From knyazev at PHYSIOL.RU  Thu Oct  1 05:22:48 2009
From: knyazev at PHYSIOL.RU (knyazev)
Date: Thu, 1 Oct 2009 10:22:48 +0700
Subject: Reference electrode in lead field
Message-ID: <THU.1.OCT.2009.102248.0700.FIELDTRIP@NIC.SURFNET.NL>

I wonder how many electrodes should be considered enough to provide a
 representative sampling of the head surface? I remember reading somewhere
that using an average reference from too few channels distorts results
severely. May someone provide an appropriate citation on the topic? Thanks
in advance.

Gennady Knyazev

----- Original Message -----
From: "Joseph Dien" <jdien07 at MAC.COM>
To: <FIELDTRIP at NIC.SURFNET.NL>
Sent: Wednesday, September 30, 2009 9:10 AM
Subject: Re: [FIELDTRIP] Reference electrode in lead field


> The reasoning behind the average reference is that it is a physics
> principle that the sum of the voltages over an enclosed surface must
> equal zero.  To the extent that the electrode locations provide a
> representative even sampling of the head surface (an important caveat)
> the sum of the voltages therefore provides an estimate of the true  zero
> voltage.  The reason for using the average reference rather than  a single
> reference site is that using a reference site arbitrarily  defines that
> point as being zero voltage (which is to say, inactive),  which is not
> biophysically reasonable as there are no inactive sites  on the head (due
> to volume conduction).  Also, to clarify, an average  reference does not
> result in a reference-free solution since, as you  say, a voltage
> measurement is by definition a relative measure  (although ideally it
> should be relatively independent of the electrode  montage, given enough
> electrodes).  It's just that the comparison  "site", which is the zero
> equipotential line (as estimated by the  average reference computation),
> is a more biophysically reasonable one  (given enough recording sites)
> than arbitrarily picking a single fixed  electrode site as the reference.
>
> For an extended discussion of these issues, see:
>
> Dien, J. (1998). Issues in the application of the average reference:
> Review, critiques, and recommendations. Behavior Research Methods,
> Instruments, and Computers, 30(1), 34-43.
>
> Cheers!
>
> Joe
>
>
> On Sep 28, 2009, at 3:29 PM, Mark Drakesmith wrote:
>
>> Hi all
>>
>> I am experimenting with source reconstruction and was wondering how  a
>> reference electrode is defined in the lead field. Looking through  the
>> scripts it looks like the average reference is used, but this is  a
>> physical impossibility, as there must be a physical reference to  which
>> differences in electrical potential can be measured. The lead  field will
>> be differ depending on the location of the reference  electrode.
>>
>> Firstly, is there a way to specify a reference electrode when
>> constructing an EEG lead field in fieldtri p and not jsut use the
>> average reference.
>>
>> Secondly, looking through  the code for  'inf_medium_leadfield' (called
>> from prepare_leadfield ->  compute_leadfield -> eeg_leadfieldb), the
>> equations used for  calculating the lead field look a little strange:
>>
>> radius = position (vox) - position(elec)
>> R (resistivity?) = 4 x pi x conductivity x sum(radius^2)^(1.5)
>> lead field(vox,elec)=radius / R.
>>
>> Where the the exponential to 1.5 come from? Is there a reference to
>> somewhere where this method is used. I'm confused as to sure how  this
>> calculation works.
>>
>> Many thanks
>>
>> Mark
>>
>> --
>>
>> Mark Drakesmith
>> PhD Student
>>
>> Neuroscience and Aphasia Research Unit (NARU)
>> University of Manchester
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users  of
>> the FieldTrip  toolbox, to share experiences and to discuss new  ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/neuroimaging/fieldtrip.
>
>
> --------------------------------------------------------------------------------
>
> Joseph Dien,
> Senior Research Scientist
> Center for Advanced Study of Language
> University of Maryland
> 7005 52nd Avenue
> College Park, MD 20742-0025
>
> E-mail: jdien07 at mac.com
> Phone: 301-226-8848
> Fax: 301-226-8811
> http://homepage.mac.com/jdien07/
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/neuroimaging/fieldtrip.

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


From r.oostenveld at FCDONDERS.RU.NL  Thu Oct  1 12:38:46 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 1 Oct 2009 12:38:46 +0200
Subject: Reference electrode in lead field
In-Reply-To: <4AC10E84.50708@postgrad.manchester.ac.uk>
Message-ID: <THU.1.OCT.2009.123846.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Mark

On 28 Sep 2009, at 21:29, Mark Drakesmith wrote:
> I am experimenting with source reconstruction and was wondering how
> a reference electrode is defined in the lead field. Looking through
> the scripts it looks like the average reference is used, but this is
> a physical impossibility, as there must be a physical reference to
> which differences in electrical potential can be measured. The lead
> field will be differ depending on the location of the reference
> electrode.
>
> Firstly, is there a way to specify a reference electrode when
> constructing an EEG lead field in fieldtri p and not jsut use the
> average reference.

At the moment there is no other reference choise for EEG source
modelling than the average over all electrodes. However, more
elaborate bipolar referencing schemes are since recently needed for
out own research and for that we'll implement a very flexible
referencing scheme. You can expect that to be included in the
fieldtrip release in a month or so. However, the average reference
will remain the defaulty, as it has been shown in simulations to give
the most robust results (although it makes little difference). I don't
immediately know the reference for that, but you should be able to
find it in pubmed.

See also the reply from Burkhard and yesterdays message from Joseph.

> Secondly, looking through  the code for
> 'inf_medium_leadfield' (called from prepare_leadfield ->
> compute_leadfield -> eeg_leadfieldb), the equations used for
> calculating the lead field look a little strange:
>
> radius = position (vox) - position(elec)
> R (resistivity?) = 4 x pi x conductivity x sum(radius^2)^(1.5)
> lead field(vox,elec)=radius / R.
>
> Where the the exponential to 1.5 come from? Is there a reference to
> somewhere where this method is used. I'm confused as to sure how
> this calculation works.

R is not a single physical value, it is just a shord-hand notation for
one of the terms in the equation. See the reference to implemented
methods on the fieldtrip wiki for publication details.

best
Robert

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


From megjim1 at GMAIL.COM  Fri Oct  2 06:07:18 2009
From: megjim1 at GMAIL.COM (Jim Li)
Date: Fri, 2 Oct 2009 06:07:18 +0200
Subject: how to plot the direction and amplitude of the planar gradient
Message-ID: <FRI.2.OCT.2009.060718.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear all,

I want to view the direction and amplitude of the planar gradient  near each 
sensor location and create a plot like what's shown in the  attached file (more 
or less).  Is it possible to do it? If so, how?

Our MEG sensors are 248 axial gradiometers. After running "megplanar" I got 
A1_dH...A248_dH,A1_dV...A248_dV for my channels. If, say, in the plane 
tangential to a given channel we have the Horizontal (x axis) and Vertical (y 
axis) directions. Then for the channel of interest, say A1,  I can run sqrt
(A1_dH^2+A1_dV^2) to get the amplitude of the planar gradient, and I can 
run atan2(A1_dV,A1_dH)*180/pi) to get the angle between the field vector 
and x-axis. What I'm not sure  about is how fieldtrip defines the Horizontal (x 
axis) and Vertical (y axis) for each channel (in a plane tangential to that 
channel). So it's hard to create the plot I want...

Thanks a lot.

Jim

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From j.schoffelen at PSY.GLA.AC.UK  Fri Oct  2 11:46:25 2009
From: j.schoffelen at PSY.GLA.AC.UK (Jan-Mathijs Schoffelen)
Date: Fri, 2 Oct 2009 09:46:25 +0000
Subject: how to plot the direction and amplitude of the planar gradient
In-Reply-To: <LISTSERV%200910020607189850.0FFE@NIC.SURFNET.NL>
Message-ID: <FRI.2.OCT.2009.094625.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Jim,

As far as I know, this is not possible in fieldtrip ... yet. Do I read
between the lines that you wouldn't mind giving it a try? I agree that
it's a very useful way to visualize planar gradient data.
First of all, it is indeed important to know the local coordinate
system for each of the planar gradient channels. For megplanar I
always use the 'sincos' method. You can see how the coordinate system
is defined at line 419 and beyond. As far as I can see the local x-
axis is taken as the vector orthogonal to the plane defined by the
coil's orientation, and the vector [0 0 1] (which is the z-axis of the
coordinate system in which your sensors are defined; assuming your
sensors are defined in headspace, this one points to the top of the
head). The local z-axis is the vector perpendicular to the coil's
plane (=orientation), and the y-axis is perpendicular to the local xz-
plane.
I guess that for the other planarmethods it's possible to figure out
the local coordinate systems as well. One think which we could think
of, is to adjust megplanar such that the output data contains
information about the local x and y axes directly.
Of course, it would also be nice if a hypothetical plotting function
would work for data acquired with hardware planar gradiometers. Here
it is usually straightforward to reconstruct the local coordinate
systems from the header-information. Perhaps people working with
Elekta-systems already have some matlab code for the plotting...
Once the local coordinate systems are known (and the angles defined
accordingly), it should be possible to warp these values to a
headspace based coordinate system for plotting (in 3D, or in 2D after
an appropriate projection).

Best,

Jan-Mathijs

On 2 Oct 2009, at 04:07, Jim Li wrote:

> Dear all,
>
> I want to view the direction and amplitude of the planar gradient
> near each
> sensor location and create a plot like what's shown in the  attached
> file (more
> or less).  Is it possible to do it? If so, how?
>
> Our MEG sensors are 248 axial gradiometers. After running
> "megplanar" I got
> A1_dH...A248_dH,A1_dV...A248_dV for my channels. If, say, in the plane
> tangential to a given channel we have the Horizontal (x axis) and
> Vertical (y
> axis) directions. Then for the channel of interest, say A1,  I can
> run sqrt
> (A1_dH^2+A1_dV^2) to get the amplitude of the planar gradient, and I
> can
> run atan2(A1_dV,A1_dH)*180/pi) to get the angle between the field
> vector
> and x-axis. What I'm not sure  about is how fieldtrip defines the
> Horizontal (x
> axis) and Vertical (y axis) for each channel (in a plane tangential
> to that
> channel). So it's hard to create the plot I want...
>
> Thanks a lot.
>
> Jim
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.
> <PlotGoal.TIF>

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


From Nina.Kahlbrock at UNI-DUESSELDORF.DE  Fri Oct  2 09:54:44 2009
From: Nina.Kahlbrock at UNI-DUESSELDORF.DE (Nina)
Date: Fri, 2 Oct 2009 09:54:44 +0200
Subject: Freqanalysis - clusterthreshold and neighbourselection
Message-ID: <FRI.2.OCT.2009.095444.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear all,



I have two questions regarding clusteranalysis.



1.	When running 'freqstatistics' on time frequency/frequency data with
the method 'montecarlo' which clusterthreshold would you use? I would think
that with the data usually not being normally distributed you would use a
nonparametric threshold. However, the default value for clusterthreshold is
'parametric'.

a.	Is there documentation about what 'nonparametric_individual' and
'nonparametric_common' mean? If yes, where can I find it?

2.	I am looking at data from our old Neuromag 122 system and used the
function 'neighbourselection' to define neighbouring channels. When checking
what 'neighbourselection' did I found that the neighbours identified were
not only the sensors surrounding the sensor of interest, but also sensors
lying far away from it. Also, not all sensors surrounding the one of
interest were included as neighbours. I used the gradfile generated by
'mne2grad122' as cfg.grad and different values for neighbourdist (4 and 3).
Does anybody have a solution for this?



Thanks in advance for your help!



Nina




----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From e.maris at DONDERS.RU.NL  Fri Oct  2 11:51:06 2009
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Fri, 2 Oct 2009 11:51:06 +0200
Subject: Freqanalysis - clusterthreshold and neighbourselection
In-Reply-To: <000901ca4335$9ad839f0$cd136386@VMED.UKD>
Message-ID: <FRI.2.OCT.2009.115106.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Nina,









I have two questions regarding clusteranalysis.



1.	When running 'freqstatistics' on time frequency/frequency data with
the method 'montecarlo' which clusterthreshold would you use? I would think
that with the data usually not being normally distributed you would use a
nonparametric threshold. However, the default value for clusterthreshold is
'parametric'.

a.	Is there documentation about what 'nonparametric_individual' and
'nonparametric_common' mean? If yes, where can I find it?



You can safely use the parametric threshold, regardless of the probability
distribution of your data. The reason is that this threshold only affects
the type of effect for which you test statistic is sensitive. The false
alarm rate does not depend on it. See Maris & Oostenveld (2007).



You only use the two other clusterthreshold options if you use a
non-normalized channel-level statistic. If you construct clusters by
thresholding channel-level T-statistics, go ahead with the parametric
threshold.





2.	I am looking at data from our old Neuromag 122 system and used the
function 'neighbourselection' to define neighbouring channels. When checking
what 'neighbourselection' did I found that the neighbours identified were
not only the sensors surrounding the sensor of interest, but also sensors
lying far away from it. Also, not all sensors surrounding the one of
interest were included as neighbours. I used the gradfile generated by
'mne2grad122' as cfg.grad and different values for neighbourdist (4 and 3).
Does anybody have a solution for this?





I guess Neuromag 122 system has planar gradiometers. For this sensor
configuration, the definition of a neighbourhood-metric requires some
thinking (because you are actually measuring spatial gradients with
different orientations). I contributed to a recent thread on the Fieldtrip
Discussion list about cluster-based permutation tests for the Vectorview
system. If I'm not mistaken, a scientist from an imaging center in Paris
initiated this thread. Have a look in the archive of the Fieldtrip
Discussion list (keywords: planar, cluster, Vectorview).





Good luck,











Thanks in advance for your help!



Nina



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

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

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

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


----------------------------------
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From r.oostenveld at FCDONDERS.RU.NL  Fri Oct  2 12:19:30 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 2 Oct 2009 12:19:30 +0200
Subject: Fwd: [FIELDTRIP] Reference electrode in lead field
Message-ID: <FRI.2.OCT.2009.121930.0200.FIELDTRIP@NIC.SURFNET.NL>

Begin forwarded message:

> From: "Dr. Georges Otte" <georges.otte at telenet.be>
> Date: 1 October 2009 13:49:13 GMT+02:00
> To: r.oostenveld at FCDONDERS.RU.NL
> Subject: reference
>
> ...
> I have followed the discussion on reference and already contacted
> Dien. I agree but what about non ERP data ? Phase information and
> coherence. Can we safely use the averaged common reference for that.
> Robert Thatcher (neuroguide) quoting rappelsberger is opoosed to it
> and shows in his neuroguide package that in small channel systems
> (19-22) a ACR scrambles phase information between channels.
>
> Sincerely
>
> Dr. Georges Otte
> P.C dr. Guislain instit
> Gent
> Belgium
>
>
> PS How can I get back on the list ?
>
> Ransscipt
> no problem!  I haven't been working in the frequency domain and am
> not very familiar with spectral analyses so I can't say.  Sorry!
>
> Joe
>
>
> On Sep 30, 2009, at 2:20 AM, Dr. Georges Otte wrote:
>
>
> If the reference is not close to zero (fi using an average reference
> on to low an electrodeset fi 19 ch with prefrontal channels likely
> to be contaminated by occasional quite lagre eye blink or eye
> movement artifacts) what would be the effect on phase calculations ?
> From point to point the reference value that is substracted from
> each channel would be different from zero. Would that not wreck
> havoc to interchannel phase information or post stimulus coherence
> mapping ? Untrusthworthy ?
>
> Same qyuestion: if people use PCA or ICA to eliminate these
> artifacts and inverse reconstruct their EEG, can they still rely on
> phase calculations without errors ?
>
> Sincerely,
>
> Georges Otte
>
> PS Sorry to mail You personally but for some reason (perhaps change
> of email adres or long period of inactivity ) I seem to be  cutoff
> from the fieldtrip listserv
>
>


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From r.oostenveld at FCDONDERS.RU.NL  Fri Oct  2 12:58:09 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 2 Oct 2009 12:58:09 +0200
Subject: Fwd: [FIELDTRIP] Reference electrode in lead field
In-Reply-To: <0EEFD9A0-12F8-4751-A69D-62D61655E8BD@FCDONDERS.RU.NL>
Message-ID: <FRI.2.OCT.2009.125809.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Georges,

Thanks for raising this very good point.

As discussed before, the choise of the reference is quite irrelevant
for most analysis that involve a **linear transformation** of the
data, such as the computation and visualisation of the topography of
an ERP. But for non-linear transformations, the reference becomes
relevant.

Consider a simple statistics example. If you want to show a
significant effect in an auditory evoked potential (AEP) given a
standard and deviant tone, the optimal reference is the mastoid, which
maximizes the potential at Cz. So Cz minus M1, or Cz minus (M1+M2)/2,
i.e. linked ears, results in the largest signal on Cz. Subsequently
you compute the average ERP in both conditions and you compute the
variance from which you can compute the standard-error of the mean.
Then you compute the t-value, i.e. the difference in means  divided by
the pooled standard-error of the mean. That is all for the values
recorded in the Cz channel. Had you referenced Cz to the tip of the
nose, then the spatial topography of the AEPs and the spatial
topography of the AEP difference would not be qualitatively different
(only a difference in the color scale, but that color scale is
arbitarry chosen anyway). But the noise over trials in the Cz AEP
would probably be larger for the nose reference than for the linked
ears  reference. That noise is expressed in the variance, which is in
the denominator of the t-value. So the t-value would be less. The t-
value would become even smaller for a Fz reference.

Another example: if you compute spectral power using a FFT or warevelt
transform, the power is expressed as a squared number. At the
reference electrode the power is zero (per definition), whereas around
the reference electrode it would increase. Had I measured oscillatory
activity from auditory cotrex using a linked-ears reference, I would
see the maximum over the vertex, i.e. Cz. For a nose reference, the
maximum in power probably still would be over the vertex. But had I
choosen Cz itself as the reference, then at the vertex there would be
no power any more. Or less extreme, had I choosen Fz as reference,
then probably the power would _not_ be maximal over the vertex any
more, but rather along the lower electrode rim (T3/T4 a.k.a. C7/C8 and
the lower occipital electrodes). The spatial topography of the power
would also be qualitatively different for the different references.
You can think of it like "pushing the maximum in the power topography
around over the scalp" by changing the reference. In general, the
power will be largest further away from the reference and small close
to the reference. Of course the true power distrubution depends on the
underlying source activity, so this is a bit of a simplification.

In both examples above a non-linear transformation on the data is
involved. Offline rereferencing is a linear transformation of the
data, i.e. it only involves the addition and/or subtraction of some
value. The computations above (t-value, spectral power) are non-
linear, and they are non commutative (see http://en.wikipedia.org/wiki/Commutativity)
. In short (1+1)^2 is not equal to (1)^2+(1)^2.

The estimation of the phase from a signal is also a non-linear
transformation of the signal. After decomposing it into a sine and
cosine contribution at a specific frequency (with the FFT), the sine
and cosine contribution are combined to get the phasae (i.e. using the
arctangent, or using the complex-number representation). Everything
that is subsequently derived from the phase is therefore also non-
linear. So coherence and phase-locking values will be qualitatively
different depending on the choise of reference. One cannot simply
first compute coherence, and then afterwards apply a re-referencing.

Note that the estimation of the source strength of a dipole using any
source reconstruction technique (dipole fitting, beamforming, minimum
norm linear estimation) is a linear operation. It assumes a linear
mixing model (data = leadfield*source + noise) and a linear unmixing
model. In the estimate of the "unmixing matrix" for most techniques
there is a particular choise for dealing with the noise (i.e.
beamformer: try to suppress it, dipole fit: try to minimize the
squared error). Dealing with the noise and with the fact that the
linear system is either underdetermined or overdetermined causes a non-
linear effect. So there is some influence of the choise of reference
on the result of the source estimate, but in general not too much. If
you take a really extreme referencing scheme, i.e. all bipolar
electrodes over the scalp from the front to the back (a so-called
banana montage) which is more sensitive for superficial sources, then
the source reconstruction will be biassed for these superficial
contributions. For a linked mastoid reference, the source
reconstruction will be slightly biased for deep sources. For an
average reference, there is no specific bias to be expected. Overall,
the effect of the reference electrode will be quite small, and be the
least biassed for an avereage reference. Therefore, the average
reference is de facto the default in all source reconstruction
packages for EEG (commercial and non-commercial).

best regards,
Robert

PS for people who want to see these effects: you can use
DIPOLESIMULATION to generate simulated raw data with added noise, and
pass that through PREPROCESSING to re-reference to a reference of
choise. Subsequently you try the various  analysies discussed above,
i.e. TIMELOCKANALYSIS, TIMELOCKSTATISTICS, FREQANALYSIS and
SOURCEANALYSIS or DIPOLEFITTING.


On 2 Oct 2009, at 12:19, Robert Oostenveld wrote:

>> From: "Dr. Georges Otte" <georges.otte at telenet.be>
>>
>> ...
>> I have followed the discussion on reference and already contacted
>> Dien. I agree but what about non ERP data ? Phase information and
>> coherence. Can we safely use the averaged common reference for
>> that. Robert Thatcher (neuroguide) quoting rappelsberger is opoosed
>> to it and shows in his neuroguide package that in small channel
>> systems (19-22) a ACR scrambles phase information between channels.

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


From megjim1 at GMAIL.COM  Mon Oct  5 15:26:56 2009
From: megjim1 at GMAIL.COM (Jim Li)
Date: Mon, 5 Oct 2009 15:26:56 +0200
Subject: how to plot the direction and amplitude of the planar gradient
Message-ID: <MON.5.OCT.2009.152656.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs ,

Thanks a lot for your information. I'll take a look at the script to see what I 
can do.


