 11 subjects, over 6
conditions. That value happens to be coherence, but could as well
have been something else. Since you have manipulated the conditions
with each subject, you can use a dependent-samples test: the observed
values depend on the subject (an example of a dependent-samples test
is a paired-t test).

If the number of trials varies between subjects and/or sessions, it
will be preferable to transform your coherence values to z-scores
manually prior to submitting the values to clusterrandanalysis.

Now about the 6 conditions, am I right that you have a 1x6 factorial
design, or is there more strucure in the design? Do you have a
specific hypothesis about the different conditions? If you only want
to reject the null-hypothesis "the observed value (coherence) is the
same (more accurately: stems from the same distribution) in all my 6
conditions", you would use an omnibus F-statistic, i.e.
'depsamplesF'. It might be that your hypothesis is more specific, or
also in case you find an omnibus effect, then you would probably want
to perform explicit tests between two subsets of your 6 conditions
using a 'depsamplesT' test.

best regards,
Robert


From jurij.dreo at GUEST.ARNES.SI  Mon Jun 19 17:31:46 2006
From: jurij.dreo at GUEST.ARNES.SI (Jurij Dreo)
Date: Mon, 19 Jun 2006 17:31:46 +0200
Subject: Statistics for coherence in a within-subject experiment
Message-ID: <MON.19.JUN.2006.173146.0200.FIELDTRIP@NIC.SURFNET.NL>

Hello!

Thank you for your answers. Here are my replies to them:

To avoid any misunderstandings here is again a summary of my study design
- I have 11 subjects. 
- Each of them performed 6 tasks related to working memory.
- Each subject performed anywehere from 25 to 60 repeats (trial) of each condition (the standard number of trials per task was 30 - but some subjects performed the entire experiment twice (ergo 60 potential trials) .... and in some some of their trials are unusable - artifacts ... ergo 25 min number of possible trials)

Given my study design I thought something like a one-way ANOVA for correlated samples would be in order.
(as I am comparing 6 conditions within-subjects as every subject performed all sets)


-----------------
> In your case you have observed a "value" in 11 subjects, over 6  
> conditions. That value happens to be coherence, but could as well  
> have been something else. Since you have manipulated the conditions  
> with each subject, you can use a dependent-samples test: the observed  
> values depend on the subject (an example of a dependent-samples test  
> is a paired-t test).
-------------------

I´m not sure what you are saying here.... I agree with the dependent samples idea... but I cannot preform a t-test ... ie. more of them as that would inflate my p-rate overall.

I thought that I would first do an ANOVA and then something like the Tukey HSD Test to cimpare individual conditions

--------------------
> If the number of trials varies between subjects and/or sessions, it  
> will be preferable to transform your coherence values to z-scores  
> manually prior to submitting the values to clusterrandanalysis.
--------------------
Yes I agree that would need to be done manually.

-----------
> Now about the 6 conditions, am I right that you have a 1x6 factorial  
> design, or is there more strucure in the design? Do you have a  
> specific hypothesis about the different conditions? If you only want  
> to reject the null-hypothesis "the observed value (coherence) is the  
> same (more accurately: stems from the same distribution) in all my 6  
> conditions", you would use an omnibus F-statistic, i.e.  
> 'depsamplesF'. It might be that your hypothesis is more specific, or  
> also in case you find an omnibus effect, then you would probably want  
> to perform explicit tests between two subsets of your 6 conditions  
> using a 'depsamplesT' test.
> 
----------

I want to contrast all conditions at once (f -test anova) AND also each combination of conditions (say a post- ANOVA Q-test)

But Im still not sure which statistic to use and even if the one I use will be able to deal with the fact that I have a different number of conditions per condition per subject

As far as I understand it... we must use some kind of ANOVA here... A simple "paired" t-test will not do... as we are comparing more than 2 conditions at once and I do not want to inflate my p-rate.

Thank you for your help!

Regards,
Jurij Dreo
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From muthuraman10 at HOTMAIL.COM  Tue Jun 20 10:40:17 2006
From: muthuraman10 at HOTMAIL.COM (Muthuraman Muthuraman)
Date: Tue, 20 Jun 2006 08:40:17 +0000
Subject: query on coherence analysis
Message-ID: <TUE.20.JUN.2006.084017.0000.FIELDTRIP@NIC.SURFNET.NL>

Hello Jan

The answers for the questions you have asked
and also i have attached some figures with this mail
1-using welch periodogram method
2-using fieldtrip 'mtmfft'
3-using fieldtrip 'mtmwelch'

Did you have a look into fd.powspctrm, and fd.cohspctrm?
-yes,both look the same so something is surely going wrong

Does it contain normal numbers, zeros, or nan?
-yes, it has normal numbers but the vlaues are from 1.0 to 10.0 not as
normal in the case of 0.1 to 1 in coherence spectrum

Did you try out other methods, to be specified in cfg.method?
-yes using 'mtmfft' i have attached the figure in the mail in which i dont
get the correct frequency content and the values are less

-In the 'mtmwelch' method i get a error when i am plotting, even then i am
able to see the figure
??? Error using ==> char
Cell elements must be character arrays.

