SV: [FIELDTRIP] multiplotTFR for 128 channel Neuroscan EEG data ???

Thu Jun 1 13:21:11 CEST 2006

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);
>