Cheers,

Jim

On Fri, 2 Oct 2009 09:46:25 +0000, Jan-Mathijs Schoffelen 
<j.schoffelen at PSY.GLA.AC.UK> wrote:

>Dear Jim,
>
>As far as I know, this is not possible in fieldtrip ... yet. Do I read
>between the lines that you wouldn't mind giving it a try? I agree that
>it's a very useful way to visualize planar gradient data.
>First of all, it is indeed important to know the local coordinate
>system for each of the planar gradient channels. For megplanar I
>always use the 'sincos' method. You can see how the coordinate system
>is defined at line 419 and beyond. As far as I can see the local x-
>axis is taken as the vector orthogonal to the plane defined by the
>coil's orientation, and the vector [0 0 1] (which is the z-axis of the
>coordinate system in which your sensors are defined; assuming your
>sensors are defined in headspace, this one points to the top of the
>head). The local z-axis is the vector perpendicular to the coil's
>plane (=orientation), and the y-axis is perpendicular to the local xz-
>plane.
>I guess that for the other planarmethods it's possible to figure out
>the local coordinate systems as well. One think which we could think
>of, is to adjust megplanar such that the output data contains
>information about the local x and y axes directly.
>Of course, it would also be nice if a hypothetical plotting function
>would work for data acquired with hardware planar gradiometers. Here
>it is usually straightforward to reconstruct the local coordinate
>systems from the header-information. Perhaps people working with
>Elekta-systems already have some matlab code for the plotting...
>Once the local coordinate systems are known (and the angles defined
>accordingly), it should be possible to warp these values to a
>headspace based coordinate system for plotting (in 3D, or in 2D after
>an appropriate projection).
>
>Best,
>
>Jan-Mathijs
>
>On 2 Oct 2009, at 04:07, Jim Li wrote:
>
>> Dear all,
>>
>> I want to view the direction and amplitude of the planar gradient
>> near each
>> sensor location and create a plot like what's shown in the  attached
>> file (more
>> or less).  Is it possible to do it? If so, how?
>>
>> Our MEG sensors are 248 axial gradiometers. After running
>> "megplanar" I got
>> A1_dH...A248_dH,A1_dV...A248_dV for my channels. If, say, in the plane
>> tangential to a given channel we have the Horizontal (x axis) and
>> Vertical (y
>> axis) directions. Then for the channel of interest, say A1,  I can
>> run sqrt
>> (A1_dH^2+A1_dV^2) to get the amplitude of the planar gradient, and I
>> can
>> run atan2(A1_dV,A1_dH)*180/pi) to get the angle between the field
>> vector
>> and x-axis. What I'm not sure  about is how fieldtrip defines the
>> Horizontal (x
>> axis) and Vertical (y axis) for each channel (in a plane tangential
>> to that
>> channel). So it's hard to create the plot I want...
>>
>> Thanks a lot.
>>
>> Jim
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also 
http://listserv.surfnet.nl/archives/fieldtrip.html
>>  and http://www.ru.nl/neuroimaging/fieldtrip.
>> <PlotGoal.TIF>
>
>----------------------------------
>The aim of this list is to facilitate the discussion between users of the 
FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and 
EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and 
http://www.ru.nl/neuroimaging/fieldtrip.

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


From Juergen.Fell at UKB.UNI-BONN.DE  Wed Oct  7 10:14:30 2009
From: Juergen.Fell at UKB.UNI-BONN.DE (Juergen Fell)
Date: Wed, 7 Oct 2009 10:14:30 +0200
Subject: complex wavelet output
Message-ID: <WED.7.OCT.2009.101430.0200.FIELDTRIP@NIC.SURFNET.NL>



Dear fieldtrip users:

I've just started digging into fieldtrip and came across the following
question: is it possible to obtain the complex output of the continuous
wavelet transform, i.e. the original wavelet-transformed complex signal
(instead of power and/or cross-spectral density)?

Any help would be greatly appreciated.

Juergen.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From pacodiaz at UB.EDU  Wed Oct  7 10:59:26 2009
From: pacodiaz at UB.EDU (=?ISO-8859-1?Q?Paco_D=EDaz?=)
Date: Wed, 7 Oct 2009 10:59:26 +0200
Subject: complex wavelet output
In-Reply-To: <OF86C3BE7E.9A337D32-ONC1257648.002C950C-C1257648.002D7751@ukb.uni-bonn.de>
Message-ID: <WED.7.OCT.2009.105926.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Juergen,

   I made it by using "freqanalysis" with (basically)

cfg.output='pow'
cfg.method='tfr'

   and then you have to edit the freqanalysis_tfr function and suppress
the following lines:

   cTmp = (2*abs(cTmp)/data.fsample).^2;

in the main body of the function, and this one:

   y = (2*abs(y)/Fs).^2;

in the SUBFUNCTION for waveletanalysis.

Doing this you will avoid the power calculation and will end up with the
complex morlet coefficients.

Hope this helps,
F.J.

Juergen Fell escribió:
>
> Dear fieldtrip users:
>
> I've just started digging into fieldtrip and came across the following
> question: is it possible to obtain the complex output of the
> continuous wavelet transform, i.e. the original wavelet-transformed
> complex signal (instead of power and/or cross-spectral density)?
>
> Any help would be greatly appreciated.
>
> Juergen.
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>

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


From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE  Wed Oct  7 11:24:36 2009
From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke Van Dijk)
Date: Wed, 7 Oct 2009 11:24:36 +0200
Subject: AW: [FIELDTRIP] complex wavelet output
Message-ID: <WED.7.OCT.2009.112436.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Juergen,

As far as I can see, you can specify cfg.output = 'fourier' for the cfg.method = 'mtmconvol' when you want to have a time axis as well (it's also possible for 'mtmfft'). It will give you the fourierspectrum. You can set the parameters of mtmconvol such that it operates simmilar to a wavelet transform as you can see on this website:

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

An example of the parameters could be:

cfg = [];
cfg.output     = 'fourier';
cfg.channel    = 'MEG';
cfg.method     = 'mtmconvol';
cfg.taper      = 'dpss';        % sleppian taper but you can use different tapers/windows here.
cfg.foi        = 1:2:30;        % frequencies of interest.
cfg.t_ftimwin  = 5./cfg.foi;    % the window length is 5 cycles of the specified frequency long.
cfg.tapsmofrq  = 0.4 *cfg.foi;  % frequency smoothing of +/- 0.4*the specified frequency.
cfg.toi        = -0.5:0.05:1.5; % time of interest.
cfg.pad        = 'maxperlen';  
TFRmult = freqanalysis(cfg, dataFIC);

Hope it helps!

Yours,

Hanneke


-----Ursprüngliche Nachricht-----
Von: FieldTrip discussion list im Auftrag von Juergen Fell
Gesendet: Mi 07.10.2009 10:14
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: [FIELDTRIP] complex wavelet output
 


Dear fieldtrip users:

I've just started digging into fieldtrip and came across the following
question: is it possible to obtain the complex output of the continuous
wavelet transform, i.e. the original wavelet-transformed complex signal
(instead of power and/or cross-spectral density)?

Any help would be greatly appreciated.

Juergen.

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


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


From brian.roach at YALE.EDU  Wed Oct  7 22:10:52 2009
From: brian.roach at YALE.EDU (Brian Roach)
Date: Wed, 7 Oct 2009 13:10:52 -0700
Subject: AW: [FIELDTRIP] complex wavelet output
In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B0F34E5@Mail2-UKD.VMED.UKD>
Message-ID: <WED.7.OCT.2009.131052.0700.FIELDTRIP@NIC.SURFNET.NL>

Hi Juergen,

You can also use cfg.method = 'wltconvol', but you need to change a line
of code in the freqanalysis_wltconvol.m script.  When you use
cfg.keeptrials = 'yes', it will normally return single trial power data
(not complex numbers), but in the script search for:

elseif keep == 2
            powdum = XYZ ;

make sure that XYZ does not have any squaring or abs calls around it.
These change complex numbers to real ones.

Brian
Hanneke Van Dijk wrote:
> Dear Juergen,
>
> As far as I can see, you can specify cfg.output = 'fourier' for the cfg.method = 'mtmconvol' when you want to have a time axis as well (it's also possible for 'mtmfft'). It will give you the fourierspectrum. You can set the parameters of mtmconvol such that it operates simmilar to a wavelet transform as you can see on this website:
>
> http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis
>
> An example of the parameters could be:
>
> cfg = [];
> cfg.output     = 'fourier';
> cfg.channel    = 'MEG';
> cfg.method     = 'mtmconvol';
> cfg.taper      = 'dpss';        % sleppian taper but you can use different tapers/windows here.
> cfg.foi        = 1:2:30;        % frequencies of interest.
> cfg.t_ftimwin  = 5./cfg.foi;    % the window length is 5 cycles of the specified frequency long.
> cfg.tapsmofrq  = 0.4 *cfg.foi;  % frequency smoothing of +/- 0.4*the specified frequency.
> cfg.toi        = -0.5:0.05:1.5; % time of interest.
> cfg.pad        = 'maxperlen';
> TFRmult = freqanalysis(cfg, dataFIC);
>
> Hope it helps!
>
> Yours,
>
> Hanneke
>
>
> -----Ursprüngliche Nachricht-----
> Von: FieldTrip discussion list im Auftrag von Juergen Fell
> Gesendet: Mi 07.10.2009 10:14
> An: FIELDTRIP at NIC.SURFNET.NL
> Betreff: [FIELDTRIP] complex wavelet output
>
>
>
> Dear fieldtrip users:
>
> I've just started digging into fieldtrip and came across the following
> question: is it possible to obtain the complex output of the continuous
> wavelet transform, i.e. the original wavelet-transformed complex signal
> (instead of power and/or cross-spectral density)?
>
> Any help would be greatly appreciated.
>
> Juergen.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>
>

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


From julian.keil at GMAIL.COM  Fri Oct  9 14:04:08 2009
From: julian.keil at GMAIL.COM (Julian Keil)
Date: Fri, 9 Oct 2009 14:04:08 +0200
Subject: Freqstatistics plv
Message-ID: <FRI.9.OCT.2009.140408.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrippers,

I have a question regarding the use of freqstatistics and phase
locking values:
Is it possible to use freqstatistics to compare phase-locking values?
If not, is there any other option to compare plv between conditions

I use the following code:

cfg=[];
cfg.statistic='depsamplesT';
cfg.method='analytic';
cfg.parameter='plvspctrm';
cfg.channel={'all'};  % 5 channels -> 10 channelcmb
cfg.tail=0;
cfg.alpha=0.05;
cfg.ivar=2;
cfg.uvar=1;
cfg.frequency   = [10 50];

cfg.design=[1:12,1:12;ones(1,12),ones(1,12)*2];

[stats_fus_vi]=freqstatistics(cfg,plv_fu{:},plv_vi{:});

I get the information:
renaming parameter 'plvspctrm' into 'powspctrm'
selected 5 channels
selected 201 time bins
selected 21 frequency bins

As I don't get any error message, I assume this works fine so far but
I'm confused about what is computed here: Is "powspctrm" used instead
of "plvspctrm" (i.e. the test is computed between power estimates
instead of phase locking values)? Why are only 5 channels selected
instead of the 10 combinations?

I already tried renaming "plvspctrm" and "labelcmb" to "powspctrm" and
"label" but then I get an error message, as freqstatistics selects 20
channels.

Thanks a lot for any advise

Julian


Dipl. Psych. Julian Keil

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

Tel: ++49 - (0)7531 - 88 42 50
Fax: ++49 - (0)7531 - 88 28 91
Email: julian.keil at uni-konstanz.de
Homepage: http://www.uni-konstanz.de/obob








----------------------------------
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From julian.keil at GMAIL.COM  Fri Oct  9 14:49:37 2009
From: julian.keil at GMAIL.COM (Julian Keil)
Date: Fri, 9 Oct 2009 14:49:37 +0200
Subject: Freqstatistics plv -> solved
Message-ID: <FRI.9.OCT.2009.144937.0200.FIELDTRIP@NIC.SURFNET.NL>

hi,

sorry for your time, problem solved: creating a new label-structure
worked.

greetings

Julian

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


From tobias.donner at NYU.EDU  Tue Oct 13 15:13:11 2009
From: tobias.donner at NYU.EDU (Tobias Donner)
Date: Tue, 13 Oct 2009 15:13:11 +0200
Subject: PhD position in Cognitive Neuroscience in Amsterdam
Message-ID: <TUE.13.OCT.2009.151311.0200.FIELDTRIP@NIC.SURFNET.NL>

The Psychology Department of the University of Amsterdam is currently
hiring a PhD student to study the neural basis of visual awareness
and visual decision-making in humans. The project is a collaboration
of Tobias H. Donner and Victor A.F. Lamme. We plan to combine visual
psychophysics, neuroimaging (MEG, fMRI), and pharmacological
manipulation to (i) characterize decision-related feedback signals in
human early visual cortex, (ii) localize the source of these signals
in the brain, and (iii) study their role in shaping the contents of
perception.

We are looking for highly motivated candidates with a strong interest
in Cognitive Neuroscience and interdisciplinary research. Candidates
must have an MA (or equivalent) in Cognitive Science, Neuroscience,
Psychology, Physics, or Engineering, or an MD. Experience in computer
programming (e.g., MATLAB) and in EEG/MEG and/or fMRI will be a
significant plus.

Further information about the post and how to apply is available at:
http://www.uva.nl/vacatures/vacatures.cfm/E19032FD-1321-
B0BE-685E8B8E55A5AD26

Inquiries are welcomed. Please contact Tobias Donner: t.h.donner at uva.nl
Application deadline: November 1, 2009.

----------------------------------
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From Sara.GonzalezAndino at HCUGE.CH  Thu Oct 15 10:21:58 2009
From: Sara.GonzalezAndino at HCUGE.CH (GONZALEZ ANDINO Sara)
Date: Thu, 15 Oct 2009 10:21:58 +0200
Subject: TR: paper announcement
Message-ID: <THU.15.OCT.2009.102158.0200.FIELDTRIP@NIC.SURFNET.NL>

-----Message d'origine-----
De : GRAVE DE PERALTA Rolando 
Envoyé : jeudi, 15. octobre 2009 10:19

Objet : paper announcement

Dear Colleagues,

We would like to call your attention to the recent publication:
http://dx.doi.org/10.1016/j.jphysparis.2009.07.004 
that, among other things,  provide the theoretical and experimental evidences to refute claims that Very High Frequencies are not measurable at the scalp surface. 


Electrical neuroimaging of single trials to identify laterality and brain regions involved in finger movements 

by:
Rolando Grave de Peralta, Theodor Landis and Sara Gonzalez Andino

Abstract
Thought-controlled neuroprostheses could allow paralyzed patients to interact with the external world using brain waves. Thus far, the fastest and more accurate control of neuroprostheses is achieved through direct recordings of neural activity [Nicolelis, M.A., 2001. Actions from thoughts. Nature 409, 403-407; Donoghue, J.P., 2002. Connecting cortex to machines: recent advances in brain interfaces. Nat. Neurosci. 5 (Suppl.), 1085-1088]. However, invasive recordings have inherent medical risks. Here we discuss some approaches that could enhance the speed and accuracy of non-invasive devices, namely, (1) enlarging the spectral analysis to include higher frequency oscillations, able to transmit substantial information over short analysis windows; (2) using spectral analysis procedures that minimize the variance of the estimates; and (3) transforming EEG recorded activity into local field potential estimates (eLFP). Theoretical and experimental arguments are used to explain why it is erroneous to think that scalp EEG cannot sense high frequency oscillations and how this might hinders further developments. We further illustrate how non-invasive eLFPs derived from the scalp-recorded electroencephalogram (EEG) can be combined with robust, broad band spectral analysis to accurately detect (off-line) the laterality of upcoming hand movements. Interestingly, the use of pattern recognition to select the brain voxels differentially engaged by the explored tasks leads to sound neural activation images. Consequently, our results indicate that both research lines, i.e., neuroprosthetics and electrical neuroimaging, might effectively benefit from their mutual interaction.



regards
rolando
www.electrical-neuroimaging.ch 

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


From fredericroux at HOTMAIL.DE  Fri Oct 16 12:26:29 2009
From: fredericroux at HOTMAIL.DE (Frederic Roux)
Date: Fri, 16 Oct 2009 12:26:29 +0200
Subject: error using freqanalysis_mtmfft
Message-ID: <FRI.16.OCT.2009.122629.0200.FIELDTRIP@NIC.SURFNET.NL>


Hi everyone,
 
I am using freqanalysis with the following cfg structure
 
cfg             = [];
cfg.output      = 'pow';
cfg.channel     = {'MEG'};
cfg.method      = 'mtmfft';
cfg.taper       = 'dpss';
cfg.foi         = 1:200; 
cfg.t_ftimwin   = .5*ones(1,length(cfg.foi));
cfg.toi         = [-1.5:.5:2.5]; 
cfg.tapsmofrq   = 5.*ones(1,length(cfg.foi)); 
cfg.pad         = 'maxperlen';
 
and I get the following error message
 
??? Error using ==> dpss
The Time-bandwidth product NW must be a scalar.
 
Error in ==> freqanalysis_mtmfft>double_dpss at 594
tap = dpss(double(a), double(b), varargin{:});
 
Error in ==> freqanalysis_mtmfft at 421
    tap =
double_dpss(numdatbns,numdatbns*(cfg.tapsmofrq./data.fsample))';
 
Error in ==> freqanalysis at 192


K should be equal to 2*(.5*5)-1 = 4 tapers so I don't really understand what's going wrong here.
And before diving into the code I thought that maybe someone could provide me with a simple answer/solution. 
Any help with this would be greatly apreciated!
 
Frederic
  		 	   		  
_________________________________________________________________
http://redirect.gimas.net/?n=M0910xHerbstmode2
So gehst du mir nicht vor die Tür! Herbsttrends entdecken
----------------------------------
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From hungptit at GMAIL.COM  Sat Oct 24 08:39:35 2009
From: hungptit at GMAIL.COM (Hung Dang)
Date: Sat, 24 Oct 2009 00:39:35 -0600
Subject: How to generate the EEG background noise and interference
In-Reply-To: <SNT107-W7ED61CCCB8F2C15B0C398B7C40@phx.gbl>
Message-ID: <SAT.24.OCT.2009.003935.0600.FIELDTRIP@NIC.SURFNET.NL>

Dear all,
Many researchers have been using Gaussian white noise as the additive
noise for the  MEG/EEG signals to evaluate their inverse algorithm,
however, this assumption may not true for the real MEG/EEG signals. I
try to google for a while and have not find any good reference.
So my question is how could we generate a more realistic MEG/EEG signal,
interference, and noise to obtain a better judgment of how good are
inverse solutions?

Have a nice weekend
Hung

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


From v.litvak at ION.UCL.AC.UK  Sat Oct 24 10:05:25 2009
From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak)
Date: Sat, 24 Oct 2009 09:05:25 +0100
Subject: How to generate the EEG background noise and interference
In-Reply-To: <4AE2A127.905@gmail.com>
Message-ID: <SAT.24.OCT.2009.090525.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Hung,

A simple and convincing thing to do would be to combine simulated data
with real data. For instance if you are talking about ERP, you can add
your simulated responses  to a real recording at times random with
respect to the original triggers. Then you will get your simulated ERP
with noise as real as it gets. By controlling the relative scaling of
the real and simulated data you can test different SNRs.

Best,

Vladimir

On Sat, Oct 24, 2009 at 7:39 AM, Hung Dang <hungptit at gmail.com> wrote:
> Dear all,
> Many researchers have been using Gaussian white noise as the additive
> noise for the  MEG/EEG signals to evaluate their inverse algorithm,
> however, this assumption may not true for the real MEG/EEG signals. I
> try to google for a while and have not find any good reference.
> So my question is how could we generate a more realistic MEG/EEG signal,
> interference, and noise to obtain a better judgment of how good are
> inverse solutions?
>
> Have a nice weekend
> Hung
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>
>

----------------------------------
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From hungptit at GMAIL.COM  Sat Oct 24 19:53:20 2009
From: hungptit at GMAIL.COM (Hung Dang)
Date: Sat, 24 Oct 2009 11:53:20 -0600
Subject: How to generate the EEG background noise and interference
In-Reply-To: <e1e7c57c0910240105r5d5b683fh6e3bb56cac175a8f@mail.gmail.com>
Message-ID: <SAT.24.OCT.2009.115320.0600.FIELDTRIP@NIC.SURFNET.NL>

Dear Vladimir,
Thanks a lot for an insightful and quick reply. That will definitely
help me a lot for my simulation studies.

Regards,
Hung



Vladimir Litvak wrote:
> Dear Hung,
>
> A simple and convincing thing to do would be to combine simulated data
> with real data. For instance if you are talking about ERP, you can add
> your simulated responses  to a real recording at times random with
> respect to the original triggers. Then you will get your simulated ERP
> with noise as real as it gets. By controlling the relative scaling of
> the real and simulated data you can test different SNRs.
>
> Best,
>
> Vladimir
>
> On Sat, Oct 24, 2009 at 7:39 AM, Hung Dang <hungptit at gmail.com> wrote:
>
>> Dear all,
>> Many researchers have been using Gaussian white noise as the additive
>> noise for the  MEG/EEG signals to evaluate their inverse algorithm,
>> however, this assumption may not true for the real MEG/EEG signals. I
>> try to google for a while and have not find any good reference.
>> So my question is how could we generate a more realistic MEG/EEG signal,
>> interference, and noise to obtain a better judgment of how good are
>> inverse solutions?
>>
>> Have a nice weekend
>> Hung
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>>
>>
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>

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


From marco.rotonda at GMAIL.COM  Mon Oct 26 14:42:28 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Mon, 26 Oct 2009 14:42:28 +0100
Subject: importing raw data
Message-ID: <MON.26.OCT.2009.144228.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi there,
I'm trying to import a raw data file to perform artifacting.
The file I have is quite simple: 2 channels and only data sampled at 256.
I did the following operations:

FF = (csvread('FF.txt', 2, 0))';
data.trial{1} = FF;
data.time{1} = linspace(0,180,46080);
data.fsample=256;
data.label={'F3';'F4'};
data.cfg.trl=[1,46080,0];
cfg.continuous='yes';
cfg.trl=[1,46080,0];
cfg.channel={'F3';'F4'};
cfg2=artifact_eog(cfg,data);

but then I have the following message error:

??? Error using ==> artifact_zvalue at 202
no channels selected

Error in ==> artifact_eog at 179
   [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
   data);

What I miss?

in artifact_zvalue from 197:

cfg.artfctdef.zvalue.channel =
channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
sgnind        = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
numsgn        = length(sgnind);

if numsgn<1
 error('no channels selected');
else
 fprintf('searching for artifacts in %d channels\n', numsgn);
end


So I added:

cfg.artfctdef.zvalue.channel={'F3';'F4'};

but I get the same error
it seems that I need the header... but I have not.
is it?

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


From P.Toffanin at RUG.NL  Mon Oct 26 15:08:43 2009
From: P.Toffanin at RUG.NL (Paolo Toffanin)
Date: Mon, 26 Oct 2009 15:08:43 +0100
Subject: importing raw data
In-Reply-To: <LISTSERV%200910261442283870.8413@NIC.SURFNET.NL>
Message-ID: <MON.26.OCT.2009.150843.0100.FIELDTRIP@NIC.SURFNET.NL>

Did you try including also eye channels into the analysis?

Paolo

On Monday 26 October 2009 02:42:28 pm Marco Rotonda wrote:
> Hi there,
> I'm trying to import a raw data file to perform artifacting.
> The file I have is quite simple: 2 channels and only data sampled at 256.
> I did the following operations:
>
> FF = (csvread('FF.txt', 2, 0))';
> data.trial{1} = FF;
> data.time{1} = linspace(0,180,46080);
> data.fsample=256;
> data.label={'F3';'F4'};
> data.cfg.trl=[1,46080,0];
> cfg.continuous='yes';
> cfg.trl=[1,46080,0];
> cfg.channel={'F3';'F4'};
> cfg2=artifact_eog(cfg,data);
>
> but then I have the following message error:
>
> ??? Error using ==> artifact_zvalue at 202
> no channels selected
>
> Error in ==> artifact_eog at 179
>    [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
>    data);
>
> What I miss?
>
> in artifact_zvalue from 197:
>
> cfg.artfctdef.zvalue.channel =
> channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
> sgnind        = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
> numsgn        = length(sgnind);
>
> if numsgn<1
>  error('no channels selected');
> else
>  fprintf('searching for artifacts in %d channels\n', numsgn);
> end
>
>
> So I added:
>
> cfg.artfctdef.zvalue.channel={'F3';'F4'};
>
> but I get the same error
> it seems that I need the header... but I have not.
> is it?
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/neuroimaging/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From marco.rotonda at GMAIL.COM  Mon Oct 26 15:15:26 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Mon, 26 Oct 2009 15:15:26 +0100
Subject: importing raw data
In-Reply-To: <200910261508.43870.p233228@rug.nl>
Message-ID: <MON.26.OCT.2009.151526.0100.FIELDTRIP@NIC.SURFNET.NL>

nope... only 2 channels...