Error in ==> singleplotER at 326
  t=[char(cfg.channelname) ' / ' num2str(cfg.channelindex) ];

-In the 'mtmconvol' i am not able to plot i get a error
selected 60 channels for coherence
??? Error using ==> plot
Vectors must be the same lengths.

Error in ==> singleplotER at 272
  plot(varargin{k-1}.(cfg.xparam), P, style);


please go through it and give your comments

and one more question for the source analysis
what are the values we need,when i open the elec1010 there are four values
x,y,z values and what is the fourth value

with regards
muthu

>From: Jan Mathijs Schoffelen <Jan.Schoffelen at FCDONDERS.RU.NL>
>Reply-To: FieldTrip discussion list <FIELDTRIP at NIC.SURFNET.NL>
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence analysis
>Date: Fri, 16 Jun 2006 09:15:15 +0200
>
>Dear Muthuraman,
>
>At first glance I don't have a clue what's going on.
>Did you have a look into fd.powspctrm, and fd.cohspctrm?
>Does it contain normal numbers, zeros, or nan?
>It might be a bug in freqanalysis_mtmwelch.
>Did you try out other methods, to be specified in cfg.method?
>If yes, did this also give strange results? If no, could you try out
>cfg.method = 'mtmconvol' instead of 'mtmwelch'? Please have a look at the
>documentation which additional options you have to specify.
>What matlab-version do you use? Do you use the latest fieldtrip-version?
>
>One additional thing: please note that you specified the odd frequencies
>1:2:29, whereas your time-window is half a second wide. These are not
>optimal settings, since the frequency-resolution of your time-window is 2
>Hz. This means that your time-window never contains an integer amount of
>cycles of the frequency you want to estimate. This might lead to strange
>results, though I don't think it has anything to do with your present
>problem. However, I would use cfg.freq = 2:2:30 in combination with a
>time-window of 0.5 s
>
>Yours,
>
>Jan-Mathijs
>
>-----Original Message-----
>From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
>Of Muthuraman Muthuraman
>Sent: Thursday, June 15, 2006 4:00 PM
>To: FIELDTRIP at NIC.SURFNET.NL
>Subject: Re: [FIELDTRIP] query on coherence analysis
>
>Hello
>
>Thankyou for the previous help it works now
>i am able to proceed further to calculate the coherence
>
>The problem now the coherence obtained using the mtmwelch
>when i plot the coherence figures for the channels
>all the coherence figures for the different channel looks the same
>is there is a bug in how i am calculating the coherence
>
>These are the steps i carried out in calculating the coherence
>
>headerfile='pd_mof_tr0_c_0306.cnt';
>hdr = read_fcdc_header(headerfile);
>cfg.trl = [];
>for i=1:floor(hdr.nSamples/hdr.Fs)
>   cfg.trl(i,1) = (i-1)*hdr.Fs + 1;
>   cfg.trl(i,2) = (i  )*hdr.Fs;
>   cfg.trl(i,3) = 0;
>end
>
>cfg.headerfile=headerfile;
> >>cfg.datafile=headerfile;
> >>[data] = preprocessing(cfg);
>
>-and after the data is preprocessed i change the channel labels from actual
>cz to eeg26 and so on
>
>
>
>cfg=[];
>cfg.output='powandcsd';
>cfg.method='mtmwelch';
>cfg.foi=1:2:30;
>numfoi = length(cfg.foi);
>cfg.taper='hanning';
>cfg.t_ftimwin=zeros(1,numfoi);
>cfg.t_ftimwin(:)=0.5;
>cfg.channel=channelselection({'EEG' 'EMG2'},data.label);
>cfg.channelcmb={'EEG' 'EMG2'};
>freq=freqanalysis(cfg,data);
>
>
>-when i calculate using freqanalysis i get these warnings
>
>1.000 Hz : WARNING - using only one taper for specified smoothing
>Warning: Size vector should be a row vector with integer elements.
> >In freqanalysis_mtmconvol at 360
>   In freqanalysis at 182
>   In freqanalysis_mtmwelch at 67
>   In freqanalysis at 182
>and so on till 30.000 hz
>
>-and while processing
>
>processing trial 2: 1000 samples
>Warning: Size vector should be a row vector with integer elements.
> >In freqanalysis_mtmconvol at 398
>   In freqanalysis at 182
>   In freqanalysis_mtmwelch at 67
>   In freqanalysis at 182
>
>
>
>fd=freqdescriptives([],freq);
>
>
>cfg=[];
>cfg.xparam='freq';
>cfg.yparam='cohspctrm';
>cfg.xlim=[3 30];
>cfg.cohrefchannel='EMG2';
>cfg.box='yes';
>cfg.showlabels='yes';
>
>cfg.channelname='EEG27';
>singleplotER(cfg,fd);
>-when i try to plot i get this error
>??? Error using ==> char
>Cell elements must be character arrays.
>
>Error in ==> singleplotER at 326
>   t=[char(cfg.channelname) ' / ' num2str(cfg.channelindex) ];
>
>
>please , look at it and help me in this regard
>
>thanking you
>with regards
>muthuraman

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From Jan.Schoffelen at FCDONDERS.RU.NL  Wed Jun 21 11:31:07 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Wed, 21 Jun 2006 11:31:07 +0200
Subject: query on coherence analysis
In-Reply-To: <BAY121-F3382C80D92ABF19D39C798CE840@phx.gbl>
Message-ID: <WED.21.JUN.2006.113107.0200.FIELDTRIP@NIC.SURFNET.NL>

>the other question i have asked in the previous mail
>i would like to do the source analysis
>and the values specified in for ex:elec1010
>it has four values and the channel label
>the first three values are x,y,z position values
>what is the fourth value?

Dear Muthuraman,

Please have a look at the FAQ-section of the fieldtrip-website. It is
explained what is specified in the layout-files.

Yours,

Jan-M


From Jan.Schoffelen at FCDONDERS.RU.NL  Wed Jun 21 12:32:15 2006
From: Jan.Schoffelen at FCDONDERS.RU.NL (Jan Mathijs Schoffelen)
Date: Wed, 21 Jun 2006 12:32:15 +0200
Subject: query on coherence analysis
In-Reply-To: <BAY121-F3382C80D92ABF19D39C798CE840@phx.gbl>
Message-ID: <WED.21.JUN.2006.123215.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Muthuraman,

Please find attached a script and a figure.
I compared the 'mtmfft' with 'mtmwelch', and the results look very similar.
I did not test the 'mtmconvol' method, since this function is called when
you specify 'mtmwelch'. I guess you have to check your configuration in that
respect. I would say that the code is doing what it should do.
Please make sure that you use the latest fieldtrip-version.

Yours,

Jan-Mathijs

-----Original Message-----
From: Muthuraman Muthuraman [mailto:muthuraman10 at hotmail.com]
Sent: Wednesday, June 21, 2006 11:05 AM
To: Jan.Schoffelen at fcdonders.ru.nl
Subject: RE: [FIELDTRIP] query on coherence analysis

Hello Jan

Thanks for the suggestions

I have tried 'mtmconvol' and also plotting using singleplotTFR
the figure looks totally blue
i have attached the figure with this mail for the same channel combination
Figure-mtmconvol

and also i have uploaded two files
one is the CNT file of a patient
and the other file is data structure after preprocessing and changing the
channel label

If u have any different results from the data
please let me know
my aim is to do the coherence analysis followed by the source analysis using

'DICS'


the other question i have asked in the previous mail
i would like to do the source analysis
and the values specified in for ex:elec1010
it has four values and the channel label
the first three values are x,y,z position values
what is the fourth value?


thanking you
with regards
muthu
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From srampp at TISCALI.DE  Wed Jun 21 23:07:50 2006
From: srampp at TISCALI.DE (Stefan Rampp)
Date: Wed, 21 Jun 2006 23:07:50 +0200
Subject: Missing minimumnormestimate etc
Message-ID: <WED.21.JUN.2006.230750.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi everyone,

I was just trying to do source localization of epilepsy MEG data using mne, however, it appears that some functions are missing: minimumnormestimate, music, loreta and rv are used in sourceanalysis.m, but I can't find the implementations (and neither can matlab). Do I need to download additional libraries/toolboxes?

Thank you,
Stefan Rampp.
Epilepsycenter Erlangen
Germany
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From t.montez at VUMC.NL  Thu Jun 22 01:27:29 2006
From: t.montez at VUMC.NL (Montez, T.)
Date: Thu, 22 Jun 2006 01:27:29 +0200
Subject: channel location file to import planar to EEGLAB
Message-ID: <THU.22.JUN.2006.012729.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtripers,

I am using EEGLAB to compute ICA of CTF 151 channels data.

I used to read the data in EEGLAB directly from the CTF format, 
but some components are affected by the bad channels. 

Since removing the bad channels will reduce the number of components
and will give problems later at the planar transformation;
I tried using megrepair first and then importing the matlab array
of data.trial{1}. I use the channel locations of a previous 
dataset opened from the CTF format.

- I still get some components reflecting the bad channels, 
should I increase the cfg.neighbourdist?  
(I was using the default of 4 cm).

- To import the data after the planar transformation I need 
a channel location file for the dH and dV pairs, 
can you help me with that? 

Thanks in advance,
Teresa Montez

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From srampp at TISCALI.DE  Thu Jun 22 01:51:25 2006
From: srampp at TISCALI.DE (Stefan Rampp)
Date: Thu, 22 Jun 2006 01:51:25 +0200
Subject: channel location file to import planar to EEGLAB
Message-ID: <THU.22.JUN.2006.015125.0200.FIELDTRIP@NIC.SURFNET.NL>

channel location file to import planar to EEGLABDear Teresa,

I can't really provide much info regarding your first question, however, I might be able to help you with the second: 
Have you applied 'combineplanar' after the planar transformation? This will combine the dH and dV pairs into one channel per pair, e.g.

cfg = [];
combplan = combineplanar(cfg, plan);

were plan is the planar transformed data set. combineplanar allows to choose the method for combination of the pairs. For further details, you might want to have a look at the tutorial about event related averaging:
http://www2.ru.nl/fcdonders/fieldtrip/doku.php?id=fieldtrip:documentation:tutorial:eventrelatedaveraging

Sincerely,
Stefan Rampp
Epilepsycenter Erlangen
Germany.
  ----- Original Message ----- 
  From: Montez, T. 
  To: FIELDTRIP at NIC.SURFNET.NL 
  Sent: Thursday, June 22, 2006 1:27 AM
  Subject: [FIELDTRIP] channel location file to import planar to EEGLAB


  Dear Fieldtripers,

  I am using EEGLAB to compute ICA of CTF 151 channels data.