On 26/ott/2009, at 15.08, Paolo Toffanin wrote:

> Did you try including also eye channels into the analysis?
>
> Paolo
>
> On Monday 26 October 2009 02:42:28 pm Marco Rotonda wrote:
> > Hi there,
> > I'm trying to import a raw data file to perform artifacting.
> > The file I have is quite simple: 2 channels and only data sampled
> at 256.
> > I did the following operations:
> >
> > FF = (csvread('FF.txt', 2, 0))';
> > data.trial{1} = FF;
> > data.time{1} = linspace(0,180,46080);
> > data.fsample=256;
> > data.label={'F3';'F4'};
> > data.cfg.trl=[1,46080,0];
> > cfg.continuous='yes';
> > cfg.trl=[1,46080,0];
> > cfg.channel={'F3';'F4'};
> > cfg2=artifact_eog(cfg,data);
> >
> > but then I have the following message error:
> >
> > ??? Error using ==> artifact_zvalue at 202
> > no channels selected
> >
> > Error in ==> artifact_eog at 179
> > [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
> > data);
> >
> > What I miss?
> >
> > in artifact_zvalue from 197:
> >
> > cfg.artfctdef.zvalue.channel =
> > channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
> > sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
> > numsgn = length(sgnind);
> >
> > if numsgn<1
> > error('no channels selected');
> > else
> > fprintf('searching for artifacts in %d channels\n', numsgn);
> > end
> >
> >
> > So I added:
> >
> > cfg.artfctdef.zvalue.channel={'F3';'F4'};
> >
> > but I get the same error
> > it seems that I need the header... but I have not.
> > is it?
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of the
> > FieldTrip toolbox, to share experiences and to discuss new ideas
> for MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/neuroimaging/fieldtrip.
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
>   http://listserv.surfnet.nl/archives/fieldtrip.html
>
>   http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From Nina.Kahlbrock at UNI-DUESSELDORF.DE  Mon Oct 26 15:18:42 2009
From: Nina.Kahlbrock at UNI-DUESSELDORF.DE (Nina)
Date: Mon, 26 Oct 2009 15:18:42 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <200910261508.43870.p233228@rug.nl>
Message-ID: <MON.26.OCT.2009.151842.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi Marco,

you might want to try:



cfg.artfctdef.eog.channel = {your EOG channel(s)};



Nina



  _____

Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag
von Paolo Toffanin
Gesendet: Montag, 26. Oktober 2009 15:09
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: Re: [FIELDTRIP] importing raw data



Did you try including also eye channels into the analysis?





Paolo





On Monday 26 October 2009 02:42:28 pm Marco Rotonda wrote:
> Hi there,
> I'm trying to import a raw data file to perform artifacting.
> The file I have is quite simple: 2 channels and only data sampled at 256.
> I did the following operations:
>
> FF = (csvread('FF.txt', 2, 0))';
> data.trial{1} = FF;
> data.time{1} = linspace(0,180,46080);
> data.fsample=256;
> data.label={'F3';'F4'};
> data.cfg.trl=[1,46080,0];
> cfg.continuous='yes';
> cfg.trl=[1,46080,0];
> cfg.channel={'F3';'F4'};
> cfg2=artifact_eog(cfg,data);
>
> but then I have the following message error:
>
> ??? Error using ==> artifact_zvalue at 202
> no channels selected
>
> Error in ==> artifact_eog at 179
> [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
> data);
>
> What I miss?
>
> in artifact_zvalue from 197:
>
> cfg.artfctdef.zvalue.channel =
> channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
> sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
> numsgn = length(sgnind);
>
> if numsgn<1
> error('no channels selected');
> else
> fprintf('searching for artifacts in %d channels\n', numsgn);
> end
>
>
> So I added:
>
> cfg.artfctdef.zvalue.channel={'F3';'F4'};
>
> but I get the same error
> it seems that I need the header... but I have not.
> is it?
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/neuroimaging/fieldtrip.





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

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

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

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


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From marco.rotonda at GMAIL.COM  Mon Oct 26 17:20:12 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Mon, 26 Oct 2009 17:20:12 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <001a01ca5647$38b652a0$cd136386@VMED.UKD>
Message-ID: <MON.26.OCT.2009.172012.0100.FIELDTRIP@NIC.SURFNET.NL>

So I need eog channels other than the 2 I have?


On 26/ott/2009, at 15.18, Nina wrote:

> Hi Marco,
> you might want to try:
>
> cfg.artfctdef.eog.channel
> = {your EOG channel(s)};
>
> Nina
>
> Von: FieldTrip
> discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von
> Paolo Toffanin
>
> Gesendet: Montag, 26. Oktober 2009
> 15:09
>
> An: FIELDTRIP at NIC.SURFNET.NL
>
> Betreff: Re: [FIELDTRIP] importing
> raw data
>
> Did you try including also eye channels into the
> analysis?
>
>
>
>
> Paolo
>
>
>
>
> On Monday 26 October 2009 02:42:28 pm Marco Rotonda
> wrote:
>
> > Hi there,
>
> > I'm trying to import a raw data file to perform artifacting.
>
> > The file I have is quite simple: 2 channels and only data sampled
> at 256.
>
> > I did the following operations:
>
> >
>
> > FF = (csvread('FF.txt', 2, 0))';
>
> > data.trial{1} = FF;
>
> > data.time{1} = linspace(0,180,46080);
>
> > data.fsample=256;
>
> > data.label={'F3';'F4'};
>
> > data.cfg.trl=[1,46080,0];
>
> > cfg.continuous='yes';
>
> > cfg.trl=[1,46080,0];
>
> > cfg.channel={'F3';'F4'};
>
> > cfg2=artifact_eog(cfg,data);
>
> >
>
> > but then I have the following message error:
>
> >
>
> > ??? Error using ==> artifact_zvalue at 202
>
> > no channels selected
>
> >
>
> > Error in ==> artifact_eog at 179
>
> > [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
>
> > data);
>
> >
>
> > What I miss?
>
> >
>
> > in artifact_zvalue from 197:
>
> >
>
> > cfg.artfctdef.zvalue.channel =
>
> > channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
>
> > sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
>
> > numsgn = length(sgnind);
>
> >
>
> > if numsgn<1
>
> > error('no channels selected');
>
> > else
>
> > fprintf('searching for artifacts in %d channels\n', numsgn);
>
> > end
>
> >
>
> >
>
> > So I added:
>
> >
>
> > cfg.artfctdef.zvalue.channel={'F3';'F4'};
>
> >
>
> > but I get the same error
>
> > it seems that I need the header... but I have not.
>
> > is it?
>
> >
>
> > ----------------------------------
>
> > The aim of this list is to facilitate the discussion between users
> of the
>
> > FieldTrip toolbox, to share experiences and to discuss new ideas
> for MEG
>
> > and EEG analysis. See also
>
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
>
> > http://www.ru.nl/neuroimaging/fieldtrip.
>
>
>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
>   http://listserv.surfnet.nl/archives/fieldtrip.html
>
>   http://www.ru.nl/fcdonders/fieldtrip/
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
>   http://listserv.surfnet.nl/archives/fieldtrip.html
>
>   http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From P.Toffanin at RUG.NL  Mon Oct 26 20:02:06 2009
From: P.Toffanin at RUG.NL (Paolo Toffanin)
Date: Mon, 26 Oct 2009 21:02:06 +0200
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <A75DF2B4-3129-41CE-9EB4-E4BBC1784BB0@gmail.com>
Message-ID: <MON.26.OCT.2009.210206.0200.FIELDTRIP@NIC.SURFNET.NL>

That's the idea.

Paolo

On Mon, 26 Oct 2009 17:20:12 +0100
  Marco Rotonda <marco.rotonda at GMAIL.COM> wrote:
> So I need eog channels other than the 2 I have?
>
>
> On 26/ott/2009, at 15.18, Nina wrote:
>
>> Hi Marco,
>> you might want to try:
>>
>> cfg.artfctdef.eog.channel
>> = {your EOG channel(s)};
>>
>> Nina
>>
>> Von: FieldTrip
>> discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von
>> Paolo Toffanin
>>
>> Gesendet: Montag, 26. Oktober 2009
>> 15:09
>>
>> An: FIELDTRIP at NIC.SURFNET.NL
>>
>> Betreff: Re: [FIELDTRIP] importing
>> raw data
>>
>> Did you try including also eye channels into the
>> analysis?
>>
>>
>>
>>
>> Paolo
>>
>>
>>
>>
>> On Monday 26 October 2009 02:42:28 pm Marco Rotonda
>> wrote:
>>
>> > Hi there,
>>
>> > I'm trying to import a raw data file to perform artifacting.
>>
>> > The file I have is quite simple: 2 channels and only data sampled
>>
>> at 256.
>>
>> > I did the following operations:
>>
>> >
>>
>> > FF = (csvread('FF.txt', 2, 0))';
>>
>> > data.trial{1} = FF;
>>
>> > data.time{1} = linspace(0,180,46080);
>>
>> > data.fsample=256;
>>
>> > data.label={'F3';'F4'};
>>
>> > data.cfg.trl=[1,46080,0];
>>
>> > cfg.continuous='yes';
>>
>> > cfg.trl=[1,46080,0];
>>
>> > cfg.channel={'F3';'F4'};
>>
>> > cfg2=artifact_eog(cfg,data);
>>
>> >
>>
>> > but then I have the following message error:
>>
>> >
>>
>> > ??? Error using ==> artifact_zvalue at 202
>>
>> > no channels selected
>>
>> >
>>
>> > Error in ==> artifact_eog at 179
>>
>> > [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
>>
>> > data);
>>
>> >
>>
>> > What I miss?
>>
>> >
>>
>> > in artifact_zvalue from 197:
>>
>> >
>>
>> > cfg.artfctdef.zvalue.channel =
>>
>> > channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
>>
>> > sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
>>
>> > numsgn = length(sgnind);
>>
>> >
>>
>> > if numsgn<1
>>
>> > error('no channels selected');
>>
>> > else
>>
>> > fprintf('searching for artifacts in %d channels\n', numsgn);
>>
>> > end
>>
>> >
>>
>> >
>>
>> > So I added:
>>
>> >
>>
>> > cfg.artfctdef.zvalue.channel={'F3';'F4'};
>>
>> >
>>
>> > but I get the same error
>>
>> > it seems that I need the header... but I have not.
>>
>> > is it?
>>
>> >
>>
>> > ----------------------------------
>>
>> > The aim of this list is to facilitate the discussion between users
>>
>> of the
>>
>> > FieldTrip toolbox, to share experiences and to discuss new ideas
>> for MEG
>>
>> > and EEG analysis. See also
>>
>> > http://listserv.surfnet.nl/archives/fieldtrip.html and
>>
>> > http://www.ru.nl/neuroimaging/fieldtrip.
>>
>>
>>
>>
>> ----------------------------------
>>
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis.
>>
>>   http://listserv.surfnet.nl/archives/fieldtrip.html
>>
>>   http://www.ru.nl/fcdonders/fieldtrip/
>>
>> ----------------------------------
>>
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis.
>>
>>   http://listserv.surfnet.nl/archives/fieldtrip.html
>>
>>   http://www.ru.nl/fcdonders/fieldtrip/
>>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
>of the FieldTrip  toolbox, to share experiences and to discuss new
>ideas for MEG and EEG analysis. See also
>http://listserv.surfnet.nl/archives/fieldtrip.html and
>http://www.ru.nl/neuroimaging/fieldtrip.

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


From marco.rotonda at GMAIL.COM  Mon Oct 26 20:04:20 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Mon, 26 Oct 2009 20:04:20 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <web-127111963@mail3.rug.nl>
Message-ID: <MON.26.OCT.2009.200420.0100.FIELDTRIP@NIC.SURFNET.NL>

so I could not do zvalue artifact on 2 channels only?

On 26/ott/2009, at 20.02, Paolo Toffanin wrote:

> That's the idea.
>
> Paolo
>
> On Mon, 26 Oct 2009 17:20:12 +0100
> Marco Rotonda <marco.rotonda at GMAIL.COM> wrote:
>> So I need eog channels other than the 2 I have?
>> On 26/ott/2009, at 15.18, Nina wrote:
>>> Hi Marco,
>>> you might want to try:
>>>
>>> cfg.artfctdef.eog.channel
>>> = {your EOG channel(s)};
>>>
>>> Nina
>>>
>>> Von: FieldTrip
>>> discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von
>>> Paolo Toffanin
>>>
>>> Gesendet: Montag, 26. Oktober 2009
>>> 15:09
>>>
>>> An: FIELDTRIP at NIC.SURFNET.NL
>>>
>>> Betreff: Re: [FIELDTRIP] importing
>>> raw data
>>>
>>> Did you try including also eye channels into the
>>> analysis?
>>>
>>>
>>>
>>>
>>> Paolo
>>>
>>>
>>>
>>>
>>> On Monday 26 October 2009 02:42:28 pm Marco Rotonda
>>> wrote:
>>>
>>> > Hi there,
>>>
>>> > I'm trying to import a raw data file to perform artifacting.
>>>
>>> > The file I have is quite simple: 2 channels and only data
>>> sampled at 256.
>>>
>>> > I did the following operations:
>>>
>>> >
>>>
>>> > FF = (csvread('FF.txt', 2, 0))';
>>>
>>> > data.trial{1} = FF;
>>>
>>> > data.time{1} = linspace(0,180,46080);
>>>
>>> > data.fsample=256;
>>>
>>> > data.label={'F3';'F4'};
>>>
>>> > data.cfg.trl=[1,46080,0];
>>>
>>> > cfg.continuous='yes';
>>>
>>> > cfg.trl=[1,46080,0];
>>>
>>> > cfg.channel={'F3';'F4'};
>>>
>>> > cfg2=artifact_eog(cfg,data);
>>>
>>> >
>>>
>>> > but then I have the following message error:
>>>
>>> >
>>>
>>> > ??? Error using ==> artifact_zvalue at 202
>>>
>>> > no channels selected
>>>
>>> >
>>>
>>> > Error in ==> artifact_eog at 179
>>>
>>> > [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
>>>
>>> > data);
>>>
>>> >
>>>
>>> > What I miss?
>>>
>>> >
>>>
>>> > in artifact_zvalue from 197:
>>>
>>> >
>>>
>>> > cfg.artfctdef.zvalue.channel =
>>>
>>> > channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
>>>
>>> > sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
>>>
>>> > numsgn = length(sgnind);
>>>
>>> >
>>>
>>> > if numsgn<1
>>>
>>> > error('no channels selected');
>>>
>>> > else
>>>
>>> > fprintf('searching for artifacts in %d channels\n', numsgn);
>>>
>>> > end
>>>
>>> >
>>>
>>> >
>>>
>>> > So I added:
>>>
>>> >
>>>
>>> > cfg.artfctdef.zvalue.channel={'F3';'F4'};
>>>
>>> >
>>>
>>> > but I get the same error
>>>
>>> > it seems that I need the header... but I have not.
>>>
>>> > is it?
>>>
>>> >
>>>
>>> > ----------------------------------
>>>
>>> > The aim of this list is to facilitate the discussion between
>>> users of the
>>>
>>> > FieldTrip toolbox, to share experiences and to discuss new
>>> ideas  for MEG
>>>
>>> > and EEG analysis. See also
>>>
>>> > http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>
>>> > http://www.ru.nl/neuroimaging/fieldtrip.
>>>
>>>
>>>
>>>
>>> ----------------------------------
>>>
>>> The aim of this list is to facilitate the discussion between
>>> users  of the FieldTrip  toolbox, to share experiences and to
>>> discuss new  ideas for MEG and EEG analysis.
>>>
>>>  http://listserv.surfnet.nl/archives/fieldtrip.html
>>>
>>>  http://www.ru.nl/fcdonders/fieldtrip/
>>>
>>> ----------------------------------
>>>
>>> The aim of this list is to facilitate the discussion between
>>> users  of the FieldTrip  toolbox, to share experiences and to
>>> discuss new  ideas for MEG and EEG analysis.
>>>
>>>  http://listserv.surfnet.nl/archives/fieldtrip.html
>>>
>>>  http://www.ru.nl/fcdonders/fieldtrip/
>>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>>  and http://www.ru.nl/neuroimaging/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.

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


From nathanweisz at MAC.COM  Mon Oct 26 21:17:31 2009
From: nathanweisz at MAC.COM (Nathan Weisz)
Date: Mon, 26 Oct 2009 21:17:31 +0100
Subject: data.label wrong after componentanalysis?
Message-ID: <MON.26.OCT.2009.211731.0100.>

hi everyone,

for an analysis of EEG data i'm doing some ICA cleaning. since there
are many conditions / epochs, i do the ICA on a subset of trials and
then apply the calculated mixing matrix to the individual conditions.

i noticed (and i'm quite sure it's no user related error) that after
rejecting components and reconstructing the preprocessing data
structure, that the sequence in data.label has changed (apparently
into alphabetical order). however that rows in the 2-D matrices making
up data.trial(xy) have not changed, accordingly. i noticed because the
topography of the auditory N1 was a huge mess.

changing the labels solved the problem, i.e.:
ica_cleaned_data.label = data_before_ica_cleaning.label;

for those interested here the original code:

load([outdir '/dataB1F1.mat'], 'dataB1F1') %load data for one condition

cfg=[];
cfg.topo=comp.topo;
cfg.topolabel=comp.topolabel;

tmpcomp=componentanalysis(cfg,dataB1F1); %apply precomputed ICA to
condition

cfg=[];
cfg.component=ncmp;

dataB1F1=rejectcomponent(cfg, tmpcomp); %reject components obviously
representing artefacts

 >> [comp.cfg.channel(1:5) tmpcomp.cfg.channel(1:5)] %demonstrate
channel label mismatch

ans =

     'Lm'     'L1'
     'LE1'    'L10'
     'LE2'    'L11'
     'LE3'    'L12'
     'LD2'    'L13'

the crucial line appears to be in componentanalysis line 220:
cfg.channel = intersect(cfg.channel, cfg.topolabel);

intersect sorts the outcome:
 >> a=randperm(10)

a =

      7     1     9     3     6     2     5     4    10     8

 >> b=randperm(10)

b =

      6     3     5     1     8     2    10     4     9     7

 >> intersect(a,b)

ans =

      1     2     3     4     5     6     7     8     9    10

since i use all channels, simply replacing the label-field with the
original label-field works for me.

best,
nathan

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


From r.oostenveld at FCDONDERS.RU.NL  Wed Oct 28 14:11:35 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Wed, 28 Oct 2009 14:11:35 +0100
Subject: data.label wrong after componentanalysis?
In-Reply-To: <2B0C43B0-93FD-455C-BE01-D7B8002A7425@mac.com>
Message-ID: <WED.28.OCT.2009.141135.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Nathan,

thanks for the notification. It sounds like a potentially nasty bug,
so we'll look into it.

best,
Robert


On 26 Oct 2009, at 21:17, Nathan Weisz wrote:

> hi everyone,
>
> for an analysis of EEG data i'm doing some ICA cleaning. since there
> are many conditions / epochs, i do the ICA on a subset of trials and
> then apply the calculated mixing matrix to the individual conditions.
>
> i noticed (and i'm quite sure it's no user related error) that after
> rejecting components and reconstructing the preprocessing data
> structure, that the sequence in data.label has changed (apparently
> into alphabetical order). however that rows in the 2-D matrices
> making up data.trial(xy) have not changed, accordingly. i noticed
> because the topography of the auditory N1 was a huge mess.
>
> changing the labels solved the problem, i.e.:
> ica_cleaned_data.label = data_before_ica_cleaning.label;
>
> for those interested here the original code:
>
> load([outdir '/dataB1F1.mat'], 'dataB1F1') %load data for one
> condition
>
> cfg=[];
> cfg.topo=comp.topo;
> cfg.topolabel=comp.topolabel;
>
> tmpcomp=componentanalysis(cfg,dataB1F1); %apply precomputed ICA to
> condition
>
> cfg=[];
> cfg.component=ncmp;
>
> dataB1F1=rejectcomponent(cfg, tmpcomp); %reject components obviously
> representing artefacts
>
> >> [comp.cfg.channel(1:5) tmpcomp.cfg.channel(1:5)] %demonstrate
> channel label mismatch
>
> ans =
>
>    'Lm'     'L1'
>    'LE1'    'L10'
>    'LE2'    'L11'
>    'LE3'    'L12'
>    'LD2'    'L13'
>
> the crucial line appears to be in componentanalysis line 220:
> cfg.channel = intersect(cfg.channel, cfg.topolabel);
>
> intersect sorts the outcome:
> >> a=randperm(10)
>
> a =
>
>     7     1     9     3     6     2     5     4    10     8
>
> >> b=randperm(10)
>
> b =
>
>     6     3     5     1     8     2    10     4     9     7
>
> >> intersect(a,b)
>
> ans =
>
>     1     2     3     4     5     6     7     8     9    10
>
> since i use all channels, simply replacing the label-field with the
> original label-field works for me.
>
> best,
> nathan
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.
>

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


From r.oostenveld at FCDONDERS.RU.NL  Wed Oct 28 14:17:33 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Wed, 28 Oct 2009 14:17:33 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <2173B9D8-114C-476C-9759-0D042CD2A9A7@gmail.com>
Message-ID: <WED.28.OCT.2009.141733.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi Marco

On 26 Oct 2009, at 20:04, Marco Rotonda wrote:
> so I could not do zvalue artifact on 2 channels only?

you can in principle compute the z-value, but I don't think that that
will help you much. If it were only a single channel, it would just be
a scaling of the data in that channel with the standard deviation.
Since you have two, it is also the accumulation of the z-value over
teh two channels.

However, I think that for your 2-channel data it is much more robust
to manually (i.e. visually) identify the artifact time-windows. You
can use the new DATABROWSER function for that.

best,
Robert

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


From marco.rotonda at GMAIL.COM  Wed Oct 28 14:21:36 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Wed, 28 Oct 2009 14:21:36 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <B50DE1AF-891D-4935-BF73-161C1D1C2A22@fcdonders.ru.nl>
Message-ID: <WED.28.OCT.2009.142136.0100.FIELDTRIP@NIC.SURFNET.NL>

thank you very much! I'll try...



On 28/ott/2009, at 14.17, Robert Oostenveld wrote:

> Hi Marco
>
> On 26 Oct 2009, at 20:04, Marco Rotonda wrote:
>> so I could not do zvalue artifact on 2 channels only?
>
> you can in principle compute the z-value, but I don't think that
> that will help you much. If it were only a single channel, it would
> just be a scaling of the data in that channel with the standard
> deviation. Since you have two, it is also the accumulation of the z-
> value over teh two channels.
>
> However, I think that for your 2-channel data it is much more robust
> to manually (i.e. visually) identify the artifact time-windows. You
> can use the new DATABROWSER function for that.
>
> best,
> Robert
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.