  I used to read the data in EEGLAB directly from the CTF format,
  but some components are affected by the bad channels.

  Since removing the bad channels will reduce the number of components
  and will give problems later at the planar transformation;
  I tried using megrepair first and then importing the matlab array
  of data.trial{1}. I use the channel locations of a previous
  dataset opened from the CTF format.

  - I still get some components reflecting the bad channels,
  should I increase the cfg.neighbourdist? 
  (I was using the default of 4 cm).

  - To import the data after the planar transformation I need
  a channel location file for the dH and dV pairs,
  can you help me with that?

  Thanks in advance,
  Teresa Montez


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From r.oostenveld at FCDONDERS.RU.NL  Thu Jun 22 09:25:56 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 22 Jun 2006 09:25:56 +0200
Subject: Statistics for coherence in a within-subject experiment
In-Reply-To: <000901c693b5$79d47c10$0200a8c0@laptop>
Message-ID: <THU.22.JUN.2006.092556.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Jurij

The parametric tests that you suggest are not implemented in  
FieldTrip. In the clusterrandanalysis function we use a randomization  
approach for statistical testing. It is a non-parametrical approach,  
and the test statistic consists of a parametrtical statistic per time- 
frequency-channel, which is clustered and summed over neighbouring  
timepoints/frequencies/channels. Not the single-sample statistic, but  
the clustersum is used for the statistical test, thereby increasing  
sensitivity and controlling for  multiple comparisons. The single  
sample (time-frequency-channel) statistic has to be chosen to match  
with the experimental design (e.g. F or F) and the randomization/ 
permutation of the data between the subjects and conditions has to be  
adequate (in your case you want to shuffle data between conditions  
but only within each subject). That determines the statistic to use.  
I suggest that you go over the clusterrandanalysis tutorial at
http://www2.ru.nl/fcdonders/fieldtrip/doku.php? 
id=fieldtrip:documentation:tutorial:clusterrandanalysis

best regards,
Robert


On 19 Jun 2006, at 17:31, Jurij Dreo wrote:

> Hello!
>
> Thank you for your answers. Here are my replies to them:
>
> To avoid any misunderstandings here is again a summary of my study  
> design
> - I have 11 subjects.
> - Each of them performed 6 tasks related to working memory.
> - Each subject performed anywehere from 25 to 60 repeats (trial) of  
> each condition (the standard number of trials per task was 30 - but  
> some subjects performed the entire experiment twice (ergo 60  
> potential trials) .... and in some some of their trials are  
> unusable - artifacts ... ergo 25 min number of possible trials)
>
> Given my study design I thought something like a one-way ANOVA for  
> correlated samples would be in order.
> (as I am comparing 6 conditions within-subjects as every subject  
> performed all sets)
>
>
> -----------------
> > In your case you have observed a "value" in 11 subjects, over 6
> > conditions. That value happens to be coherence, but could as well
> > have been something else. Since you have manipulated the conditions
> > with each subject, you can use a dependent-samples test: the  
> observed
> > values depend on the subject (an example of a dependent-samples test
> > is a paired-t test).
> -------------------
>
> I´m not sure what you are saying here.... I agree with the  
> dependent samples idea... but I cannot preform a t-test ... ie.  
> more of them as that would inflate my p-rate overall.
>
> I thought that I would first do an ANOVA and then something like  
> the Tukey HSD Test to cimpare individual conditions
>
> --------------------
> > If the number of trials varies between subjects and/or sessions, it
> > will be preferable to transform your coherence values to z-scores
> > manually prior to submitting the values to clusterrandanalysis.
> --------------------
> Yes I agree that would need to be done manually.
>
> -----------
> > Now about the 6 conditions, am I right that you have a 1x6 factorial
> > design, or is there more strucure in the design? Do you have a
> > specific hypothesis about the different conditions? If you only want
> > to reject the null-hypothesis "the observed value (coherence) is the
> > same (more accurately: stems from the same distribution) in all my 6
> > conditions", you would use an omnibus F-statistic, i.e.
> > 'depsamplesF'. It might be that your hypothesis is more specific, or
> > also in case you find an omnibus effect, then you would probably  
> want
> > to perform explicit tests between two subsets of your 6 conditions
> > using a 'depsamplesT' test.
> >
> ----------
>
> I want to contrast all conditions at once (f -test anova) AND also  
> each combination of conditions (say a post- ANOVA Q-test)
>
> But Im still not sure which statistic to use and even if the one I  
> use will be able to deal with the fact that I have a different  
> number of conditions per condition per subject
>
> As far as I understand it... we must use some kind of ANOVA here...  
> A simple "paired" t-test will not do... as we are comparing more  
> than 2 conditions at once and I do not want to inflate my p-rate.
>
> Thank you for your help!
>
> Regards,
> Jurij Dreo
>


From r.oostenveld at FCDONDERS.RU.NL  Thu Jun 22 09:31:10 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 22 Jun 2006 09:31:10 +0200
Subject: Missing minimumnormestimate etc
In-Reply-To: <006c01c69576$c1d13270$14b2a8c0@mirandola>
Message-ID: <THU.22.JUN.2006.093110.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Stefan,

The SOURCEANALYSIS function is used as wrapper for various
distributed or scanning inverse approaches, and DIPOLEFITTING is used
for underdetermined model fitting to the data. The only underlying
functions for SOURCEANALYSIS that are released on the ftp server are
the lcmv and the dics beamformer methods. The functions that you
refer to are implemented in our in-house version of FieldTrip but
have not been tested thouroughly. I can give you a pre-release if you
are willing to aid in the testing of those functions.

best regards,
Robert


On 21 Jun 2006, at 23:07, Stefan Rampp wrote:

> Hi everyone,
>
> I was just trying to do source localization of epilepsy MEG data
> using mne, however, it appears that some functions are missing:
> minimumnormestimate, music, loreta and rv are used in
> sourceanalysis.m, but I can't find the implementations (and neither
> can matlab). Do I need to download additional libraries/toolboxes?
>
> Thank you,
> Stefan Rampp.
> Epilepsycenter Erlangen
> Germany
>


From r.oostenveld at FCDONDERS.RU.NL  Thu Jun 22 09:40:31 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 22 Jun 2006 09:40:31 +0200
Subject: channel location file to import planar to EEGLAB
In-Reply-To: <28FF6B8D22C94B44A55E4E1325A94AF2348059@vumc-mb02.vumc.nl>
Message-ID: <THU.22.JUN.2006.094031.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Theresa

On 22 Jun 2006, at 1:27, Montez, T. wrote:
> I am using EEGLAB to compute ICA of CTF 151 channels data.
>
> I used to read the data in EEGLAB directly from the CTF format,
> but some components are affected by the bad channels.
The bad channels do not reflect a linear mixture of underlying
sources, therefore you should remove them prior to ICA. You should
also remove all trials containing anomalous artifacts.
> Since removing the bad channels will reduce the number of components
> and will give problems later at the planar transformation;
> I tried using megrepair first and then importing the matlab array
> of data.trial{1}. I use the channel locations of a previous
> dataset opened from the CTF format.
MEGREPAIR uses a nearest-neighbour approach for fixing the missing
channels. The "repaired" channels are linear combinations (i.e. a
linear mixture) of the neighbours and hence do not add any
information (i.e. components) to the data, doing ICA on the repaired
dataset does not give you all 151 components.
> - I still get some components reflecting the bad channels,
> should I increase the cfg.neighbourdist?
> (I was using the default of 4 cm).
>
> - To import the data after the planar transformation I need
> a channel location file for the dH and dV pairs,
> can you help me with that?
The planar transformation in MEGPLANAR also results in a linear
estimation of the horizontal and vertical gradients, i.e. if you
start with 151 axial channels and you do MEGPLANAR, you will have 302
planar channels, but the dimensionality of that data will still be
151. That means that ICA on the 302-channel planar data will result
in a maximum of 151 components.

I suggest to do the ICA on the axial data with the bad channels
removed. Subsequently you can switch from EEGLAB to FieldTrip and
compute the planar representation of the ICA components using the
MEGPLANAR function (I am not sure whether megplanar knows how to deal
with ICA data, but it is easy to convert the ICA data into something
that resembles an average ERF or alternatively to add support for the
ICA data in megplanar).

best regards,
Robert


From srampp at TISCALI.DE  Thu Jun 22 10:43:01 2006
From: srampp at TISCALI.DE (Stefan Rampp)
Date: Thu, 22 Jun 2006 10:43:01 +0200
Subject: Missing minimumnormestimate etc
Message-ID: <THU.22.JUN.2006.104301.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Robert,

Thank you for the fast answer. Since I'm interested in comparing various
methods, I'd greatly appreciate a pre-release version. And of course I could
contribute to Fieldtrip as a betatester for these functions like that.