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


From wibral at BIC.UNI-FRANKFURT.DE  Fri Oct 30 10:36:05 2009
From: wibral at BIC.UNI-FRANKFURT.DE (Michael Wibral)
Date: Fri, 30 Oct 2009 10:36:05 +0100
Subject: PhD position in the areas of cognitive neuroscience an d
 neuroimaging
Message-ID: <FRI.30.OCT.2009.103605.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrip users,

the Institute for Medical Psychology in Frankfurt (Prof. Jochen Kaiser) is offering a PhD position in the areas of cognitive neuroscience and neuroimaging (see below). Please also feel free to forward this message to interested colleagues.

Best Regards,
Michael Wibral

Job offer: PhD Student in Cognitive Neuroscience
The Institute of Medical Psychology at the University of Frankfurt/Germany invites applications for a PhD student position in the areas of cognitive neuroscience and neuroimaging. Employment duration will initially be limited to 2 years but can be extended*.
The work focuses on investigating auditory and visual memory processing employing magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI). The successful candidate will plan and conduct MEG, fMRI and behavioral experiments, perform data analyses, and publish the results.
The Institute of Medical Psychology provides access to state of the art research facilities of the Frankfurt Brain Imaging Center including two 3-Tesla research scanners, a 275-channel MEG system, and a 128-channel EEG system. We offer excellent supervision by experienced researchers and possibilities for participation in training courses and international scientific conferences. Last but not least, we provide a positive and highly productive working atmosphere!
Candidates should have a background and hold a Masters Degree in neuroscience, psychology, biology, or a related field. The candidate should enjoy experimental neuroscience, interdisciplinary collaboration and should be motivated to acquire new skills and knowledge. Furthermore, the candidate should be fluent in English both orally and written. Experience with fMRI or EEG/MEG, and good knowledge of statistics and programming skills are highly desirable.
Applications of women are specifically invited. In case of similar qualifications, competence, and specific achievements, women will be considered on preferential terms within the framework of the legal possibilities. Disabled candidates with equivalent qualifications will be given preference.
Please send your application (deadline: 30th November, 2009) to: 
Prof. Jochen Kaiser
Institut für Medizinische Psychologie
Goethe-Universität
Heinrich-Hoffmann-Straße 10
D-60528 Frankfurt am Main
Germany
j.kaiser at med.uni-frankfurt.de
URL: http://www.imp.uni-frankfurt.de

*The limitation of the contract is based upon the regulations of the "Wissenschaftszeitvertragsgesetz" in conjunction with the "Hessisches Hochschulgesetz". The salary will be based on BAT or the tariffs for German civil service employees.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From knyazev at PHYSIOL.RU  Thu Oct  1 05:22:48 2009
From: knyazev at PHYSIOL.RU (knyazev)
Date: Thu, 1 Oct 2009 10:22:48 +0700
Subject: Reference electrode in lead field
Message-ID: <THU.1.OCT.2009.102248.0700.FIELDTRIP@NIC.SURFNET.NL>

I wonder how many electrodes should be considered enough to provide a
 representative sampling of the head surface? I remember reading somewhere
that using an average reference from too few channels distorts results
severely. May someone provide an appropriate citation on the topic? Thanks
in advance.

Gennady Knyazev

----- Original Message -----
From: "Joseph Dien" <jdien07 at MAC.COM>
To: <FIELDTRIP at NIC.SURFNET.NL>
Sent: Wednesday, September 30, 2009 9:10 AM
Subject: Re: [FIELDTRIP] Reference electrode in lead field


> The reasoning behind the average reference is that it is a physics
> principle that the sum of the voltages over an enclosed surface must
> equal zero.  To the extent that the electrode locations provide a
> representative even sampling of the head surface (an important caveat)
> the sum of the voltages therefore provides an estimate of the true  zero
> voltage.  The reason for using the average reference rather than  a single
> reference site is that using a reference site arbitrarily  defines that
> point as being zero voltage (which is to say, inactive),  which is not
> biophysically reasonable as there are no inactive sites  on the head (due
> to volume conduction).  Also, to clarify, an average  reference does not
> result in a reference-free solution since, as you  say, a voltage
> measurement is by definition a relative measure  (although ideally it
> should be relatively independent of the electrode  montage, given enough
> electrodes).  It's just that the comparison  "site", which is the zero
> equipotential line (as estimated by the  average reference computation),
> is a more biophysically reasonable one  (given enough recording sites)
> than arbitrarily picking a single fixed  electrode site as the reference.
>
> For an extended discussion of these issues, see:
>
> Dien, J. (1998). Issues in the application of the average reference:
> Review, critiques, and recommendations. Behavior Research Methods,
> Instruments, and Computers, 30(1), 34-43.
>
> Cheers!
>
> Joe
>
>
> On Sep 28, 2009, at 3:29 PM, Mark Drakesmith wrote:
>
>> Hi all
>>
>> I am experimenting with source reconstruction and was wondering how  a
>> reference electrode is defined in the lead field. Looking through  the
>> scripts it looks like the average reference is used, but this is  a
>> physical impossibility, as there must be a physical reference to  which
>> differences in electrical potential can be measured. The lead  field will
>> be differ depending on the location of the reference  electrode.
>>
>> Firstly, is there a way to specify a reference electrode when
>> constructing an EEG lead field in fieldtri p and not jsut use the
>> average reference.
>>
>> Secondly, looking through  the code for  'inf_medium_leadfield' (called
>> from prepare_leadfield ->  compute_leadfield -> eeg_leadfieldb), the
>> equations used for  calculating the lead field look a little strange:
>>
>> radius = position (vox) - position(elec)
>> R (resistivity?) = 4 x pi x conductivity x sum(radius^2)^(1.5)
>> lead field(vox,elec)=radius / R.
>>
>> Where the the exponential to 1.5 come from? Is there a reference to
>> somewhere where this method is used. I'm confused as to sure how  this
>> calculation works.
>>
>> Many thanks
>>
>> Mark
>>
>> --
>>
>> Mark Drakesmith
>> PhD Student
>>
>> Neuroscience and Aphasia Research Unit (NARU)
>> University of Manchester
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users  of
>> the FieldTrip  toolbox, to share experiences and to discuss new  ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/neuroimaging/fieldtrip.
>
>
> --------------------------------------------------------------------------------
>
> Joseph Dien,
> Senior Research Scientist
> Center for Advanced Study of Language
> University of Maryland
> 7005 52nd Avenue
> College Park, MD 20742-0025
>
> E-mail: jdien07 at mac.com
> Phone: 301-226-8848
> Fax: 301-226-8811
> http://homepage.mac.com/jdien07/
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/neuroimaging/fieldtrip.

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


From r.oostenveld at FCDONDERS.RU.NL  Thu Oct  1 12:38:46 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 1 Oct 2009 12:38:46 +0200
Subject: Reference electrode in lead field
In-Reply-To: <4AC10E84.50708@postgrad.manchester.ac.uk>
Message-ID: <THU.1.OCT.2009.123846.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Mark

On 28 Sep 2009, at 21:29, Mark Drakesmith wrote:
> I am experimenting with source reconstruction and was wondering how
> a reference electrode is defined in the lead field. Looking through
> the scripts it looks like the average reference is used, but this is
> a physical impossibility, as there must be a physical reference to
> which differences in electrical potential can be measured. The lead
> field will be differ depending on the location of the reference
> electrode.
>
> Firstly, is there a way to specify a reference electrode when
> constructing an EEG lead field in fieldtri p and not jsut use the
> average reference.

At the moment there is no other reference choise for EEG source
modelling than the average over all electrodes. However, more
elaborate bipolar referencing schemes are since recently needed for
out own research and for that we'll implement a very flexible
referencing scheme. You can expect that to be included in the
fieldtrip release in a month or so. However, the average reference
will remain the defaulty, as it has been shown in simulations to give
the most robust results (although it makes little difference). I don't
immediately know the reference for that, but you should be able to
find it in pubmed.

See also the reply from Burkhard and yesterdays message from Joseph.

> Secondly, looking through  the code for
> 'inf_medium_leadfield' (called from prepare_leadfield ->
> compute_leadfield -> eeg_leadfieldb), the equations used for
> calculating the lead field look a little strange:
>
> radius = position (vox) - position(elec)
> R (resistivity?) = 4 x pi x conductivity x sum(radius^2)^(1.5)
> lead field(vox,elec)=radius / R.
>
> Where the the exponential to 1.5 come from? Is there a reference to
> somewhere where this method is used. I'm confused as to sure how
> this calculation works.

R is not a single physical value, it is just a shord-hand notation for
one of the terms in the equation. See the reference to implemented
methods on the fieldtrip wiki for publication details.

best
Robert

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


From megjim1 at GMAIL.COM  Fri Oct  2 06:07:18 2009
From: megjim1 at GMAIL.COM (Jim Li)
Date: Fri, 2 Oct 2009 06:07:18 +0200
Subject: how to plot the direction and amplitude of the planar gradient
Message-ID: <FRI.2.OCT.2009.060718.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear all,

I want to view the direction and amplitude of the planar gradient  near each 
sensor location and create a plot like what's shown in the  attached file (more 
or less).  Is it possible to do it? If so, how?

Our MEG sensors are 248 axial gradiometers. After running "megplanar" I got 
A1_dH...A248_dH,A1_dV...A248_dV for my channels. If, say, in the plane 
tangential to a given channel we have the Horizontal (x axis) and Vertical (y 
axis) directions. Then for the channel of interest, say A1,  I can run sqrt
(A1_dH^2+A1_dV^2) to get the amplitude of the planar gradient, and I can 
run atan2(A1_dV,A1_dH)*180/pi) to get the angle between the field vector 
and x-axis. What I'm not sure  about is how fieldtrip defines the Horizontal (x 
axis) and Vertical (y axis) for each channel (in a plane tangential to that 
channel). So it's hard to create the plot I want...

Thanks a lot.

Jim

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From j.schoffelen at PSY.GLA.AC.UK  Fri Oct  2 11:46:25 2009
From: j.schoffelen at PSY.GLA.AC.UK (Jan-Mathijs Schoffelen)
Date: Fri, 2 Oct 2009 09:46:25 +0000
Subject: how to plot the direction and amplitude of the planar gradient
In-Reply-To: <LISTSERV%200910020607189850.0FFE@NIC.SURFNET.NL>
Message-ID: <FRI.2.OCT.2009.094625.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Jim,

As far as I know, this is not possible in fieldtrip ... yet. Do I read
between the lines that you wouldn't mind giving it a try? I agree that
it's a very useful way to visualize planar gradient data.
First of all, it is indeed important to know the local coordinate
system for each of the planar gradient channels. For megplanar I
always use the 'sincos' method. You can see how the coordinate system
is defined at line 419 and beyond. As far as I can see the local x-
axis is taken as the vector orthogonal to the plane defined by the
coil's orientation, and the vector [0 0 1] (which is the z-axis of the
coordinate system in which your sensors are defined; assuming your
sensors are defined in headspace, this one points to the top of the
head). The local z-axis is the vector perpendicular to the coil's
plane (=orientation), and the y-axis is perpendicular to the local xz-
plane.
I guess that for the other planarmethods it's possible to figure out
the local coordinate systems as well. One think which we could think
of, is to adjust megplanar such that the output data contains
information about the local x and y axes directly.
Of course, it would also be nice if a hypothetical plotting function
would work for data acquired with hardware planar gradiometers. Here
it is usually straightforward to reconstruct the local coordinate
systems from the header-information. Perhaps people working with
Elekta-systems already have some matlab code for the plotting...
Once the local coordinate systems are known (and the angles defined
accordingly), it should be possible to warp these values to a
headspace based coordinate system for plotting (in 3D, or in 2D after
an appropriate projection).

Best,

Jan-Mathijs

On 2 Oct 2009, at 04:07, Jim Li wrote:

> Dear all,
>
> I want to view the direction and amplitude of the planar gradient
> near each
> sensor location and create a plot like what's shown in the  attached
> file (more
> or less).  Is it possible to do it? If so, how?
>
> Our MEG sensors are 248 axial gradiometers. After running
> "megplanar" I got
> A1_dH...A248_dH,A1_dV...A248_dV for my channels. If, say, in the plane
> tangential to a given channel we have the Horizontal (x axis) and
> Vertical (y
> axis) directions. Then for the channel of interest, say A1,  I can
> run sqrt
> (A1_dH^2+A1_dV^2) to get the amplitude of the planar gradient, and I
> can
> run atan2(A1_dV,A1_dH)*180/pi) to get the angle between the field
> vector
> and x-axis. What I'm not sure  about is how fieldtrip defines the
> Horizontal (x
> axis) and Vertical (y axis) for each channel (in a plane tangential
> to that
> channel). So it's hard to create the plot I want...
>
> Thanks a lot.
>
> Jim
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.
> <PlotGoal.TIF>

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


From Nina.Kahlbrock at UNI-DUESSELDORF.DE  Fri Oct  2 09:54:44 2009
From: Nina.Kahlbrock at UNI-DUESSELDORF.DE (Nina)
Date: Fri, 2 Oct 2009 09:54:44 +0200
Subject: Freqanalysis - clusterthreshold and neighbourselection
Message-ID: <FRI.2.OCT.2009.095444.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear all,



I have two questions regarding clusteranalysis.



1.	When running 'freqstatistics' on time frequency/frequency data with
the method 'montecarlo' which clusterthreshold would you use? I would think
that with the data usually not being normally distributed you would use a
nonparametric threshold. However, the default value for clusterthreshold is
'parametric'.

a.	Is there documentation about what 'nonparametric_individual' and
'nonparametric_common' mean? If yes, where can I find it?

2.	I am looking at data from our old Neuromag 122 system and used the
function 'neighbourselection' to define neighbouring channels. When checking
what 'neighbourselection' did I found that the neighbours identified were
not only the sensors surrounding the sensor of interest, but also sensors
lying far away from it. Also, not all sensors surrounding the one of
interest were included as neighbours. I used the gradfile generated by
'mne2grad122' as cfg.grad and different values for neighbourdist (4 and 3).
Does anybody have a solution for this?



Thanks in advance for your help!



Nina




----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From e.maris at DONDERS.RU.NL  Fri Oct  2 11:51:06 2009
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Fri, 2 Oct 2009 11:51:06 +0200
Subject: Freqanalysis - clusterthreshold and neighbourselection
In-Reply-To: <000901ca4335$9ad839f0$cd136386@VMED.UKD>
Message-ID: <FRI.2.OCT.2009.115106.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Nina,









I have two questions regarding clusteranalysis.



1.	When running 'freqstatistics' on time frequency/frequency data with
the method 'montecarlo' which clusterthreshold would you use? I would think
that with the data usually not being normally distributed you would use a
nonparametric threshold. However, the default value for clusterthreshold is
'parametric'.

a.	Is there documentation about what 'nonparametric_individual' and
'nonparametric_common' mean? If yes, where can I find it?



You can safely use the parametric threshold, regardless of the probability
distribution of your data. The reason is that this threshold only affects
the type of effect for which you test statistic is sensitive. The false
alarm rate does not depend on it. See Maris & Oostenveld (2007).



You only use the two other clusterthreshold options if you use a
non-normalized channel-level statistic. If you construct clusters by
thresholding channel-level T-statistics, go ahead with the parametric
threshold.





2.	I am looking at data from our old Neuromag 122 system and used the
function 'neighbourselection' to define neighbouring channels. When checking
what 'neighbourselection' did I found that the neighbours identified were
not only the sensors surrounding the sensor of interest, but also sensors
lying far away from it. Also, not all sensors surrounding the one of
interest were included as neighbours. I used the gradfile generated by
'mne2grad122' as cfg.grad and different values for neighbourdist (4 and 3).
Does anybody have a solution for this?





I guess Neuromag 122 system has planar gradiometers. For this sensor
configuration, the definition of a neighbourhood-metric requires some
thinking (because you are actually measuring spatial gradients with
different orientations). I contributed to a recent thread on the Fieldtrip
Discussion list about cluster-based permutation tests for the Vectorview
system. If I'm not mistaken, a scientist from an imaging center in Paris
initiated this thread. Have a look in the archive of the Fieldtrip
Discussion list (keywords: planar, cluster, Vectorview).





Good luck,











Thanks in advance for your help!



Nina



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

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

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

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


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From r.oostenveld at FCDONDERS.RU.NL  Fri Oct  2 12:19:30 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 2 Oct 2009 12:19:30 +0200
Subject: Fwd: [FIELDTRIP] Reference electrode in lead field
Message-ID: <FRI.2.OCT.2009.121930.0200.FIELDTRIP@NIC.SURFNET.NL>

Begin forwarded message:

> From: "Dr. Georges Otte" <georges.otte at telenet.be>
> Date: 1 October 2009 13:49:13 GMT+02:00
> To: r.oostenveld at FCDONDERS.RU.NL
> Subject: reference
>
> ...
> I have followed the discussion on reference and already contacted
> Dien. I agree but what about non ERP data ? Phase information and
> coherence. Can we safely use the averaged common reference for that.
> Robert Thatcher (neuroguide) quoting rappelsberger is opoosed to it
> and shows in his neuroguide package that in small channel systems
> (19-22) a ACR scrambles phase information between channels.
>
> Sincerely
>
> Dr. Georges Otte
> P.C dr. Guislain instit
> Gent
> Belgium
>
>
> PS How can I get back on the list ?
>
> Ransscipt
> no problem!  I haven't been working in the frequency domain and am
> not very familiar with spectral analyses so I can't say.  Sorry!
>
> Joe
>
>
> On Sep 30, 2009, at 2:20 AM, Dr. Georges Otte wrote:
>
>
> If the reference is not close to zero (fi using an average reference
> on to low an electrodeset fi 19 ch with prefrontal channels likely
> to be contaminated by occasional quite lagre eye blink or eye
> movement artifacts) what would be the effect on phase calculations ?
> From point to point the reference value that is substracted from
> each channel would be different from zero. Would that not wreck
> havoc to interchannel phase information or post stimulus coherence
> mapping ? Untrusthworthy ?
>
> Same qyuestion: if people use PCA or ICA to eliminate these
> artifacts and inverse reconstruct their EEG, can they still rely on
> phase calculations without errors ?
>
> Sincerely,
>
> Georges Otte
>
> PS Sorry to mail You personally but for some reason (perhaps change
> of email adres or long period of inactivity ) I seem to be  cutoff
> from the fieldtrip listserv
>
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From r.oostenveld at FCDONDERS.RU.NL  Fri Oct  2 12:58:09 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 2 Oct 2009 12:58:09 +0200
Subject: Fwd: [FIELDTRIP] Reference electrode in lead field
In-Reply-To: <0EEFD9A0-12F8-4751-A69D-62D61655E8BD@FCDONDERS.RU.NL>
Message-ID: <FRI.2.OCT.2009.125809.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Georges,

Thanks for raising this very good point.

As discussed before, the choise of the reference is quite irrelevant
for most analysis that involve a **linear transformation** of the
data, such as the computation and visualisation of the topography of
an ERP. But for non-linear transformations, the reference becomes
relevant.

Consider a simple statistics example. If you want to show a
significant effect in an auditory evoked potential (AEP) given a
standard and deviant tone, the optimal reference is the mastoid, which
maximizes the potential at Cz. So Cz minus M1, or Cz minus (M1+M2)/2,
i.e. linked ears, results in the largest signal on Cz. Subsequently
you compute the average ERP in both conditions and you compute the
variance from which you can compute the standard-error of the mean.
Then you compute the t-value, i.e. the difference in means  divided by
the pooled standard-error of the mean. That is all for the values
recorded in the Cz channel. Had you referenced Cz to the tip of the
nose, then the spatial topography of the AEPs and the spatial
topography of the AEP difference would not be qualitatively different
(only a difference in the color scale, but that color scale is
arbitarry chosen anyway). But the noise over trials in the Cz AEP
would probably be larger for the nose reference than for the linked
ears  reference. That noise is expressed in the variance, which is in
the denominator of the t-value. So the t-value would be less. The t-
value would become even smaller for a Fz reference.

Another example: if you compute spectral power using a FFT or warevelt
transform, the power is expressed as a squared number. At the
reference electrode the power is zero (per definition), whereas around
the reference electrode it would increase. Had I measured oscillatory
activity from auditory cotrex using a linked-ears reference, I would
see the maximum over the vertex, i.e. Cz. For a nose reference, the
maximum in power probably still would be over the vertex. But had I
choosen Cz itself as the reference, then at the vertex there would be
no power any more. Or less extreme, had I choosen Fz as reference,
then probably the power would _not_ be maximal over the vertex any
more, but rather along the lower electrode rim (T3/T4 a.k.a. C7/C8 and
the lower occipital electrodes). The spatial topography of the power
would also be qualitatively different for the different references.
You can think of it like "pushing the maximum in the power topography
around over the scalp" by changing the reference. In general, the
power will be largest further away from the reference and small close
to the reference. Of course the true power distrubution depends on the
underlying source activity, so this is a bit of a simplification.

In both examples above a non-linear transformation on the data is
involved. Offline rereferencing is a linear transformation of the
data, i.e. it only involves the addition and/or subtraction of some
value. The computations above (t-value, spectral power) are non-
linear, and they are non commutative (see http://en.wikipedia.org/wiki/Commutativity)
. In short (1+1)^2 is not equal to (1)^2+(1)^2.

The estimation of the phase from a signal is also a non-linear
transformation of the signal. After decomposing it into a sine and
cosine contribution at a specific frequency (with the FFT), the sine
and cosine contribution are combined to get the phasae (i.e. using the
arctangent, or using the complex-number representation). Everything
that is subsequently derived from the phase is therefore also non-
linear. So coherence and phase-locking values will be qualitatively
different depending on the choise of reference. One cannot simply
first compute coherence, and then afterwards apply a re-referencing.

Note that the estimation of the source strength of a dipole using any
source reconstruction technique (dipole fitting, beamforming, minimum
norm linear estimation) is a linear operation. It assumes a linear
mixing model (data = leadfield*source + noise) and a linear unmixing
model. In the estimate of the "unmixing matrix" for most techniques
there is a particular choise for dealing with the noise (i.e.
beamformer: try to suppress it, dipole fit: try to minimize the
squared error). Dealing with the noise and with the fact that the
linear system is either underdetermined or overdetermined causes a non-
linear effect. So there is some influence of the choise of reference
on the result of the source estimate, but in general not too much. If
you take a really extreme referencing scheme, i.e. all bipolar
electrodes over the scalp from the front to the back (a so-called
banana montage) which is more sensitive for superficial sources, then
the source reconstruction will be biassed for these superficial
contributions. For a linked mastoid reference, the source
reconstruction will be slightly biased for deep sources. For an
average reference, there is no specific bias to be expected. Overall,
the effect of the reference electrode will be quite small, and be the
least biassed for an avereage reference. Therefore, the average
reference is de facto the default in all source reconstruction
packages for EEG (commercial and non-commercial).

best regards,
Robert

PS for people who want to see these effects: you can use
DIPOLESIMULATION to generate simulated raw data with added noise, and
pass that through PREPROCESSING to re-reference to a reference of
choise. Subsequently you try the various  analysies discussed above,
i.e. TIMELOCKANALYSIS, TIMELOCKSTATISTICS, FREQANALYSIS and
SOURCEANALYSIS or DIPOLEFITTING.