Sincerely,
Stefan Rampp
Epilepsycenter Erlangen
Germany


----- Original Message -----
From: "Robert Oostenveld" <r.oostenveld at FCDONDERS.RU.NL>
To: <FIELDTRIP at NIC.SURFNET.NL>
Sent: Thursday, June 22, 2006 9:31 AM
Subject: Re: [FIELDTRIP] Missing minimumnormestimate etc


> Dear Stefan,
>
> The SOURCEANALYSIS function is used as wrapper for various  distributed or
> scanning inverse approaches, and DIPOLEFITTING is used  for
> underdetermined model fitting to the data. The only underlying  functions
> for SOURCEANALYSIS that are released on the ftp server are  the lcmv and
> the dics beamformer methods. The functions that you  refer to are
> implemented in our in-house version of FieldTrip but  have not been tested
> thouroughly. I can give you a pre-release if you  are willing to aid in
> the testing of those functions.
>
> best regards,
> Robert
>
>
> On 21 Jun 2006, at 23:07, Stefan Rampp wrote:
>
>> Hi everyone,
>>
>> I was just trying to do source localization of epilepsy MEG data  using
>> mne, however, it appears that some functions are missing:
>> minimumnormestimate, music, loreta and rv are used in  sourceanalysis.m,
>> but I can't find the implementations (and neither  can matlab). Do I need
>> to download additional libraries/toolboxes?
>>
>> Thank you,
>> Stefan Rampp.
>> Epilepsycenter Erlangen
>> Germany
>>


From MZvyagintsev at UKAACHEN.DE  Thu Jun 22 18:08:43 2006
From: MZvyagintsev at UKAACHEN.DE (Mikhail Zvyagintsev)
Date: Thu, 22 Jun 2006 18:08:43 +0200
Subject: Missing minimumnormestimate etc
In-Reply-To: <21EE19CF-BE60-4719-BC9E-C1F3737F26B5@fcdonders.ru.nl>
Message-ID: <THU.22.JUN.2006.180843.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Robert,

Would be also nice to have an implementaion of LORETA approach for
source analysis from your in-house software. I would appreciate if you
could send it to me as well.

Best regards,

Mikhail Zvyagintsev

MZvyagintsev at UKAachen.de



Robert Oostenveld wrote:

> Dear Stefan,
>
> The SOURCEANALYSIS function is used as wrapper for various
> distributed or scanning inverse approaches, and DIPOLEFITTING is used
> for underdetermined model fitting to the data. The only underlying
> functions for SOURCEANALYSIS that are released on the ftp server are
> the lcmv and the dics beamformer methods. The functions that you
> refer to are implemented in our in-house version of FieldTrip but
> have not been tested thouroughly. I can give you a pre-release if you
> are willing to aid in the testing of those functions.
>
> best regards,
> Robert


From muthuraman10 at HOTMAIL.COM  Fri Jun 23 12:54:57 2006
From: muthuraman10 at HOTMAIL.COM (Muthuraman Muthuraman)
Date: Fri, 23 Jun 2006 10:54:57 +0000
Subject: query on CTF software!!!
Message-ID: <FRI.23.JUN.2006.105457.0000.FIELDTRIP@NIC.SURFNET.NL>

Hello

For the Beamformer source analysis, do we need the CTF software
because when i am trying out the tutorial in beamforming

Matlab
>>freq=19.0;
>>Ncycles=10;
>>dTimeWin=Ncycles/freq;
>>cfg=[];
>>cfg.dataset='Subject01.ds';
>>cfg.channel={'MEG' 'STIM'};
>>cfg.trialdef.excludeConditions={'BAD'};
>>cfg.trialdef.includeTrigger=3;
>>cfg.trialdef.prestim=0.1+dTimeWin;
>>cfg.trialdef.poststim=-0.1;
>>datapre=preprocessing(cfg);

CTF_READ_RES4 [v  1.12]
....done (  0.67 sec)

i get the error

??? Error using ==> read_fcdc_header
could not read CTF res4 header file

Error in ==> preprocessing at 263
hdr = read_fcdc_header(cfg.headerfile);


with regards
muthu


From r.oostenveld at FCDONDERS.RU.NL  Fri Jun 23 15:23:22 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 23 Jun 2006 15:23:22 +0200
Subject: query on CTF software!!!
In-Reply-To: <BAY121-F290E321E30CF71939F2A00CE7A0@phx.gbl>
Message-ID: <FRI.23.JUN.2006.152322.0200.FIELDTRIP@NIC.SURFNET.NL>

dear Muthuraman

On 23 Jun 2006, at 12:54, Muthuraman Muthuraman wrote:
> For the Beamformer source analysis, do we need the CTF software
> because when i am trying out the tutorial in beamforming

You do not need the ctf software to follow the tutorial. The tutorial
is based however on a ctf MEG dataset.

> CTF_READ_RES4 [v  1.12]
> ....done (  0.67 sec)
>
> i get the error
>
> ??? Error using ==> read_fcdc_header
> could not read CTF res4 header file
>
> Error in ==> preprocessing at 263
> hdr = read_fcdc_header(cfg.headerfile);

Based on your error I suspect that matlab/fieldtrip cannot find the
dataset that you are trying to analyze, or that you matlab path is
incorrect. The function "CTF_READ_RES4" is not supposed to be called
(it is part of the NIH ctf import routines, e.g. used in EEGLAB),
since the default private/read_ctf_res4.m function can deal with the
tutorial dataset just fine. Please look into the code of
read_fcdc_header (using the matlab debugger) to figure out what your
exact problem is.

best
Robert


From r.oostenveld at FCDONDERS.RU.NL  Fri Jun 23 15:28:03 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 23 Jun 2006 15:28:03 +0200
Subject: Missing minimumnormestimate etc
In-Reply-To: <449AC08B.4080202@UKAachen.de>
Message-ID: <FRI.23.JUN.2006.152803.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Mikhail

My loreta implementation still has some problems and is not 100%
correct. I first want to fix it before I release it. If you know how
to work with KEY-LORETA (the software from Pasqual Marqui) and could
compare the two implementations, you could get a pre-release version
and help fix the bugs.

Robert


On 22 Jun 2006, at 18:08, Mikhail Zvyagintsev wrote:

> Dear Robert,
>
> Would be also nice to have an implementaion of LORETA approach for
> source analysis from your in-house software. I would appreciate if
> you could send it to me as well.
>
> Best regards,
>
> Mikhail Zvyagintsev
>
> MZvyagintsev at UKAachen.de


From MZvyagintsev at UKAACHEN.DE  Mon Jun 26 13:15:34 2006
From: MZvyagintsev at UKAACHEN.DE (Mikhail Zvyagintsev)
Date: Mon, 26 Jun 2006 13:15:34 +0200
Subject: Missing minimumnormestimate etc
In-Reply-To: <29758FB9-8B0E-4C41-8067-BF39410560A0@fcdonders.ru.nl>
Message-ID: <MON.26.JUN.2006.131534.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Robert,
Thank you for this encouragement. I was working with LORETA from Pasqual
Marqui only with EEG data. I hope it will help me to be useful with
fixing bugs.
Kindly,
Mikhail.

MZvyagintsev at UKAachen.de

Robert Oostenveld wrote:

> Dear Mikhail
>
> My loreta implementation still has some problems and is not 100%
> correct. I first want to fix it before I release it. If you know how
> to work with KEY-LORETA (the software from Pasqual Marqui) and could
> compare the two implementations, you could get a pre-release version
> and help fix the bugs.
>
> Robert


From esther.meeuwissen at FCDONDERS.RU.NL  Mon Jun 26 15:04:27 2006
From: esther.meeuwissen at FCDONDERS.RU.NL (Esther Meeuwissen)
Date: Mon, 26 Jun 2006 15:04:27 +0200
Subject: artifact rejection
Message-ID: <MON.26.JUN.2006.150427.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi all,

A few weeks ago I started to work with Fieldtrip. I would like use it to 
analyze EEG data.

I have a question concerning preprocessing of EEG data. I would like to do 
a artifact rejection during preprocessing partly using the functions in 
fieldtrip (detection and rejection of  muscle artifacts) and partly 
reading in artifact markers that are exported out of brain vision analyser 
(I used the raw data inspector to detect eye blinks).

I used the following script:

EEGchans = 
{'Fp2', 'F7', 'F3', 'Fz', 'F4', 'F8', 'FC5', 'FC1', 'FCz', 'FC2', 'FC6', 'T
7', 'C3', 'Cz', 'C4', 'T8', 'CP5', 'CP1', 'CP2', 'CP6', 'TP10', 'P7', 'P3',
 'Pz', 'P4', 'P8', 'O1', 'O2'};
EOGchans = {'VB','HL', 'HR', 'VO'};

files = {'GOS10B'...
    'GOS11C'};
for subject=1:2,
   
% Parameters
cfg = [];
cfg.datafile            = strcat('',files{subject},'.eeg');
cfg.headerfile          = strcat('',files{subject},'.vhdr');
cfg.trialdef.trgfile    = strcat('',files{subject},'.vmrk');
cfg.rejectfile          = strcat('',files{subject},'_Reject.Marker');
cfg.icaresultfile       = strcat('',files{subject},'.ica');
cfg.outdatafile         = strcat('',files{subject},'.mat');

cfg.channel    = {'all'};
cfg.padding    = 1.5;
cfg.bpfilter   = 'yes';
cfg.bpfreq     = [0.3 30];
cfg.blc        = 'yes';
cfg.blcwindow  = [-0.1 0.0];

% EEG options
cfg.reref      = 'no';
cfg.implicitref = [];
cfg.refchannel  = {};

% Trial definition
cfg.trialdef.stim = [1 2 3 4];   
cfg.trialdef.prestim    = 0.200;
cfg.trialdef.poststim   = 1.000;

% Artifact options (preprocessing)
cfg.artfctdef.reject            = 'complete';
cfg.artfctdef.muscle.sgn        = EEGchans;
cfg.artfctdef.muscle.feedback   = 'no';
cfg.artfctdef.muscle.cutoff     = 15;

% Do preprocessing
cfg = definetrial(cfg);
cfg = artifact_muscle(cfg)
cfg = rejectartifact(cfg);
data = preprocessing(cfg);

%Save intermediate result
save(cfg.outdatafile,'data');
clear data;
pack;
end;

and get the following error message:

 Error using ==> horzcat
CAT arguments dimensions are not consistent.