On 2 Oct 2009, at 12:19, Robert Oostenveld wrote:

>> From: "Dr. Georges Otte" <georges.otte at telenet.be>
>>
>> ...
>> I have followed the discussion on reference and already contacted
>> Dien. I agree but what about non ERP data ? Phase information and
>> coherence. Can we safely use the averaged common reference for
>> that. Robert Thatcher (neuroguide) quoting rappelsberger is opoosed
>> to it and shows in his neuroguide package that in small channel
>> systems (19-22) a ACR scrambles phase information between channels.

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


From megjim1 at GMAIL.COM  Mon Oct  5 15:26:56 2009
From: megjim1 at GMAIL.COM (Jim Li)
Date: Mon, 5 Oct 2009 15:26:56 +0200
Subject: how to plot the direction and amplitude of the planar gradient
Message-ID: <MON.5.OCT.2009.152656.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs ,

Thanks a lot for your information. I'll take a look at the script to see what I 
can do.


Cheers,

Jim

On Fri, 2 Oct 2009 09:46:25 +0000, Jan-Mathijs Schoffelen 
<j.schoffelen at PSY.GLA.AC.UK> wrote:

>Dear Jim,
>
>As far as I know, this is not possible in fieldtrip ... yet. Do I read
>between the lines that you wouldn't mind giving it a try? I agree that
>it's a very useful way to visualize planar gradient data.
>First of all, it is indeed important to know the local coordinate
>system for each of the planar gradient channels. For megplanar I
>always use the 'sincos' method. You can see how the coordinate system
>is defined at line 419 and beyond. As far as I can see the local x-
>axis is taken as the vector orthogonal to the plane defined by the
>coil's orientation, and the vector [0 0 1] (which is the z-axis of the
>coordinate system in which your sensors are defined; assuming your
>sensors are defined in headspace, this one points to the top of the
>head). The local z-axis is the vector perpendicular to the coil's
>plane (=orientation), and the y-axis is perpendicular to the local xz-
>plane.
>I guess that for the other planarmethods it's possible to figure out
>the local coordinate systems as well. One think which we could think
>of, is to adjust megplanar such that the output data contains
>information about the local x and y axes directly.
>Of course, it would also be nice if a hypothetical plotting function
>would work for data acquired with hardware planar gradiometers. Here
>it is usually straightforward to reconstruct the local coordinate
>systems from the header-information. Perhaps people working with
>Elekta-systems already have some matlab code for the plotting...
>Once the local coordinate systems are known (and the angles defined
>accordingly), it should be possible to warp these values to a
>headspace based coordinate system for plotting (in 3D, or in 2D after
>an appropriate projection).
>
>Best,
>
>Jan-Mathijs
>
>On 2 Oct 2009, at 04:07, Jim Li wrote:
>
>> Dear all,
>>
>> I want to view the direction and amplitude of the planar gradient
>> near each
>> sensor location and create a plot like what's shown in the  attached
>> file (more
>> or less).  Is it possible to do it? If so, how?
>>
>> Our MEG sensors are 248 axial gradiometers. After running
>> "megplanar" I got
>> A1_dH...A248_dH,A1_dV...A248_dV for my channels. If, say, in the plane
>> tangential to a given channel we have the Horizontal (x axis) and
>> Vertical (y
>> axis) directions. Then for the channel of interest, say A1,  I can
>> run sqrt
>> (A1_dH^2+A1_dV^2) to get the amplitude of the planar gradient, and I
>> can
>> run atan2(A1_dV,A1_dH)*180/pi) to get the angle between the field
>> vector
>> and x-axis. What I'm not sure  about is how fieldtrip defines the
>> Horizontal (x
>> axis) and Vertical (y axis) for each channel (in a plane tangential
>> to that
>> channel). So it's hard to create the plot I want...
>>
>> Thanks a lot.
>>
>> Jim
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also 
http://listserv.surfnet.nl/archives/fieldtrip.html
>>  and http://www.ru.nl/neuroimaging/fieldtrip.
>> <PlotGoal.TIF>
>
>----------------------------------
>The aim of this list is to facilitate the discussion between users of the 
FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and 
EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and 
http://www.ru.nl/neuroimaging/fieldtrip.

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


From Juergen.Fell at UKB.UNI-BONN.DE  Wed Oct  7 10:14:30 2009
From: Juergen.Fell at UKB.UNI-BONN.DE (Juergen Fell)
Date: Wed, 7 Oct 2009 10:14:30 +0200
Subject: complex wavelet output
Message-ID: <WED.7.OCT.2009.101430.0200.FIELDTRIP@NIC.SURFNET.NL>



Dear fieldtrip users:

I've just started digging into fieldtrip and came across the following
question: is it possible to obtain the complex output of the continuous
wavelet transform, i.e. the original wavelet-transformed complex signal
(instead of power and/or cross-spectral density)?

Any help would be greatly appreciated.

Juergen.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From pacodiaz at UB.EDU  Wed Oct  7 10:59:26 2009
From: pacodiaz at UB.EDU (=?ISO-8859-1?Q?Paco_D=EDaz?=)
Date: Wed, 7 Oct 2009 10:59:26 +0200
Subject: complex wavelet output
In-Reply-To: <OF86C3BE7E.9A337D32-ONC1257648.002C950C-C1257648.002D7751@ukb.uni-bonn.de>
Message-ID: <WED.7.OCT.2009.105926.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Juergen,

   I made it by using "freqanalysis" with (basically)

cfg.output='pow'
cfg.method='tfr'

   and then you have to edit the freqanalysis_tfr function and suppress
the following lines:

   cTmp = (2*abs(cTmp)/data.fsample).^2;

in the main body of the function, and this one:

   y = (2*abs(y)/Fs).^2;

in the SUBFUNCTION for waveletanalysis.

Doing this you will avoid the power calculation and will end up with the
complex morlet coefficients.

Hope this helps,
F.J.

Juergen Fell escribió:
>
> Dear fieldtrip users:
>
> I've just started digging into fieldtrip and came across the following
> question: is it possible to obtain the complex output of the
> continuous wavelet transform, i.e. the original wavelet-transformed
> complex signal (instead of power and/or cross-spectral density)?
>
> Any help would be greatly appreciated.
>
> Juergen.
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>

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


From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE  Wed Oct  7 11:24:36 2009
From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke Van Dijk)
Date: Wed, 7 Oct 2009 11:24:36 +0200
Subject: AW: [FIELDTRIP] complex wavelet output
Message-ID: <WED.7.OCT.2009.112436.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Juergen,

As far as I can see, you can specify cfg.output = 'fourier' for the cfg.method = 'mtmconvol' when you want to have a time axis as well (it's also possible for 'mtmfft'). It will give you the fourierspectrum. You can set the parameters of mtmconvol such that it operates simmilar to a wavelet transform as you can see on this website:

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

An example of the parameters could be:

cfg = [];
cfg.output     = 'fourier';
cfg.channel    = 'MEG';
cfg.method     = 'mtmconvol';
cfg.taper      = 'dpss';        % sleppian taper but you can use different tapers/windows here.
cfg.foi        = 1:2:30;        % frequencies of interest.
cfg.t_ftimwin  = 5./cfg.foi;    % the window length is 5 cycles of the specified frequency long.
cfg.tapsmofrq  = 0.4 *cfg.foi;  % frequency smoothing of +/- 0.4*the specified frequency.
cfg.toi        = -0.5:0.05:1.5; % time of interest.
cfg.pad        = 'maxperlen';  
TFRmult = freqanalysis(cfg, dataFIC);

Hope it helps!

Yours,

Hanneke


-----Ursprüngliche Nachricht-----
Von: FieldTrip discussion list im Auftrag von Juergen Fell
Gesendet: Mi 07.10.2009 10:14
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: [FIELDTRIP] complex wavelet output
 


Dear fieldtrip users:

I've just started digging into fieldtrip and came across the following
question: is it possible to obtain the complex output of the continuous
wavelet transform, i.e. the original wavelet-transformed complex signal
(instead of power and/or cross-spectral density)?

Any help would be greatly appreciated.

Juergen.

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


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


From brian.roach at YALE.EDU  Wed Oct  7 22:10:52 2009
From: brian.roach at YALE.EDU (Brian Roach)
Date: Wed, 7 Oct 2009 13:10:52 -0700
Subject: AW: [FIELDTRIP] complex wavelet output
In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B0F34E5@Mail2-UKD.VMED.UKD>
Message-ID: <WED.7.OCT.2009.131052.0700.FIELDTRIP@NIC.SURFNET.NL>

Hi Juergen,

You can also use cfg.method = 'wltconvol', but you need to change a line
of code in the freqanalysis_wltconvol.m script.  When you use
cfg.keeptrials = 'yes', it will normally return single trial power data
(not complex numbers), but in the script search for:

elseif keep == 2
            powdum = XYZ ;

make sure that XYZ does not have any squaring or abs calls around it.
These change complex numbers to real ones.

Brian
Hanneke Van Dijk wrote:
> Dear Juergen,
>
> As far as I can see, you can specify cfg.output = 'fourier' for the cfg.method = 'mtmconvol' when you want to have a time axis as well (it's also possible for 'mtmfft'). It will give you the fourierspectrum. You can set the parameters of mtmconvol such that it operates simmilar to a wavelet transform as you can see on this website:
>
> http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis
>
> An example of the parameters could be:
>
> cfg = [];
> cfg.output     = 'fourier';
> cfg.channel    = 'MEG';
> cfg.method     = 'mtmconvol';
> cfg.taper      = 'dpss';        % sleppian taper but you can use different tapers/windows here.
> cfg.foi        = 1:2:30;        % frequencies of interest.
> cfg.t_ftimwin  = 5./cfg.foi;    % the window length is 5 cycles of the specified frequency long.
> cfg.tapsmofrq  = 0.4 *cfg.foi;  % frequency smoothing of +/- 0.4*the specified frequency.
> cfg.toi        = -0.5:0.05:1.5; % time of interest.
> cfg.pad        = 'maxperlen';
> TFRmult = freqanalysis(cfg, dataFIC);
>
> Hope it helps!
>
> Yours,
>
> Hanneke
>
>
> -----Ursprüngliche Nachricht-----
> Von: FieldTrip discussion list im Auftrag von Juergen Fell
> Gesendet: Mi 07.10.2009 10:14
> An: FIELDTRIP at NIC.SURFNET.NL
> Betreff: [FIELDTRIP] complex wavelet output
>
>
>
> Dear fieldtrip users:
>
> I've just started digging into fieldtrip and came across the following
> question: is it possible to obtain the complex output of the continuous
> wavelet transform, i.e. the original wavelet-transformed complex signal
> (instead of power and/or cross-spectral density)?
>
> Any help would be greatly appreciated.
>
> Juergen.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>
>

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


From julian.keil at GMAIL.COM  Fri Oct  9 14:04:08 2009
From: julian.keil at GMAIL.COM (Julian Keil)
Date: Fri, 9 Oct 2009 14:04:08 +0200
Subject: Freqstatistics plv
Message-ID: <FRI.9.OCT.2009.140408.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrippers,

I have a question regarding the use of freqstatistics and phase
locking values:
Is it possible to use freqstatistics to compare phase-locking values?
If not, is there any other option to compare plv between conditions

I use the following code:

cfg=[];
cfg.statistic='depsamplesT';
cfg.method='analytic';
cfg.parameter='plvspctrm';
cfg.channel={'all'};  % 5 channels -> 10 channelcmb
cfg.tail=0;
cfg.alpha=0.05;
cfg.ivar=2;
cfg.uvar=1;
cfg.frequency   = [10 50];

cfg.design=[1:12,1:12;ones(1,12),ones(1,12)*2];

[stats_fus_vi]=freqstatistics(cfg,plv_fu{:},plv_vi{:});

I get the information:
renaming parameter 'plvspctrm' into 'powspctrm'
selected 5 channels
selected 201 time bins
selected 21 frequency bins

As I don't get any error message, I assume this works fine so far but
I'm confused about what is computed here: Is "powspctrm" used instead
of "plvspctrm" (i.e. the test is computed between power estimates
instead of phase locking values)? Why are only 5 channels selected
instead of the 10 combinations?

I already tried renaming "plvspctrm" and "labelcmb" to "powspctrm" and
"label" but then I get an error message, as freqstatistics selects 20
channels.

Thanks a lot for any advise

Julian


Dipl. Psych. Julian Keil

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

Tel: ++49 - (0)7531 - 88 42 50
Fax: ++49 - (0)7531 - 88 28 91
Email: julian.keil at uni-konstanz.de
Homepage: http://www.uni-konstanz.de/obob








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From julian.keil at GMAIL.COM  Fri Oct  9 14:49:37 2009
From: julian.keil at GMAIL.COM (Julian Keil)
Date: Fri, 9 Oct 2009 14:49:37 +0200
Subject: Freqstatistics plv -> solved
Message-ID: <FRI.9.OCT.2009.144937.0200.FIELDTRIP@NIC.SURFNET.NL>

hi,

sorry for your time, problem solved: creating a new label-structure
worked.

greetings

Julian

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From tobias.donner at NYU.EDU  Tue Oct 13 15:13:11 2009
From: tobias.donner at NYU.EDU (Tobias Donner)
Date: Tue, 13 Oct 2009 15:13:11 +0200
Subject: PhD position in Cognitive Neuroscience in Amsterdam
Message-ID: <TUE.13.OCT.2009.151311.0200.FIELDTRIP@NIC.SURFNET.NL>

The Psychology Department of the University of Amsterdam is currently
hiring a PhD student to study the neural basis of visual awareness
and visual decision-making in humans. The project is a collaboration
of Tobias H. Donner and Victor A.F. Lamme. We plan to combine visual
psychophysics, neuroimaging (MEG, fMRI), and pharmacological
manipulation to (i) characterize decision-related feedback signals in
human early visual cortex, (ii) localize the source of these signals
in the brain, and (iii) study their role in shaping the contents of
perception.

We are looking for highly motivated candidates with a strong interest
in Cognitive Neuroscience and interdisciplinary research. Candidates
must have an MA (or equivalent) in Cognitive Science, Neuroscience,
Psychology, Physics, or Engineering, or an MD. Experience in computer
programming (e.g., MATLAB) and in EEG/MEG and/or fMRI will be a
significant plus.

Further information about the post and how to apply is available at:
http://www.uva.nl/vacatures/vacatures.cfm/E19032FD-1321-
B0BE-685E8B8E55A5AD26

Inquiries are welcomed. Please contact Tobias Donner: t.h.donner at uva.nl
Application deadline: November 1, 2009.

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


From Sara.GonzalezAndino at HCUGE.CH  Thu Oct 15 10:21:58 2009
From: Sara.GonzalezAndino at HCUGE.CH (GONZALEZ ANDINO Sara)
Date: Thu, 15 Oct 2009 10:21:58 +0200
Subject: TR: paper announcement
Message-ID: <THU.15.OCT.2009.102158.0200.FIELDTRIP@NIC.SURFNET.NL>

-----Message d'origine-----
De : GRAVE DE PERALTA Rolando 
Envoyé : jeudi, 15. octobre 2009 10:19

Objet : paper announcement

Dear Colleagues,

We would like to call your attention to the recent publication:
http://dx.doi.org/10.1016/j.jphysparis.2009.07.004 
that, among other things,  provide the theoretical and experimental evidences to refute claims that Very High Frequencies are not measurable at the scalp surface. 


Electrical neuroimaging of single trials to identify laterality and brain regions involved in finger movements 

by:
Rolando Grave de Peralta, Theodor Landis and Sara Gonzalez Andino

Abstract
Thought-controlled neuroprostheses could allow paralyzed patients to interact with the external world using brain waves. Thus far, the fastest and more accurate control of neuroprostheses is achieved through direct recordings of neural activity [Nicolelis, M.A., 2001. Actions from thoughts. Nature 409, 403-407; Donoghue, J.P., 2002. Connecting cortex to machines: recent advances in brain interfaces. Nat. Neurosci. 5 (Suppl.), 1085-1088]. However, invasive recordings have inherent medical risks. Here we discuss some approaches that could enhance the speed and accuracy of non-invasive devices, namely, (1) enlarging the spectral analysis to include higher frequency oscillations, able to transmit substantial information over short analysis windows; (2) using spectral analysis procedures that minimize the variance of the estimates; and (3) transforming EEG recorded activity into local field potential estimates (eLFP). Theoretical and experimental arguments are used to explain why it is erroneous to think that scalp EEG cannot sense high frequency oscillations and how this might hinders further developments. We further illustrate how non-invasive eLFPs derived from the scalp-recorded electroencephalogram (EEG) can be combined with robust, broad band spectral analysis to accurately detect (off-line) the laterality of upcoming hand movements. Interestingly, the use of pattern recognition to select the brain voxels differentially engaged by the explored tasks leads to sound neural activation images. Consequently, our results indicate that both research lines, i.e., neuroprosthetics and electrical neuroimaging, might effectively benefit from their mutual interaction.



regards
rolando
www.electrical-neuroimaging.ch 

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


From fredericroux at HOTMAIL.DE  Fri Oct 16 12:26:29 2009
From: fredericroux at HOTMAIL.DE (Frederic Roux)
Date: Fri, 16 Oct 2009 12:26:29 +0200
Subject: error using freqanalysis_mtmfft
Message-ID: <FRI.16.OCT.2009.122629.0200.FIELDTRIP@NIC.SURFNET.NL>


Hi everyone,
 
I am using freqanalysis with the following cfg structure
 
cfg             = [];
cfg.output      = 'pow';
cfg.channel     = {'MEG'};
cfg.method      = 'mtmfft';
cfg.taper       = 'dpss';
cfg.foi         = 1:200; 
cfg.t_ftimwin   = .5*ones(1,length(cfg.foi));
cfg.toi         = [-1.5:.5:2.5]; 
cfg.tapsmofrq   = 5.*ones(1,length(cfg.foi)); 
cfg.pad         = 'maxperlen';
 
and I get the following error message
 
??? Error using ==> dpss
The Time-bandwidth product NW must be a scalar.
 
Error in ==> freqanalysis_mtmfft>double_dpss at 594
tap = dpss(double(a), double(b), varargin{:});
 
Error in ==> freqanalysis_mtmfft at 421
    tap =
double_dpss(numdatbns,numdatbns*(cfg.tapsmofrq./data.fsample))';
 
Error in ==> freqanalysis at 192


K should be equal to 2*(.5*5)-1 = 4 tapers so I don't really understand what's going wrong here.
And before diving into the code I thought that maybe someone could provide me with a simple answer/solution. 
Any help with this would be greatly apreciated!
 
Frederic
  		 	   		  
_________________________________________________________________
http://redirect.gimas.net/?n=M0910xHerbstmode2
So gehst du mir nicht vor die Tür! Herbsttrends entdecken
----------------------------------
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From hungptit at GMAIL.COM  Sat Oct 24 08:39:35 2009
From: hungptit at GMAIL.COM (Hung Dang)
Date: Sat, 24 Oct 2009 00:39:35 -0600
Subject: How to generate the EEG background noise and interference
In-Reply-To: <SNT107-W7ED61CCCB8F2C15B0C398B7C40@phx.gbl>
Message-ID: <SAT.24.OCT.2009.003935.0600.FIELDTRIP@NIC.SURFNET.NL>

Dear all,
Many researchers have been using Gaussian white noise as the additive
noise for the  MEG/EEG signals to evaluate their inverse algorithm,
however, this assumption may not true for the real MEG/EEG signals. I
try to google for a while and have not find any good reference.
So my question is how could we generate a more realistic MEG/EEG signal,
interference, and noise to obtain a better judgment of how good are
inverse solutions?

Have a nice weekend
Hung

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


From v.litvak at ION.UCL.AC.UK  Sat Oct 24 10:05:25 2009
From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak)
Date: Sat, 24 Oct 2009 09:05:25 +0100
Subject: How to generate the EEG background noise and interference
In-Reply-To: <4AE2A127.905@gmail.com>
Message-ID: <SAT.24.OCT.2009.090525.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Hung,

A simple and convincing thing to do would be to combine simulated data
with real data. For instance if you are talking about ERP, you can add
your simulated responses  to a real recording at times random with
respect to the original triggers. Then you will get your simulated ERP
with noise as real as it gets. By controlling the relative scaling of
the real and simulated data you can test different SNRs.

Best,

Vladimir

On Sat, Oct 24, 2009 at 7:39 AM, Hung Dang <hungptit at gmail.com> wrote:
> Dear all,
> Many researchers have been using Gaussian white noise as the additive
> noise for the  MEG/EEG signals to evaluate their inverse algorithm,
> however, this assumption may not true for the real MEG/EEG signals. I
> try to google for a while and have not find any good reference.
> So my question is how could we generate a more realistic MEG/EEG signal,
> interference, and noise to obtain a better judgment of how good are
> inverse solutions?
>
> Have a nice weekend
> Hung
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>
>

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


From hungptit at GMAIL.COM  Sat Oct 24 19:53:20 2009
From: hungptit at GMAIL.COM (Hung Dang)
Date: Sat, 24 Oct 2009 11:53:20 -0600
Subject: How to generate the EEG background noise and interference
In-Reply-To: <e1e7c57c0910240105r5d5b683fh6e3bb56cac175a8f@mail.gmail.com>
Message-ID: <SAT.24.OCT.2009.115320.0600.FIELDTRIP@NIC.SURFNET.NL>

Dear Vladimir,
Thanks a lot for an insightful and quick reply. That will definitely
help me a lot for my simulation studies.

Regards,
Hung



Vladimir Litvak wrote:
> Dear Hung,
>
> A simple and convincing thing to do would be to combine simulated data
> with real data. For instance if you are talking about ERP, you can add
> your simulated responses  to a real recording at times random with
> respect to the original triggers. Then you will get your simulated ERP
> with noise as real as it gets. By controlling the relative scaling of
> the real and simulated data you can test different SNRs.
>
> Best,
>
> Vladimir
>
> On Sat, Oct 24, 2009 at 7:39 AM, Hung Dang <hungptit at gmail.com> wrote:
>
>> Dear all,
>> Many researchers have been using Gaussian white noise as the additive
>> noise for the  MEG/EEG signals to evaluate their inverse algorithm,
>> however, this assumption may not true for the real MEG/EEG signals. I
>> try to google for a while and have not find any good reference.
>> So my question is how could we generate a more realistic MEG/EEG signal,
>> interference, and noise to obtain a better judgment of how good are
>> inverse solutions?
>>
>> Have a nice weekend
>> Hung
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>>
>>
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>

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


From marco.rotonda at GMAIL.COM  Mon Oct 26 14:42:28 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Mon, 26 Oct 2009 14:42:28 +0100
Subject: importing raw data
Message-ID: <MON.26.OCT.2009.144228.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi there,
I'm trying to import a raw data file to perform artifacting.
The file I have is quite simple: 2 channels and only data sampled at 256.
I did the following operations:

FF = (csvread('FF.txt', 2, 0))';
data.trial{1} = FF;
data.time{1} = linspace(0,180,46080);
data.fsample=256;
data.label={'F3';'F4'};
data.cfg.trl=[1,46080,0];
cfg.continuous='yes';
cfg.trl=[1,46080,0];
cfg.channel={'F3';'F4'};
cfg2=artifact_eog(cfg,data);

but then I have the following message error:

??? Error using ==> artifact_zvalue at 202
no channels selected

Error in ==> artifact_eog at 179
   [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
   data);

What I miss?

in artifact_zvalue from 197:

cfg.artfctdef.zvalue.channel =
channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
sgnind        = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
numsgn        = length(sgnind);

if numsgn<1
 error('no channels selected');
else
 fprintf('searching for artifacts in %d channels\n', numsgn);
end


So I added:

cfg.artfctdef.zvalue.channel={'F3';'F4'};

but I get the same error
it seems that I need the header... but I have not.
is it?

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


From P.Toffanin at RUG.NL  Mon Oct 26 15:08:43 2009
From: P.Toffanin at RUG.NL (Paolo Toffanin)
Date: Mon, 26 Oct 2009 15:08:43 +0100
Subject: importing raw data
In-Reply-To: <LISTSERV%200910261442283870.8413@NIC.SURFNET.NL>
Message-ID: <MON.26.OCT.2009.150843.0100.FIELDTRIP@NIC.SURFNET.NL>

Did you try including also eye channels into the analysis?

Paolo

On Monday 26 October 2009 02:42:28 pm Marco Rotonda wrote:
> Hi there,
> I'm trying to import a raw data file to perform artifacting.
> The file I have is quite simple: 2 channels and only data sampled at 256.
> I did the following operations:
>
> FF = (csvread('FF.txt', 2, 0))';
> data.trial{1} = FF;
> data.time{1} = linspace(0,180,46080);
> data.fsample=256;
> data.label={'F3';'F4'};
> data.cfg.trl=[1,46080,0];
> cfg.continuous='yes';
> cfg.trl=[1,46080,0];
> cfg.channel={'F3';'F4'};
> cfg2=artifact_eog(cfg,data);
>
> but then I have the following message error:
>
> ??? Error using ==> artifact_zvalue at 202
> no channels selected
>
> Error in ==> artifact_eog at 179
>    [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
>    data);
>
> What I miss?
>
> in artifact_zvalue from 197:
>
> cfg.artfctdef.zvalue.channel =
> channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
> sgnind        = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
> numsgn        = length(sgnind);
>
> if numsgn<1
>  error('no channels selected');
> else
>  fprintf('searching for artifacts in %d channels\n', numsgn);
> end
>
>
> So I added:
>
> cfg.artfctdef.zvalue.channel={'F3';'F4'};
>
> but I get the same error
> it seems that I need the header... but I have not.
> is it?
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/neuroimaging/fieldtrip.


----------------------------------
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From marco.rotonda at GMAIL.COM  Mon Oct 26 15:15:26 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Mon, 26 Oct 2009 15:15:26 +0100
Subject: importing raw data
In-Reply-To: <200910261508.43870.p233228@rug.nl>
Message-ID: <MON.26.OCT.2009.151526.0100.FIELDTRIP@NIC.SURFNET.NL>

nope... only 2 channels...


On 26/ott/2009, at 15.08, Paolo Toffanin wrote:

> Did you try including also eye channels into the analysis?
>
> Paolo
>
> On Monday 26 October 2009 02:42:28 pm Marco Rotonda wrote:
> > Hi there,
> > I'm trying to import a raw data file to perform artifacting.
> > The file I have is quite simple: 2 channels and only data sampled
> at 256.
> > I did the following operations:
> >
> > FF = (csvread('FF.txt', 2, 0))';
> > data.trial{1} = FF;
> > data.time{1} = linspace(0,180,46080);
> > data.fsample=256;
> > data.label={'F3';'F4'};
> > data.cfg.trl=[1,46080,0];
> > cfg.continuous='yes';
> > cfg.trl=[1,46080,0];
> > cfg.channel={'F3';'F4'};
> > cfg2=artifact_eog(cfg,data);
> >
> > but then I have the following message error:
> >
> > ??? Error using ==> artifact_zvalue at 202
> > no channels selected
> >
> > Error in ==> artifact_eog at 179
> > [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
> > data);
> >
> > What I miss?
> >
> > in artifact_zvalue from 197:
> >
> > cfg.artfctdef.zvalue.channel =
> > channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
> > sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
> > numsgn = length(sgnind);
> >
> > if numsgn<1
> > error('no channels selected');
> > else
> > fprintf('searching for artifacts in %d channels\n', numsgn);
> > end
> >
> >
> > So I added:
> >
> > cfg.artfctdef.zvalue.channel={'F3';'F4'};
> >
> > but I get the same error
> > it seems that I need the header... but I have not.
> > is it?
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of the
> > FieldTrip toolbox, to share experiences and to discuss new ideas
> for MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/neuroimaging/fieldtrip.
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
>   http://listserv.surfnet.nl/archives/fieldtrip.html
>
>   http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
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From Nina.Kahlbrock at UNI-DUESSELDORF.DE  Mon Oct 26 15:18:42 2009
From: Nina.Kahlbrock at UNI-DUESSELDORF.DE (Nina)
Date: Mon, 26 Oct 2009 15:18:42 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <200910261508.43870.p233228@rug.nl>
Message-ID: <MON.26.OCT.2009.151842.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi Marco,

you might want to try:



cfg.artfctdef.eog.channel = {your EOG channel(s)};



Nina



  _____

Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag
von Paolo Toffanin
Gesendet: Montag, 26. Oktober 2009 15:09
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: Re: [FIELDTRIP] importing raw data



Did you try including also eye channels into the analysis?





Paolo





On Monday 26 October 2009 02:42:28 pm Marco Rotonda wrote:
> Hi there,
> I'm trying to import a raw data file to perform artifacting.
> The file I have is quite simple: 2 channels and only data sampled at 256.
> I did the following operations:
>
> FF = (csvread('FF.txt', 2, 0))';
> data.trial{1} = FF;
> data.time{1} = linspace(0,180,46080);
> data.fsample=256;
> data.label={'F3';'F4'};
> data.cfg.trl=[1,46080,0];
> cfg.continuous='yes';
> cfg.trl=[1,46080,0];
> cfg.channel={'F3';'F4'};
> cfg2=artifact_eog(cfg,data);
>
> but then I have the following message error:
>
> ??? Error using ==> artifact_zvalue at 202
> no channels selected
>
> Error in ==> artifact_eog at 179
> [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
> data);
>
> What I miss?
>
> in artifact_zvalue from 197:
>
> cfg.artfctdef.zvalue.channel =
> channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
> sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
> numsgn = length(sgnind);
>
> if numsgn<1
> error('no channels selected');
> else
> fprintf('searching for artifacts in %d channels\n', numsgn);
> end
>
>
> So I added:
>
> cfg.artfctdef.zvalue.channel={'F3';'F4'};
>
> but I get the same error
> it seems that I need the header... but I have not.
> is it?
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/neuroimaging/fieldtrip.





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

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

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

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


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From marco.rotonda at GMAIL.COM  Mon Oct 26 17:20:12 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Mon, 26 Oct 2009 17:20:12 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <001a01ca5647$38b652a0$cd136386@VMED.UKD>
Message-ID: <MON.26.OCT.2009.172012.0100.FIELDTRIP@NIC.SURFNET.NL>

So I need eog channels other than the 2 I have?


On 26/ott/2009, at 15.18, Nina wrote:

> Hi Marco,
> you might want to try:
>
> cfg.artfctdef.eog.channel
> = {your EOG channel(s)};
>
> Nina
>
> Von: FieldTrip
> discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von
> Paolo Toffanin
>
> Gesendet: Montag, 26. Oktober 2009
> 15:09
>
> An: FIELDTRIP at NIC.SURFNET.NL
>
> Betreff: Re: [FIELDTRIP] importing
> raw data
>
> Did you try including also eye channels into the
> analysis?
>
>
>
>
> Paolo
>
>
>
>
> On Monday 26 October 2009 02:42:28 pm Marco Rotonda
> wrote:
>
> > Hi there,
>
> > I'm trying to import a raw data file to perform artifacting.
>
> > The file I have is quite simple: 2 channels and only data sampled
> at 256.
>
> > I did the following operations:
>
> >
>
> > FF = (csvread('FF.txt', 2, 0))';
>
> > data.trial{1} = FF;
>
> > data.time{1} = linspace(0,180,46080);
>
> > data.fsample=256;
>
> > data.label={'F3';'F4'};
>
> > data.cfg.trl=[1,46080,0];
>
> > cfg.continuous='yes';
>
> > cfg.trl=[1,46080,0];
>
> > cfg.channel={'F3';'F4'};
>
> > cfg2=artifact_eog(cfg,data);
>
> >
>
> > but then I have the following message error:
>
> >
>
> > ??? Error using ==> artifact_zvalue at 202
>
> > no channels selected
>
> >
>
> > Error in ==> artifact_eog at 179
>
> > [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
>
> > data);
>
> >
>
> > What I miss?
>
> >
>
> > in artifact_zvalue from 197:
>
> >
>
> > cfg.artfctdef.zvalue.channel =
>
> > channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
>
> > sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
>
> > numsgn = length(sgnind);
>
> >
>
> > if numsgn<1
>
> > error('no channels selected');
>
> > else
>
> > fprintf('searching for artifacts in %d channels\n', numsgn);
>
> > end
>
> >
>
> >
>
> > So I added:
>
> >
>
> > cfg.artfctdef.zvalue.channel={'F3';'F4'};
>
> >
>
> > but I get the same error
>
> > it seems that I need the header... but I have not.
>
> > is it?
>
> >
>
> > ----------------------------------
>
> > The aim of this list is to facilitate the discussion between users
> of the
>
> > FieldTrip toolbox, to share experiences and to discuss new ideas
> for MEG
>
> > and EEG analysis. See also
>
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
>
> > http://www.ru.nl/neuroimaging/fieldtrip.
>
>
>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
>   http://listserv.surfnet.nl/archives/fieldtrip.html
>
>   http://www.ru.nl/fcdonders/fieldtrip/
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
>   http://listserv.surfnet.nl/archives/fieldtrip.html
>
>   http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From P.Toffanin at RUG.NL  Mon Oct 26 20:02:06 2009
From: P.Toffanin at RUG.NL (Paolo Toffanin)
Date: Mon, 26 Oct 2009 21:02:06 +0200
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <A75DF2B4-3129-41CE-9EB4-E4BBC1784BB0@gmail.com>
Message-ID: <MON.26.OCT.2009.210206.0200.FIELDTRIP@NIC.SURFNET.NL>

That's the idea.

Paolo

On Mon, 26 Oct 2009 17:20:12 +0100
  Marco Rotonda <marco.rotonda at GMAIL.COM> wrote:
> So I need eog channels other than the 2 I have?
>
>
> On 26/ott/2009, at 15.18, Nina wrote:
>
>> Hi Marco,
>> you might want to try:
>>
>> cfg.artfctdef.eog.channel
>> = {your EOG channel(s)};
>>
>> Nina
>>
>> Von: FieldTrip
>> discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von
>> Paolo Toffanin
>>
>> Gesendet: Montag, 26. Oktober 2009
>> 15:09
>>
>> An: FIELDTRIP at NIC.SURFNET.NL
>>
>> Betreff: Re: [FIELDTRIP] importing
>> raw data
>>
>> Did you try including also eye channels into the
>> analysis?
>>
>>
>>
>>
>> Paolo
>>
>>
>>
>>
>> On Monday 26 October 2009 02:42:28 pm Marco Rotonda
>> wrote:
>>
>> > Hi there,
>>
>> > I'm trying to import a raw data file to perform artifacting.
>>
>> > The file I have is quite simple: 2 channels and only data sampled
>>
>> at 256.
>>
>> > I did the following operations:
>>
>> >
>>
>> > FF = (csvread('FF.txt', 2, 0))';
>>
>> > data.trial{1} = FF;
>>
>> > data.time{1} = linspace(0,180,46080);
>>
>> > data.fsample=256;
>>
>> > data.label={'F3';'F4'};
>>
>> > data.cfg.trl=[1,46080,0];
>>
>> > cfg.continuous='yes';
>>
>> > cfg.trl=[1,46080,0];
>>
>> > cfg.channel={'F3';'F4'};
>>
>> > cfg2=artifact_eog(cfg,data);
>>
>> >
>>
>> > but then I have the following message error:
>>
>> >
>>
>> > ??? Error using ==> artifact_zvalue at 202
>>
>> > no channels selected
>>
>> >
>>
>> > Error in ==> artifact_eog at 179
>>
>> > [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
>>
>> > data);
>>
>> >
>>
>> > What I miss?
>>
>> >
>>
>> > in artifact_zvalue from 197:
>>
>> >
>>
>> > cfg.artfctdef.zvalue.channel =
>>
>> > channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
>>
>> > sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
>>
>> > numsgn = length(sgnind);
>>
>> >
>>
>> > if numsgn<1
>>
>> > error('no channels selected');
>>
>> > else
>>
>> > fprintf('searching for artifacts in %d channels\n', numsgn);
>>
>> > end
>>
>> >
>>
>> >
>>
>> > So I added:
>>
>> >
>>
>> > cfg.artfctdef.zvalue.channel={'F3';'F4'};
>>
>> >
>>
>> > but I get the same error
>>
>> > it seems that I need the header... but I have not.
>>
>> > is it?
>>
>> >
>>
>> > ----------------------------------
>>
>> > The aim of this list is to facilitate the discussion between users
>>
>> of the
>>
>> > FieldTrip toolbox, to share experiences and to discuss new ideas
>> for MEG
>>
>> > and EEG analysis. See also
>>
>> > http://listserv.surfnet.nl/archives/fieldtrip.html and
>>
>> > http://www.ru.nl/neuroimaging/fieldtrip.
>>
>>
>>
>>
>> ----------------------------------
>>
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis.
>>
>>   http://listserv.surfnet.nl/archives/fieldtrip.html
>>
>>   http://www.ru.nl/fcdonders/fieldtrip/
>>
>> ----------------------------------
>>
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis.
>>
>>   http://listserv.surfnet.nl/archives/fieldtrip.html
>>
>>   http://www.ru.nl/fcdonders/fieldtrip/
>>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
>of the FieldTrip  toolbox, to share experiences and to discuss new
>ideas for MEG and EEG analysis. See also
>http://listserv.surfnet.nl/archives/fieldtrip.html and
>http://www.ru.nl/neuroimaging/fieldtrip.

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


From marco.rotonda at GMAIL.COM  Mon Oct 26 20:04:20 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Mon, 26 Oct 2009 20:04:20 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <web-127111963@mail3.rug.nl>
Message-ID: <MON.26.OCT.2009.200420.0100.FIELDTRIP@NIC.SURFNET.NL>

so I could not do zvalue artifact on 2 channels only?

On 26/ott/2009, at 20.02, Paolo Toffanin wrote:

> That's the idea.
>
> Paolo
>
> On Mon, 26 Oct 2009 17:20:12 +0100
> Marco Rotonda <marco.rotonda at GMAIL.COM> wrote:
>> So I need eog channels other than the 2 I have?
>> On 26/ott/2009, at 15.18, Nina wrote:
>>> Hi Marco,
>>> you might want to try:
>>>
>>> cfg.artfctdef.eog.channel
>>> = {your EOG channel(s)};
>>>
>>> Nina
>>>
>>> Von: FieldTrip
>>> discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von
>>> Paolo Toffanin
>>>
>>> Gesendet: Montag, 26. Oktober 2009
>>> 15:09
>>>
>>> An: FIELDTRIP at NIC.SURFNET.NL
>>>
>>> Betreff: Re: [FIELDTRIP] importing
>>> raw data
>>>
>>> Did you try including also eye channels into the
>>> analysis?
>>>
>>>
>>>
>>>
>>> Paolo
>>>
>>>
>>>
>>>
>>> On Monday 26 October 2009 02:42:28 pm Marco Rotonda
>>> wrote:
>>>
>>> > Hi there,
>>>
>>> > I'm trying to import a raw data file to perform artifacting.
>>>
>>> > The file I have is quite simple: 2 channels and only data
>>> sampled at 256.
>>>
>>> > I did the following operations:
>>>
>>> >
>>>
>>> > FF = (csvread('FF.txt', 2, 0))';
>>>
>>> > data.trial{1} = FF;
>>>
>>> > data.time{1} = linspace(0,180,46080);
>>>
>>> > data.fsample=256;
>>>
>>> > data.label={'F3';'F4'};
>>>
>>> > data.cfg.trl=[1,46080,0];
>>>
>>> > cfg.continuous='yes';
>>>
>>> > cfg.trl=[1,46080,0];
>>>
>>> > cfg.channel={'F3';'F4'};
>>>
>>> > cfg2=artifact_eog(cfg,data);
>>>
>>> >
>>>
>>> > but then I have the following message error:
>>>
>>> >
>>>
>>> > ??? Error using ==> artifact_zvalue at 202
>>>
>>> > no channels selected
>>>
>>> >
>>>
>>> > Error in ==> artifact_eog at 179
>>>
>>> > [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
>>>
>>> > data);
>>>
>>> >
>>>
>>> > What I miss?
>>>
>>> >
>>>
>>> > in artifact_zvalue from 197:
>>>
>>> >
>>>
>>> > cfg.artfctdef.zvalue.channel =
>>>
>>> > channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
>>>
>>> > sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
>>>
>>> > numsgn = length(sgnind);
>>>
>>> >
>>>
>>> > if numsgn<1
>>>
>>> > error('no channels selected');
>>>
>>> > else
>>>
>>> > fprintf('searching for artifacts in %d channels\n', numsgn);
>>>
>>> > end
>>>
>>> >
>>>
>>> >
>>>
>>> > So I added:
>>>
>>> >
>>>
>>> > cfg.artfctdef.zvalue.channel={'F3';'F4'};
>>>
>>> >
>>>
>>> > but I get the same error
>>>
>>> > it seems that I need the header... but I have not.
>>>
>>> > is it?
>>>
>>> >
>>>
>>> > ----------------------------------
>>>
>>> > The aim of this list is to facilitate the discussion between
>>> users of the
>>>
>>> > FieldTrip toolbox, to share experiences and to discuss new
>>> ideas  for MEG
>>>
>>> > and EEG analysis. See also
>>>
>>> > http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>
>>> > http://www.ru.nl/neuroimaging/fieldtrip.
>>>
>>>
>>>
>>>
>>> ----------------------------------
>>>
>>> The aim of this list is to facilitate the discussion between
>>> users  of the FieldTrip  toolbox, to share experiences and to
>>> discuss new  ideas for MEG and EEG analysis.
>>>
>>>  http://listserv.surfnet.nl/archives/fieldtrip.html
>>>
>>>  http://www.ru.nl/fcdonders/fieldtrip/
>>>
>>> ----------------------------------
>>>
>>> The aim of this list is to facilitate the discussion between
>>> users  of the FieldTrip  toolbox, to share experiences and to
>>> discuss new  ideas for MEG and EEG analysis.
>>>
>>>  http://listserv.surfnet.nl/archives/fieldtrip.html
>>>
>>>  http://www.ru.nl/fcdonders/fieldtrip/
>>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>>  and http://www.ru.nl/neuroimaging/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.

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


From nathanweisz at MAC.COM  Mon Oct 26 21:17:31 2009
From: nathanweisz at MAC.COM (Nathan Weisz)
Date: Mon, 26 Oct 2009 21:17:31 +0100
Subject: data.label wrong after componentanalysis?
Message-ID: <MON.26.OCT.2009.211731.0100.>

hi everyone,

for an analysis of EEG data i'm doing some ICA cleaning. since there
are many conditions / epochs, i do the ICA on a subset of trials and
then apply the calculated mixing matrix to the individual conditions.

i noticed (and i'm quite sure it's no user related error) that after
rejecting components and reconstructing the preprocessing data
structure, that the sequence in data.label has changed (apparently
into alphabetical order). however that rows in the 2-D matrices making
up data.trial(xy) have not changed, accordingly. i noticed because the
topography of the auditory N1 was a huge mess.

changing the labels solved the problem, i.e.:
ica_cleaned_data.label = data_before_ica_cleaning.label;

for those interested here the original code:

load([outdir '/dataB1F1.mat'], 'dataB1F1') %load data for one condition

cfg=[];
cfg.topo=comp.topo;
cfg.topolabel=comp.topolabel;

tmpcomp=componentanalysis(cfg,dataB1F1); %apply precomputed ICA to
condition

cfg=[];
cfg.component=ncmp;

dataB1F1=rejectcomponent(cfg, tmpcomp); %reject components obviously
representing artefacts

 >> [comp.cfg.channel(1:5) tmpcomp.cfg.channel(1:5)] %demonstrate
channel label mismatch

ans =

     'Lm'     'L1'
     'LE1'    'L10'
     'LE2'    'L11'
     'LE3'    'L12'
     'LD2'    'L13'

the crucial line appears to be in componentanalysis line 220:
cfg.channel = intersect(cfg.channel, cfg.topolabel);

intersect sorts the outcome:
 >> a=randperm(10)

a =

      7     1     9     3     6     2     5     4    10     8

 >> b=randperm(10)

b =

      6     3     5     1     8     2    10     4     9     7

 >> intersect(a,b)

ans =

      1     2     3     4     5     6     7     8     9    10

since i use all channels, simply replacing the label-field with the
original label-field works for me.

best,
nathan

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


From r.oostenveld at FCDONDERS.RU.NL  Wed Oct 28 14:11:35 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Wed, 28 Oct 2009 14:11:35 +0100
Subject: data.label wrong after componentanalysis?
In-Reply-To: <2B0C43B0-93FD-455C-BE01-D7B8002A7425@mac.com>
Message-ID: <WED.28.OCT.2009.141135.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Nathan,

thanks for the notification. It sounds like a potentially nasty bug,
so we'll look into it.

best,
Robert


On 26 Oct 2009, at 21:17, Nathan Weisz wrote:

> hi everyone,
>
> for an analysis of EEG data i'm doing some ICA cleaning. since there
> are many conditions / epochs, i do the ICA on a subset of trials and
> then apply the calculated mixing matrix to the individual conditions.
>
> i noticed (and i'm quite sure it's no user related error) that after
> rejecting components and reconstructing the preprocessing data
> structure, that the sequence in data.label has changed (apparently
> into alphabetical order). however that rows in the 2-D matrices
> making up data.trial(xy) have not changed, accordingly. i noticed
> because the topography of the auditory N1 was a huge mess.
>
> changing the labels solved the problem, i.e.:
> ica_cleaned_data.label = data_before_ica_cleaning.label;
>
> for those interested here the original code:
>
> load([outdir '/dataB1F1.mat'], 'dataB1F1') %load data for one
> condition
>
> cfg=[];
> cfg.topo=comp.topo;
> cfg.topolabel=comp.topolabel;
>
> tmpcomp=componentanalysis(cfg,dataB1F1); %apply precomputed ICA to
> condition
>
> cfg=[];
> cfg.component=ncmp;
>
> dataB1F1=rejectcomponent(cfg, tmpcomp); %reject components obviously
> representing artefacts
>
> >> [comp.cfg.channel(1:5) tmpcomp.cfg.channel(1:5)] %demonstrate
> channel label mismatch
>
> ans =
>
>    'Lm'     'L1'
>    'LE1'    'L10'
>    'LE2'    'L11'
>    'LE3'    'L12'
>    'LD2'    'L13'
>
> the crucial line appears to be in componentanalysis line 220:
> cfg.channel = intersect(cfg.channel, cfg.topolabel);
>
> intersect sorts the outcome:
> >> a=randperm(10)
>
> a =
>
>     7     1     9     3     6     2     5     4    10     8
>
> >> b=randperm(10)
>
> b =
>
>     6     3     5     1     8     2    10     4     9     7
>
> >> intersect(a,b)
>
> ans =
>
>     1     2     3     4     5     6     7     8     9    10
>
> since i use all channels, simply replacing the label-field with the
> original label-field works for me.
>
> best,
> nathan
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.
>

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


From r.oostenveld at FCDONDERS.RU.NL  Wed Oct 28 14:17:33 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Wed, 28 Oct 2009 14:17:33 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <2173B9D8-114C-476C-9759-0D042CD2A9A7@gmail.com>
Message-ID: <WED.28.OCT.2009.141733.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi Marco

On 26 Oct 2009, at 20:04, Marco Rotonda wrote:
> so I could not do zvalue artifact on 2 channels only?

you can in principle compute the z-value, but I don't think that that
will help you much. If it were only a single channel, it would just be
a scaling of the data in that channel with the standard deviation.
Since you have two, it is also the accumulation of the z-value over
teh two channels.