Error in ==> rejectartifact at 182
    cfg.artfctdef.type = [{'file'} cfg.artfctdef.type];

Error in ==> preprocessing at 317
[cfg] = rejectartifact(cfg);

Error in ==> preproesther1 at 45
data = preprocessing(cfg);

By trying to make it work I figured out that it is possible to do both the 
artifact rejection parts separately using (parts of) the script above but  
(Fieldtrip wants to combine two matrices to 1 matrix and that is what goes 
wrong). Does anyone know how (/whether) it is possible to do a artifact 
detection/rejection in Fieldtrip partly using functions of Fieldtrip 
itself and partly read markers of EEG parts containing a artifact (the 
file made by brain vision analyzer)?

Thanks in advance for the answer(s)!
Esther Meeuwissen


From r.oostenveld at FCDONDERS.RU.NL  Mon Jun 26 17:17:49 2006
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Mon, 26 Jun 2006 17:17:49 +0200
Subject: artifact rejection
In-Reply-To: <LISTSERV%200606261504275190.1F7B@NIC.SURFNET.NL>
Message-ID: <MON.26.JUN.2006.171749.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Esther,

On 26 Jun 2006, at 15:04, Esther Meeuwissen wrote:
> and get the following error message:
>
>  Error using ==> horzcat
> CAT arguments dimensions are not consistent.
>
> Error in ==> rejectartifact at 182
>     cfg.artfctdef.type = [{'file'} cfg.artfctdef.type];

I suspect here that cfg.artfctdef.type is a cell-array with strings
represented as a vertical cell-vector, and that line 182 tries to
combine it with something that Matlab treats as horizontal cell-
vector. It is unclear to me why it does that, since the
cfg.artfctdef.type is built up internally (you did not explicitely
specify it).

> Error in ==> preprocessing at 317
> [cfg] = rejectartifact(cfg);
>
> Error in ==> preproesther1 at 45
> data = preprocessing(cfg);
>
> By trying to make it work I figured out that it is possible to do
> both the
> artifact rejection parts separately using (parts of) the script
> above but
> (Fieldtrip wants to combine two matrices to 1 matrix and that is
> what goes
> wrong). Does anyone know how (/whether) it is possible to do a
> artifact
> detection/rejection in Fieldtrip partly using functions of Fieldtrip
> itself and partly read markers of EEG parts containing a artifact (the
> file made by brain vision analyzer)?

I have tried replicating your problem (with the data that I found on /
home/electromag/estmee/GOs/analyses/datagoed), but did not encounter
any problems up to the definetrial, artifatc_muscle and
rejectartifact. However, the problem comes only in when preprocessing
is called. For backward compatibility with other peoples old scripts,
preprocessing is also calling definetrial and rejhectartifact, and
rejectartifact seems confused by being called twice.

I made a small change to rejectartifact that hopefully fixes the
problem. The updated version is on home/common now and will be on the
ftp this evening.

best regards,
Robert


From Esther.Meeuwissen at FCDONDERS.RU.NL  Tue Jun 27 09:05:21 2006
From: Esther.Meeuwissen at FCDONDERS.RU.NL (Esther Meeuwissen)
Date: Tue, 27 Jun 2006 09:05:21 +0200
Subject: artifact rejection
In-Reply-To: <442FC113-07E9-4479-9237-6D20F1D026C8@fcdonders.ru.nl>
Message-ID: <TUE.27.JUN.2006.090521.0200.FIELDTRIP@NIC.SURFNET.NL>

Robert Oostenveld wrote:
> Hi Esther,
>
> On 26 Jun 2006, at 15:04, Esther Meeuwissen wrote:
>> and get the following error message:
>>
>>  Error using ==> horzcat
>> CAT arguments dimensions are not consistent.
>>
>> Error in ==> rejectartifact at 182
>>     cfg.artfctdef.type = [{'file'} cfg.artfctdef.type];
>
> I suspect here that cfg.artfctdef.type is a cell-array with strings
> represented as a vertical cell-vector, and that line 182 tries to
> combine it with something that Matlab treats as horizontal
> cell-vector. It is unclear to me why it does that, since the
> cfg.artfctdef.type is built up internally (you did not explicitely
> specify it).
>
>> Error in ==> preprocessing at 317
>> [cfg] = rejectartifact(cfg);
>>
>> Error in ==> preproesther1 at 45
>> data = preprocessing(cfg);
>>
>> By trying to make it work I figured out that it is possible to do
>> both the
>> artifact rejection parts separately using (parts of) the script above
>> but
>> (Fieldtrip wants to combine two matrices to 1 matrix and that is what
>> goes
>> wrong). Does anyone know how (/whether) it is possible to do a artifact
>> detection/rejection in Fieldtrip partly using functions of Fieldtrip
>> itself and partly read markers of EEG parts containing a artifact (the
>> file made by brain vision analyzer)?
>
> I have tried replicating your problem (with the data that I found on
> /home/electromag/estmee/GOs/analyses/datagoed), but did not encounter
> any problems up to the definetrial, artifatc_muscle and
> rejectartifact. However, the problem comes only in when preprocessing
> is called. For backward compatibility with other peoples old scripts,
> preprocessing is also calling definetrial and rejhectartifact, and
> rejectartifact seems confused by being called twice.
>
> I made a small change to rejectartifact that hopefully fixes the
> problem. The updated version is on home/common now and will be on the
> ftp this evening.
>
> best regards,
> Robert
>