However, I think that for your 2-channel data it is much more robust
to manually (i.e. visually) identify the artifact time-windows. You
can use the new DATABROWSER function for that.

best,
Robert

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


From marco.rotonda at GMAIL.COM  Wed Oct 28 14:21:36 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Wed, 28 Oct 2009 14:21:36 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <B50DE1AF-891D-4935-BF73-161C1D1C2A22@fcdonders.ru.nl>
Message-ID: <WED.28.OCT.2009.142136.0100.FIELDTRIP@NIC.SURFNET.NL>

thank you very much! I'll try...



On 28/ott/2009, at 14.17, Robert Oostenveld wrote:

> Hi Marco
>
> On 26 Oct 2009, at 20:04, Marco Rotonda wrote:
>> so I could not do zvalue artifact on 2 channels only?
>
> you can in principle compute the z-value, but I don't think that
> that will help you much. If it were only a single channel, it would
> just be a scaling of the data in that channel with the standard
> deviation. Since you have two, it is also the accumulation of the z-
> value over teh two channels.
>
> However, I think that for your 2-channel data it is much more robust
> to manually (i.e. visually) identify the artifact time-windows. You
> can use the new DATABROWSER function for that.
>
> best,
> Robert
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.

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


From wibral at BIC.UNI-FRANKFURT.DE  Fri Oct 30 10:36:05 2009
From: wibral at BIC.UNI-FRANKFURT.DE (Michael Wibral)
Date: Fri, 30 Oct 2009 10:36:05 +0100
Subject: PhD position in the areas of cognitive neuroscience an d
 neuroimaging
Message-ID: <FRI.30.OCT.2009.103605.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrip users,

the Institute for Medical Psychology in Frankfurt (Prof. Jochen Kaiser) is offering a PhD position in the areas of cognitive neuroscience and neuroimaging (see below). Please also feel free to forward this message to interested colleagues.

Best Regards,
Michael Wibral

Job offer: PhD Student in Cognitive Neuroscience
The Institute of Medical Psychology at the University of Frankfurt/Germany invites applications for a PhD student position in the areas of cognitive neuroscience and neuroimaging. Employment duration will initially be limited to 2 years but can be extended*.
The work focuses on investigating auditory and visual memory processing employing magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI). The successful candidate will plan and conduct MEG, fMRI and behavioral experiments, perform data analyses, and publish the results.
The Institute of Medical Psychology provides access to state of the art research facilities of the Frankfurt Brain Imaging Center including two 3-Tesla research scanners, a 275-channel MEG system, and a 128-channel EEG system. We offer excellent supervision by experienced researchers and possibilities for participation in training courses and international scientific conferences. Last but not least, we provide a positive and highly productive working atmosphere!
Candidates should have a background and hold a Masters Degree in neuroscience, psychology, biology, or a related field. The candidate should enjoy experimental neuroscience, interdisciplinary collaboration and should be motivated to acquire new skills and knowledge. Furthermore, the candidate should be fluent in English both orally and written. Experience with fMRI or EEG/MEG, and good knowledge of statistics and programming skills are highly desirable.
Applications of women are specifically invited. In case of similar qualifications, competence, and specific achievements, women will be considered on preferential terms within the framework of the legal possibilities. Disabled candidates with equivalent qualifications will be given preference.
Please send your application (deadline: 30th November, 2009) to: 
Prof. Jochen Kaiser
Institut für Medizinische Psychologie
Goethe-Universität
Heinrich-Hoffmann-Straße 10
D-60528 Frankfurt am Main
Germany
j.kaiser at med.uni-frankfurt.de
URL: http://www.imp.uni-frankfurt.de

*The limitation of the contract is based upon the regulations of the "Wissenschaftszeitvertragsgesetz" in conjunction with the "Hessisches Hochschulgesetz". The salary will be based on BAT or the tariffs for German civil service employees.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From knyazev at PHYSIOL.RU  Thu Oct  1 05:22:48 2009
From: knyazev at PHYSIOL.RU (knyazev)
Date: Thu, 1 Oct 2009 10:22:48 +0700
Subject: Reference electrode in lead field
Message-ID: <THU.1.OCT.2009.102248.0700.FIELDTRIP@NIC.SURFNET.NL>

I wonder how many electrodes should be considered enough to provide a
 representative sampling of the head surface? I remember reading somewhere
that using an average reference from too few channels distorts results
severely. May someone provide an appropriate citation on the topic? Thanks
in advance.

Gennady Knyazev

----- Original Message -----
From: "Joseph Dien" <jdien07 at MAC.COM>
To: <FIELDTRIP at NIC.SURFNET.NL>
Sent: Wednesday, September 30, 2009 9:10 AM
Subject: Re: [FIELDTRIP] Reference electrode in lead field


> The reasoning behind the average reference is that it is a physics
> principle that the sum of the voltages over an enclosed surface must
> equal zero.  To the extent that the electrode locations provide a
> representative even sampling of the head surface (an important caveat)
> the sum of the voltages therefore provides an estimate of the true  zero
> voltage.  The reason for using the average reference rather than  a single
> reference site is that using a reference site arbitrarily  defines that
> point as being zero voltage (which is to say, inactive),  which is not
> biophysically reasonable as there are no inactive sites  on the head (due
> to volume conduction).  Also, to clarify, an average  reference does not
> result in a reference-free solution since, as you  say, a voltage
> measurement is by definition a relative measure  (although ideally it
> should be relatively independent of the electrode  montage, given enough
> electrodes).  It's just that the comparison  "site", which is the zero
> equipotential line (as estimated by the  average reference computation),
> is a more biophysically reasonable one  (given enough recording sites)
> than arbitrarily picking a single fixed  electrode site as the reference.
>
> For an extended discussion of these issues, see:
>
> Dien, J. (1998). Issues in the application of the average reference:
> Review, critiques, and recommendations. Behavior Research Methods,
> Instruments, and Computers, 30(1), 34-43.
>
> Cheers!
>
> Joe
>
>
> On Sep 28, 2009, at 3:29 PM, Mark Drakesmith wrote:
>
>> Hi all
>>
>> I am experimenting with source reconstruction and was wondering how  a
>> reference electrode is defined in the lead field. Looking through  the
>> scripts it looks like the average reference is used, but this is  a
>> physical impossibility, as there must be a physical reference to  which
>> differences in electrical potential can be measured. The lead  field will
>> be differ depending on the location of the reference  electrode.
>>
>> Firstly, is there a way to specify a reference electrode when
>> constructing an EEG lead field in fieldtri p and not jsut use the
>> average reference.
>>
>> Secondly, looking through  the code for  'inf_medium_leadfield' (called
>> from prepare_leadfield ->  compute_leadfield -> eeg_leadfieldb), the
>> equations used for  calculating the lead field look a little strange:
>>
>> radius = position (vox) - position(elec)
>> R (resistivity?) = 4 x pi x conductivity x sum(radius^2)^(1.5)
>> lead field(vox,elec)=radius / R.
>>
>> Where the the exponential to 1.5 come from? Is there a reference to
>> somewhere where this method is used. I'm confused as to sure how  this
>> calculation works.
>>
>> Many thanks
>>
>> Mark
>>
>> --
>>
>> Mark Drakesmith
>> PhD Student
>>
>> Neuroscience and Aphasia Research Unit (NARU)
>> University of Manchester
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users  of
>> the FieldTrip  toolbox, to share experiences and to discuss new  ideas
>> for MEG and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/neuroimaging/fieldtrip.
>
>
> --------------------------------------------------------------------------------
>
> Joseph Dien,
> Senior Research Scientist
> Center for Advanced Study of Language
> University of Maryland
> 7005 52nd Avenue
> College Park, MD 20742-0025
>
> E-mail: jdien07 at mac.com
> Phone: 301-226-8848
> Fax: 301-226-8811
> http://homepage.mac.com/jdien07/
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/neuroimaging/fieldtrip.

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


From r.oostenveld at FCDONDERS.RU.NL  Thu Oct  1 12:38:46 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Thu, 1 Oct 2009 12:38:46 +0200
Subject: Reference electrode in lead field
In-Reply-To: <4AC10E84.50708@postgrad.manchester.ac.uk>
Message-ID: <THU.1.OCT.2009.123846.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Mark

On 28 Sep 2009, at 21:29, Mark Drakesmith wrote:
> I am experimenting with source reconstruction and was wondering how
> a reference electrode is defined in the lead field. Looking through
> the scripts it looks like the average reference is used, but this is
> a physical impossibility, as there must be a physical reference to
> which differences in electrical potential can be measured. The lead
> field will be differ depending on the location of the reference
> electrode.
>
> Firstly, is there a way to specify a reference electrode when
> constructing an EEG lead field in fieldtri p and not jsut use the
> average reference.

At the moment there is no other reference choise for EEG source
modelling than the average over all electrodes. However, more
elaborate bipolar referencing schemes are since recently needed for
out own research and for that we'll implement a very flexible
referencing scheme. You can expect that to be included in the
fieldtrip release in a month or so. However, the average reference
will remain the defaulty, as it has been shown in simulations to give
the most robust results (although it makes little difference). I don't
immediately know the reference for that, but you should be able to
find it in pubmed.

See also the reply from Burkhard and yesterdays message from Joseph.

> Secondly, looking through  the code for
> 'inf_medium_leadfield' (called from prepare_leadfield ->
> compute_leadfield -> eeg_leadfieldb), the equations used for
> calculating the lead field look a little strange:
>
> radius = position (vox) - position(elec)
> R (resistivity?) = 4 x pi x conductivity x sum(radius^2)^(1.5)
> lead field(vox,elec)=radius / R.
>
> Where the the exponential to 1.5 come from? Is there a reference to
> somewhere where this method is used. I'm confused as to sure how
> this calculation works.

R is not a single physical value, it is just a shord-hand notation for
one of the terms in the equation. See the reference to implemented
methods on the fieldtrip wiki for publication details.

best
Robert

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


From megjim1 at GMAIL.COM  Fri Oct  2 06:07:18 2009
From: megjim1 at GMAIL.COM (Jim Li)
Date: Fri, 2 Oct 2009 06:07:18 +0200
Subject: how to plot the direction and amplitude of the planar gradient
Message-ID: <FRI.2.OCT.2009.060718.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear all,

I want to view the direction and amplitude of the planar gradient  near each 
sensor location and create a plot like what's shown in the  attached file (more 
or less).  Is it possible to do it? If so, how?

Our MEG sensors are 248 axial gradiometers. After running "megplanar" I got 
A1_dH...A248_dH,A1_dV...A248_dV for my channels. If, say, in the plane 
tangential to a given channel we have the Horizontal (x axis) and Vertical (y 
axis) directions. Then for the channel of interest, say A1,  I can run sqrt
(A1_dH^2+A1_dV^2) to get the amplitude of the planar gradient, and I can 
run atan2(A1_dV,A1_dH)*180/pi) to get the angle between the field vector 
and x-axis. What I'm not sure  about is how fieldtrip defines the Horizontal (x 
axis) and Vertical (y axis) for each channel (in a plane tangential to that 
channel). So it's hard to create the plot I want...

Thanks a lot.

Jim

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From j.schoffelen at PSY.GLA.AC.UK  Fri Oct  2 11:46:25 2009
From: j.schoffelen at PSY.GLA.AC.UK (Jan-Mathijs Schoffelen)
Date: Fri, 2 Oct 2009 09:46:25 +0000
Subject: how to plot the direction and amplitude of the planar gradient
In-Reply-To: <LISTSERV%200910020607189850.0FFE@NIC.SURFNET.NL>
Message-ID: <FRI.2.OCT.2009.094625.0000.FIELDTRIP@NIC.SURFNET.NL>

Dear Jim,

As far as I know, this is not possible in fieldtrip ... yet. Do I read
between the lines that you wouldn't mind giving it a try? I agree that
it's a very useful way to visualize planar gradient data.
First of all, it is indeed important to know the local coordinate
system for each of the planar gradient channels. For megplanar I
always use the 'sincos' method. You can see how the coordinate system
is defined at line 419 and beyond. As far as I can see the local x-
axis is taken as the vector orthogonal to the plane defined by the
coil's orientation, and the vector [0 0 1] (which is the z-axis of the
coordinate system in which your sensors are defined; assuming your
sensors are defined in headspace, this one points to the top of the
head). The local z-axis is the vector perpendicular to the coil's
plane (=orientation), and the y-axis is perpendicular to the local xz-
plane.
I guess that for the other planarmethods it's possible to figure out
the local coordinate systems as well. One think which we could think
of, is to adjust megplanar such that the output data contains
information about the local x and y axes directly.
Of course, it would also be nice if a hypothetical plotting function
would work for data acquired with hardware planar gradiometers. Here
it is usually straightforward to reconstruct the local coordinate
systems from the header-information. Perhaps people working with
Elekta-systems already have some matlab code for the plotting...
Once the local coordinate systems are known (and the angles defined
accordingly), it should be possible to warp these values to a
headspace based coordinate system for plotting (in 3D, or in 2D after
an appropriate projection).

Best,

Jan-Mathijs

On 2 Oct 2009, at 04:07, Jim Li wrote:

> Dear all,
>
> I want to view the direction and amplitude of the planar gradient
> near each
> sensor location and create a plot like what's shown in the  attached
> file (more
> or less).  Is it possible to do it? If so, how?
>
> Our MEG sensors are 248 axial gradiometers. After running
> "megplanar" I got
> A1_dH...A248_dH,A1_dV...A248_dV for my channels. If, say, in the plane
> tangential to a given channel we have the Horizontal (x axis) and
> Vertical (y
> axis) directions. Then for the channel of interest, say A1,  I can
> run sqrt
> (A1_dH^2+A1_dV^2) to get the amplitude of the planar gradient, and I
> can
> run atan2(A1_dV,A1_dH)*180/pi) to get the angle between the field
> vector
> and x-axis. What I'm not sure  about is how fieldtrip defines the
> Horizontal (x
> axis) and Vertical (y axis) for each channel (in a plane tangential
> to that
> channel). So it's hard to create the plot I want...
>
> Thanks a lot.
>
> Jim
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.
> <PlotGoal.TIF>

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


From Nina.Kahlbrock at UNI-DUESSELDORF.DE  Fri Oct  2 09:54:44 2009
From: Nina.Kahlbrock at UNI-DUESSELDORF.DE (Nina)
Date: Fri, 2 Oct 2009 09:54:44 +0200
Subject: Freqanalysis - clusterthreshold and neighbourselection
Message-ID: <FRI.2.OCT.2009.095444.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear all,



I have two questions regarding clusteranalysis.



1.	When running 'freqstatistics' on time frequency/frequency data with
the method 'montecarlo' which clusterthreshold would you use? I would think
that with the data usually not being normally distributed you would use a
nonparametric threshold. However, the default value for clusterthreshold is
'parametric'.

a.	Is there documentation about what 'nonparametric_individual' and
'nonparametric_common' mean? If yes, where can I find it?

2.	I am looking at data from our old Neuromag 122 system and used the
function 'neighbourselection' to define neighbouring channels. When checking
what 'neighbourselection' did I found that the neighbours identified were
not only the sensors surrounding the sensor of interest, but also sensors
lying far away from it. Also, not all sensors surrounding the one of
interest were included as neighbours. I used the gradfile generated by
'mne2grad122' as cfg.grad and different values for neighbourdist (4 and 3).
Does anybody have a solution for this?



Thanks in advance for your help!



Nina




----------------------------------
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From e.maris at DONDERS.RU.NL  Fri Oct  2 11:51:06 2009
From: e.maris at DONDERS.RU.NL (Eric Maris)
Date: Fri, 2 Oct 2009 11:51:06 +0200
Subject: Freqanalysis - clusterthreshold and neighbourselection
In-Reply-To: <000901ca4335$9ad839f0$cd136386@VMED.UKD>
Message-ID: <FRI.2.OCT.2009.115106.0200.FIELDTRIP@NIC.SURFNET.NL>

Hi Nina,









I have two questions regarding clusteranalysis.



1.	When running 'freqstatistics' on time frequency/frequency data with
the method 'montecarlo' which clusterthreshold would you use? I would think
that with the data usually not being normally distributed you would use a
nonparametric threshold. However, the default value for clusterthreshold is
'parametric'.

a.	Is there documentation about what 'nonparametric_individual' and
'nonparametric_common' mean? If yes, where can I find it?



You can safely use the parametric threshold, regardless of the probability
distribution of your data. The reason is that this threshold only affects
the type of effect for which you test statistic is sensitive. The false
alarm rate does not depend on it. See Maris & Oostenveld (2007).



You only use the two other clusterthreshold options if you use a
non-normalized channel-level statistic. If you construct clusters by
thresholding channel-level T-statistics, go ahead with the parametric
threshold.





2.	I am looking at data from our old Neuromag 122 system and used the
function 'neighbourselection' to define neighbouring channels. When checking
what 'neighbourselection' did I found that the neighbours identified were
not only the sensors surrounding the sensor of interest, but also sensors
lying far away from it. Also, not all sensors surrounding the one of
interest were included as neighbours. I used the gradfile generated by
'mne2grad122' as cfg.grad and different values for neighbourdist (4 and 3).
Does anybody have a solution for this?





I guess Neuromag 122 system has planar gradiometers. For this sensor
configuration, the definition of a neighbourhood-metric requires some
thinking (because you are actually measuring spatial gradients with
different orientations). I contributed to a recent thread on the Fieldtrip
Discussion list about cluster-based permutation tests for the Vectorview
system. If I'm not mistaken, a scientist from an imaging center in Paris
initiated this thread. Have a look in the archive of the Fieldtrip
Discussion list (keywords: planar, cluster, Vectorview).





Good luck,











Thanks in advance for your help!



Nina



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

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

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

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


----------------------------------
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From r.oostenveld at FCDONDERS.RU.NL  Fri Oct  2 12:19:30 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 2 Oct 2009 12:19:30 +0200
Subject: Fwd: [FIELDTRIP] Reference electrode in lead field
Message-ID: <FRI.2.OCT.2009.121930.0200.FIELDTRIP@NIC.SURFNET.NL>

Begin forwarded message:

> From: "Dr. Georges Otte" <georges.otte at telenet.be>
> Date: 1 October 2009 13:49:13 GMT+02:00
> To: r.oostenveld at FCDONDERS.RU.NL
> Subject: reference
>
> ...
> I have followed the discussion on reference and already contacted
> Dien. I agree but what about non ERP data ? Phase information and
> coherence. Can we safely use the averaged common reference for that.
> Robert Thatcher (neuroguide) quoting rappelsberger is opoosed to it
> and shows in his neuroguide package that in small channel systems
> (19-22) a ACR scrambles phase information between channels.
>
> Sincerely
>
> Dr. Georges Otte
> P.C dr. Guislain instit
> Gent
> Belgium
>
>
> PS How can I get back on the list ?
>
> Ransscipt
> no problem!  I haven't been working in the frequency domain and am
> not very familiar with spectral analyses so I can't say.  Sorry!
>
> Joe
>
>
> On Sep 30, 2009, at 2:20 AM, Dr. Georges Otte wrote:
>
>
> If the reference is not close to zero (fi using an average reference
> on to low an electrodeset fi 19 ch with prefrontal channels likely
> to be contaminated by occasional quite lagre eye blink or eye
> movement artifacts) what would be the effect on phase calculations ?
> From point to point the reference value that is substracted from
> each channel would be different from zero. Would that not wreck
> havoc to interchannel phase information or post stimulus coherence
> mapping ? Untrusthworthy ?
>
> Same qyuestion: if people use PCA or ICA to eliminate these
> artifacts and inverse reconstruct their EEG, can they still rely on
> phase calculations without errors ?
>
> Sincerely,
>
> Georges Otte
>
> PS Sorry to mail You personally but for some reason (perhaps change
> of email adres or long period of inactivity ) I seem to be  cutoff
> from the fieldtrip listserv
>
>


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From r.oostenveld at FCDONDERS.RU.NL  Fri Oct  2 12:58:09 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Fri, 2 Oct 2009 12:58:09 +0200
Subject: Fwd: [FIELDTRIP] Reference electrode in lead field
In-Reply-To: <0EEFD9A0-12F8-4751-A69D-62D61655E8BD@FCDONDERS.RU.NL>
Message-ID: <FRI.2.OCT.2009.125809.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Georges,

Thanks for raising this very good point.

As discussed before, the choise of the reference is quite irrelevant
for most analysis that involve a **linear transformation** of the
data, such as the computation and visualisation of the topography of
an ERP. But for non-linear transformations, the reference becomes
relevant.

Consider a simple statistics example. If you want to show a
significant effect in an auditory evoked potential (AEP) given a
standard and deviant tone, the optimal reference is the mastoid, which
maximizes the potential at Cz. So Cz minus M1, or Cz minus (M1+M2)/2,
i.e. linked ears, results in the largest signal on Cz. Subsequently
you compute the average ERP in both conditions and you compute the
variance from which you can compute the standard-error of the mean.
Then you compute the t-value, i.e. the difference in means  divided by
the pooled standard-error of the mean. That is all for the values
recorded in the Cz channel. Had you referenced Cz to the tip of the
nose, then the spatial topography of the AEPs and the spatial
topography of the AEP difference would not be qualitatively different
(only a difference in the color scale, but that color scale is
arbitarry chosen anyway). But the noise over trials in the Cz AEP
would probably be larger for the nose reference than for the linked
ears  reference. That noise is expressed in the variance, which is in
the denominator of the t-value. So the t-value would be less. The t-
value would become even smaller for a Fz reference.

Another example: if you compute spectral power using a FFT or warevelt
transform, the power is expressed as a squared number. At the
reference electrode the power is zero (per definition), whereas around
the reference electrode it would increase. Had I measured oscillatory
activity from auditory cotrex using a linked-ears reference, I would
see the maximum over the vertex, i.e. Cz. For a nose reference, the
maximum in power probably still would be over the vertex. But had I
choosen Cz itself as the reference, then at the vertex there would be
no power any more. Or less extreme, had I choosen Fz as reference,
then probably the power would _not_ be maximal over the vertex any
more, but rather along the lower electrode rim (T3/T4 a.k.a. C7/C8 and
the lower occipital electrodes). The spatial topography of the power
would also be qualitatively different for the different references.
You can think of it like "pushing the maximum in the power topography
around over the scalp" by changing the reference. In general, the
power will be largest further away from the reference and small close
to the reference. Of course the true power distrubution depends on the
underlying source activity, so this is a bit of a simplification.

In both examples above a non-linear transformation on the data is
involved. Offline rereferencing is a linear transformation of the
data, i.e. it only involves the addition and/or subtraction of some
value. The computations above (t-value, spectral power) are non-
linear, and they are non commutative (see http://en.wikipedia.org/wiki/Commutativity)
. In short (1+1)^2 is not equal to (1)^2+(1)^2.

The estimation of the phase from a signal is also a non-linear
transformation of the signal. After decomposing it into a sine and
cosine contribution at a specific frequency (with the FFT), the sine
and cosine contribution are combined to get the phasae (i.e. using the
arctangent, or using the complex-number representation). Everything
that is subsequently derived from the phase is therefore also non-
linear. So coherence and phase-locking values will be qualitatively
different depending on the choise of reference. One cannot simply
first compute coherence, and then afterwards apply a re-referencing.

Note that the estimation of the source strength of a dipole using any
source reconstruction technique (dipole fitting, beamforming, minimum
norm linear estimation) is a linear operation. It assumes a linear
mixing model (data = leadfield*source + noise) and a linear unmixing
model. In the estimate of the "unmixing matrix" for most techniques
there is a particular choise for dealing with the noise (i.e.
beamformer: try to suppress it, dipole fit: try to minimize the
squared error). Dealing with the noise and with the fact that the
linear system is either underdetermined or overdetermined causes a non-
linear effect. So there is some influence of the choise of reference
on the result of the source estimate, but in general not too much. If
you take a really extreme referencing scheme, i.e. all bipolar
electrodes over the scalp from the front to the back (a so-called
banana montage) which is more sensitive for superficial sources, then
the source reconstruction will be biassed for these superficial
contributions. For a linked mastoid reference, the source
reconstruction will be slightly biased for deep sources. For an
average reference, there is no specific bias to be expected. Overall,
the effect of the reference electrode will be quite small, and be the
least biassed for an avereage reference. Therefore, the average
reference is de facto the default in all source reconstruction
packages for EEG (commercial and non-commercial).

best regards,
Robert

PS for people who want to see these effects: you can use
DIPOLESIMULATION to generate simulated raw data with added noise, and
pass that through PREPROCESSING to re-reference to a reference of
choise. Subsequently you try the various  analysies discussed above,
i.e. TIMELOCKANALYSIS, TIMELOCKSTATISTICS, FREQANALYSIS and
SOURCEANALYSIS or DIPOLEFITTING.


On 2 Oct 2009, at 12:19, Robert Oostenveld wrote:

>> From: "Dr. Georges Otte" <georges.otte at telenet.be>
>>
>> ...
>> I have followed the discussion on reference and already contacted
>> Dien. I agree but what about non ERP data ? Phase information and
>> coherence. Can we safely use the averaged common reference for
>> that. Robert Thatcher (neuroguide) quoting rappelsberger is opoosed
>> to it and shows in his neuroguide package that in small channel
>> systems (19-22) a ACR scrambles phase information between channels.

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


From megjim1 at GMAIL.COM  Mon Oct  5 15:26:56 2009
From: megjim1 at GMAIL.COM (Jim Li)
Date: Mon, 5 Oct 2009 15:26:56 +0200
Subject: how to plot the direction and amplitude of the planar gradient
Message-ID: <MON.5.OCT.2009.152656.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Jan-Mathijs ,

Thanks a lot for your information. I'll take a look at the script to see what I 
can do.


Cheers,

Jim

On Fri, 2 Oct 2009 09:46:25 +0000, Jan-Mathijs Schoffelen 
<j.schoffelen at PSY.GLA.AC.UK> wrote:

>Dear Jim,
>
>As far as I know, this is not possible in fieldtrip ... yet. Do I read
>between the lines that you wouldn't mind giving it a try? I agree that
>it's a very useful way to visualize planar gradient data.
>First of all, it is indeed important to know the local coordinate
>system for each of the planar gradient channels. For megplanar I
>always use the 'sincos' method. You can see how the coordinate system
>is defined at line 419 and beyond. As far as I can see the local x-
>axis is taken as the vector orthogonal to the plane defined by the
>coil's orientation, and the vector [0 0 1] (which is the z-axis of the
>coordinate system in which your sensors are defined; assuming your
>sensors are defined in headspace, this one points to the top of the
>head). The local z-axis is the vector perpendicular to the coil's
>plane (=orientation), and the y-axis is perpendicular to the local xz-
>plane.
>I guess that for the other planarmethods it's possible to figure out
>the local coordinate systems as well. One think which we could think
>of, is to adjust megplanar such that the output data contains
>information about the local x and y axes directly.
>Of course, it would also be nice if a hypothetical plotting function
>would work for data acquired with hardware planar gradiometers. Here
>it is usually straightforward to reconstruct the local coordinate
>systems from the header-information. Perhaps people working with
>Elekta-systems already have some matlab code for the plotting...
>Once the local coordinate systems are known (and the angles defined
>accordingly), it should be possible to warp these values to a
>headspace based coordinate system for plotting (in 3D, or in 2D after
>an appropriate projection).
>
>Best,
>
>Jan-Mathijs
>
>On 2 Oct 2009, at 04:07, Jim Li wrote:
>
>> Dear all,
>>
>> I want to view the direction and amplitude of the planar gradient
>> near each
>> sensor location and create a plot like what's shown in the  attached
>> file (more
>> or less).  Is it possible to do it? If so, how?
>>
>> Our MEG sensors are 248 axial gradiometers. After running
>> "megplanar" I got
>> A1_dH...A248_dH,A1_dV...A248_dV for my channels. If, say, in the plane
>> tangential to a given channel we have the Horizontal (x axis) and
>> Vertical (y
>> axis) directions. Then for the channel of interest, say A1,  I can
>> run sqrt
>> (A1_dH^2+A1_dV^2) to get the amplitude of the planar gradient, and I
>> can
>> run atan2(A1_dV,A1_dH)*180/pi) to get the angle between the field
>> vector
>> and x-axis. What I'm not sure  about is how fieldtrip defines the
>> Horizontal (x
>> axis) and Vertical (y axis) for each channel (in a plane tangential
>> to that
>> channel). So it's hard to create the plot I want...
>>
>> Thanks a lot.
>>
>> Jim
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also 
http://listserv.surfnet.nl/archives/fieldtrip.html
>>  and http://www.ru.nl/neuroimaging/fieldtrip.
>> <PlotGoal.TIF>
>
>----------------------------------
>The aim of this list is to facilitate the discussion between users of the 
FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and 
EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and 
http://www.ru.nl/neuroimaging/fieldtrip.

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


From Juergen.Fell at UKB.UNI-BONN.DE  Wed Oct  7 10:14:30 2009
From: Juergen.Fell at UKB.UNI-BONN.DE (Juergen Fell)
Date: Wed, 7 Oct 2009 10:14:30 +0200
Subject: complex wavelet output
Message-ID: <WED.7.OCT.2009.101430.0200.FIELDTRIP@NIC.SURFNET.NL>



Dear fieldtrip users:

I've just started digging into fieldtrip and came across the following
question: is it possible to obtain the complex output of the continuous
wavelet transform, i.e. the original wavelet-transformed complex signal
(instead of power and/or cross-spectral density)?

Any help would be greatly appreciated.

Juergen.

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From pacodiaz at UB.EDU  Wed Oct  7 10:59:26 2009
From: pacodiaz at UB.EDU (=?ISO-8859-1?Q?Paco_D=EDaz?=)
Date: Wed, 7 Oct 2009 10:59:26 +0200
Subject: complex wavelet output
In-Reply-To: <OF86C3BE7E.9A337D32-ONC1257648.002C950C-C1257648.002D7751@ukb.uni-bonn.de>
Message-ID: <WED.7.OCT.2009.105926.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Juergen,

   I made it by using "freqanalysis" with (basically)

cfg.output='pow'
cfg.method='tfr'

   and then you have to edit the freqanalysis_tfr function and suppress
the following lines:

   cTmp = (2*abs(cTmp)/data.fsample).^2;

in the main body of the function, and this one:

   y = (2*abs(y)/Fs).^2;

in the SUBFUNCTION for waveletanalysis.

Doing this you will avoid the power calculation and will end up with the
complex morlet coefficients.

Hope this helps,
F.J.

Juergen Fell escribió:
>
> Dear fieldtrip users:
>
> I've just started digging into fieldtrip and came across the following
> question: is it possible to obtain the complex output of the
> continuous wavelet transform, i.e. the original wavelet-transformed
> complex signal (instead of power and/or cross-spectral density)?
>
> Any help would be greatly appreciated.
>
> Juergen.
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis.
>
> http://listserv.surfnet.nl/archives/fieldtrip.html
>
> http://www.ru.nl/fcdonders/fieldtrip/
>

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


From Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE  Wed Oct  7 11:24:36 2009
From: Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE (Hanneke Van Dijk)
Date: Wed, 7 Oct 2009 11:24:36 +0200
Subject: AW: [FIELDTRIP] complex wavelet output
Message-ID: <WED.7.OCT.2009.112436.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Juergen,

As far as I can see, you can specify cfg.output = 'fourier' for the cfg.method = 'mtmconvol' when you want to have a time axis as well (it's also possible for 'mtmfft'). It will give you the fourierspectrum. You can set the parameters of mtmconvol such that it operates simmilar to a wavelet transform as you can see on this website:

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

An example of the parameters could be:

cfg = [];
cfg.output     = 'fourier';
cfg.channel    = 'MEG';
cfg.method     = 'mtmconvol';
cfg.taper      = 'dpss';        % sleppian taper but you can use different tapers/windows here.
cfg.foi        = 1:2:30;        % frequencies of interest.
cfg.t_ftimwin  = 5./cfg.foi;    % the window length is 5 cycles of the specified frequency long.
cfg.tapsmofrq  = 0.4 *cfg.foi;  % frequency smoothing of +/- 0.4*the specified frequency.
cfg.toi        = -0.5:0.05:1.5; % time of interest.
cfg.pad        = 'maxperlen';  
TFRmult = freqanalysis(cfg, dataFIC);

Hope it helps!

Yours,

Hanneke


-----Ursprüngliche Nachricht-----
Von: FieldTrip discussion list im Auftrag von Juergen Fell
Gesendet: Mi 07.10.2009 10:14
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: [FIELDTRIP] complex wavelet output
 


Dear fieldtrip users:

I've just started digging into fieldtrip and came across the following
question: is it possible to obtain the complex output of the continuous
wavelet transform, i.e. the original wavelet-transformed complex signal
(instead of power and/or cross-spectral density)?

Any help would be greatly appreciated.

Juergen.

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


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


From brian.roach at YALE.EDU  Wed Oct  7 22:10:52 2009
From: brian.roach at YALE.EDU (Brian Roach)
Date: Wed, 7 Oct 2009 13:10:52 -0700
Subject: AW: [FIELDTRIP] complex wavelet output
In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B0F34E5@Mail2-UKD.VMED.UKD>
Message-ID: <WED.7.OCT.2009.131052.0700.FIELDTRIP@NIC.SURFNET.NL>

Hi Juergen,

You can also use cfg.method = 'wltconvol', but you need to change a line
of code in the freqanalysis_wltconvol.m script.  When you use
cfg.keeptrials = 'yes', it will normally return single trial power data
(not complex numbers), but in the script search for:

elseif keep == 2
            powdum = XYZ ;

make sure that XYZ does not have any squaring or abs calls around it.
These change complex numbers to real ones.

Brian
Hanneke Van Dijk wrote:
> Dear Juergen,
>
> As far as I can see, you can specify cfg.output = 'fourier' for the cfg.method = 'mtmconvol' when you want to have a time axis as well (it's also possible for 'mtmfft'). It will give you the fourierspectrum. You can set the parameters of mtmconvol such that it operates simmilar to a wavelet transform as you can see on this website:
>
> http://fieldtrip.fcdonders.nl/tutorial/timefrequencyanalysis
>
> An example of the parameters could be:
>
> cfg = [];
> cfg.output     = 'fourier';
> cfg.channel    = 'MEG';
> cfg.method     = 'mtmconvol';
> cfg.taper      = 'dpss';        % sleppian taper but you can use different tapers/windows here.
> cfg.foi        = 1:2:30;        % frequencies of interest.
> cfg.t_ftimwin  = 5./cfg.foi;    % the window length is 5 cycles of the specified frequency long.
> cfg.tapsmofrq  = 0.4 *cfg.foi;  % frequency smoothing of +/- 0.4*the specified frequency.
> cfg.toi        = -0.5:0.05:1.5; % time of interest.
> cfg.pad        = 'maxperlen';
> TFRmult = freqanalysis(cfg, dataFIC);
>
> Hope it helps!
>
> Yours,
>
> Hanneke
>
>
> -----Ursprüngliche Nachricht-----
> Von: FieldTrip discussion list im Auftrag von Juergen Fell
> Gesendet: Mi 07.10.2009 10:14
> An: FIELDTRIP at NIC.SURFNET.NL
> Betreff: [FIELDTRIP] complex wavelet output
>
>
>
> Dear fieldtrip users:
>
> I've just started digging into fieldtrip and came across the following
> question: is it possible to obtain the complex output of the continuous
> wavelet transform, i.e. the original wavelet-transformed complex signal
> (instead of power and/or cross-spectral density)?
>
> Any help would be greatly appreciated.
>
> Juergen.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>
>

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


From julian.keil at GMAIL.COM  Fri Oct  9 14:04:08 2009
From: julian.keil at GMAIL.COM (Julian Keil)
Date: Fri, 9 Oct 2009 14:04:08 +0200
Subject: Freqstatistics plv
Message-ID: <FRI.9.OCT.2009.140408.0200.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrippers,

I have a question regarding the use of freqstatistics and phase
locking values:
Is it possible to use freqstatistics to compare phase-locking values?
If not, is there any other option to compare plv between conditions

I use the following code:

cfg=[];
cfg.statistic='depsamplesT';
cfg.method='analytic';
cfg.parameter='plvspctrm';
cfg.channel={'all'};  % 5 channels -> 10 channelcmb
cfg.tail=0;
cfg.alpha=0.05;
cfg.ivar=2;
cfg.uvar=1;
cfg.frequency   = [10 50];

cfg.design=[1:12,1:12;ones(1,12),ones(1,12)*2];

[stats_fus_vi]=freqstatistics(cfg,plv_fu{:},plv_vi{:});

I get the information:
renaming parameter 'plvspctrm' into 'powspctrm'
selected 5 channels
selected 201 time bins
selected 21 frequency bins

As I don't get any error message, I assume this works fine so far but
I'm confused about what is computed here: Is "powspctrm" used instead
of "plvspctrm" (i.e. the test is computed between power estimates
instead of phase locking values)? Why are only 5 channels selected
instead of the 10 combinations?

I already tried renaming "plvspctrm" and "labelcmb" to "powspctrm" and
"label" but then I get an error message, as freqstatistics selects 20
channels.

Thanks a lot for any advise

Julian


Dipl. Psych. Julian Keil

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

Tel: ++49 - (0)7531 - 88 42 50
Fax: ++49 - (0)7531 - 88 28 91
Email: julian.keil at uni-konstanz.de
Homepage: http://www.uni-konstanz.de/obob








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From julian.keil at GMAIL.COM  Fri Oct  9 14:49:37 2009
From: julian.keil at GMAIL.COM (Julian Keil)
Date: Fri, 9 Oct 2009 14:49:37 +0200
Subject: Freqstatistics plv -> solved
Message-ID: <FRI.9.OCT.2009.144937.0200.FIELDTRIP@NIC.SURFNET.NL>

hi,

sorry for your time, problem solved: creating a new label-structure
worked.

greetings

Julian

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


From tobias.donner at NYU.EDU  Tue Oct 13 15:13:11 2009
From: tobias.donner at NYU.EDU (Tobias Donner)
Date: Tue, 13 Oct 2009 15:13:11 +0200
Subject: PhD position in Cognitive Neuroscience in Amsterdam
Message-ID: <TUE.13.OCT.2009.151311.0200.FIELDTRIP@NIC.SURFNET.NL>

The Psychology Department of the University of Amsterdam is currently
hiring a PhD student to study the neural basis of visual awareness
and visual decision-making in humans. The project is a collaboration
of Tobias H. Donner and Victor A.F. Lamme. We plan to combine visual
psychophysics, neuroimaging (MEG, fMRI), and pharmacological
manipulation to (i) characterize decision-related feedback signals in
human early visual cortex, (ii) localize the source of these signals
in the brain, and (iii) study their role in shaping the contents of
perception.

We are looking for highly motivated candidates with a strong interest
in Cognitive Neuroscience and interdisciplinary research. Candidates
must have an MA (or equivalent) in Cognitive Science, Neuroscience,
Psychology, Physics, or Engineering, or an MD. Experience in computer
programming (e.g., MATLAB) and in EEG/MEG and/or fMRI will be a
significant plus.

Further information about the post and how to apply is available at:
http://www.uva.nl/vacatures/vacatures.cfm/E19032FD-1321-
B0BE-685E8B8E55A5AD26

Inquiries are welcomed. Please contact Tobias Donner: t.h.donner at uva.nl
Application deadline: November 1, 2009.

----------------------------------
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From Sara.GonzalezAndino at HCUGE.CH  Thu Oct 15 10:21:58 2009
From: Sara.GonzalezAndino at HCUGE.CH (GONZALEZ ANDINO Sara)
Date: Thu, 15 Oct 2009 10:21:58 +0200
Subject: TR: paper announcement
Message-ID: <THU.15.OCT.2009.102158.0200.FIELDTRIP@NIC.SURFNET.NL>

-----Message d'origine-----
De : GRAVE DE PERALTA Rolando 
Envoyé : jeudi, 15. octobre 2009 10:19

Objet : paper announcement

Dear Colleagues,

We would like to call your attention to the recent publication:
http://dx.doi.org/10.1016/j.jphysparis.2009.07.004 
that, among other things,  provide the theoretical and experimental evidences to refute claims that Very High Frequencies are not measurable at the scalp surface. 


Electrical neuroimaging of single trials to identify laterality and brain regions involved in finger movements 

by:
Rolando Grave de Peralta, Theodor Landis and Sara Gonzalez Andino

Abstract
Thought-controlled neuroprostheses could allow paralyzed patients to interact with the external world using brain waves. Thus far, the fastest and more accurate control of neuroprostheses is achieved through direct recordings of neural activity [Nicolelis, M.A., 2001. Actions from thoughts. Nature 409, 403-407; Donoghue, J.P., 2002. Connecting cortex to machines: recent advances in brain interfaces. Nat. Neurosci. 5 (Suppl.), 1085-1088]. However, invasive recordings have inherent medical risks. Here we discuss some approaches that could enhance the speed and accuracy of non-invasive devices, namely, (1) enlarging the spectral analysis to include higher frequency oscillations, able to transmit substantial information over short analysis windows; (2) using spectral analysis procedures that minimize the variance of the estimates; and (3) transforming EEG recorded activity into local field potential estimates (eLFP). Theoretical and experimental arguments are used to explain why it is erroneous to think that scalp EEG cannot sense high frequency oscillations and how this might hinders further developments. We further illustrate how non-invasive eLFPs derived from the scalp-recorded electroencephalogram (EEG) can be combined with robust, broad band spectral analysis to accurately detect (off-line) the laterality of upcoming hand movements. Interestingly, the use of pattern recognition to select the brain voxels differentially engaged by the explored tasks leads to sound neural activation images. Consequently, our results indicate that both research lines, i.e., neuroprosthetics and electrical neuroimaging, might effectively benefit from their mutual interaction.



regards
rolando
www.electrical-neuroimaging.ch 

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From fredericroux at HOTMAIL.DE  Fri Oct 16 12:26:29 2009
From: fredericroux at HOTMAIL.DE (Frederic Roux)
Date: Fri, 16 Oct 2009 12:26:29 +0200
Subject: error using freqanalysis_mtmfft
Message-ID: <FRI.16.OCT.2009.122629.0200.FIELDTRIP@NIC.SURFNET.NL>


Hi everyone,
 
I am using freqanalysis with the following cfg structure
 
cfg             = [];
cfg.output      = 'pow';
cfg.channel     = {'MEG'};
cfg.method      = 'mtmfft';
cfg.taper       = 'dpss';
cfg.foi         = 1:200; 
cfg.t_ftimwin   = .5*ones(1,length(cfg.foi));
cfg.toi         = [-1.5:.5:2.5]; 
cfg.tapsmofrq   = 5.*ones(1,length(cfg.foi)); 
cfg.pad         = 'maxperlen';
 
and I get the following error message
 
??? Error using ==> dpss
The Time-bandwidth product NW must be a scalar.
 
Error in ==> freqanalysis_mtmfft>double_dpss at 594
tap = dpss(double(a), double(b), varargin{:});
 
Error in ==> freqanalysis_mtmfft at 421
    tap =
double_dpss(numdatbns,numdatbns*(cfg.tapsmofrq./data.fsample))';
 
Error in ==> freqanalysis at 192


K should be equal to 2*(.5*5)-1 = 4 tapers so I don't really understand what's going wrong here.
And before diving into the code I thought that maybe someone could provide me with a simple answer/solution. 
Any help with this would be greatly apreciated!
 
Frederic
  		 	   		  
_________________________________________________________________
http://redirect.gimas.net/?n=M0910xHerbstmode2
So gehst du mir nicht vor die Tür! Herbsttrends entdecken
----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From hungptit at GMAIL.COM  Sat Oct 24 08:39:35 2009
From: hungptit at GMAIL.COM (Hung Dang)
Date: Sat, 24 Oct 2009 00:39:35 -0600
Subject: How to generate the EEG background noise and interference
In-Reply-To: <SNT107-W7ED61CCCB8F2C15B0C398B7C40@phx.gbl>
Message-ID: <SAT.24.OCT.2009.003935.0600.FIELDTRIP@NIC.SURFNET.NL>

Dear all,
Many researchers have been using Gaussian white noise as the additive
noise for the  MEG/EEG signals to evaluate their inverse algorithm,
however, this assumption may not true for the real MEG/EEG signals. I
try to google for a while and have not find any good reference.
So my question is how could we generate a more realistic MEG/EEG signal,
interference, and noise to obtain a better judgment of how good are
inverse solutions?

Have a nice weekend
Hung

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


From v.litvak at ION.UCL.AC.UK  Sat Oct 24 10:05:25 2009
From: v.litvak at ION.UCL.AC.UK (Vladimir Litvak)
Date: Sat, 24 Oct 2009 09:05:25 +0100
Subject: How to generate the EEG background noise and interference
In-Reply-To: <4AE2A127.905@gmail.com>
Message-ID: <SAT.24.OCT.2009.090525.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Hung,

A simple and convincing thing to do would be to combine simulated data
with real data. For instance if you are talking about ERP, you can add
your simulated responses  to a real recording at times random with
respect to the original triggers. Then you will get your simulated ERP
with noise as real as it gets. By controlling the relative scaling of
the real and simulated data you can test different SNRs.

Best,

Vladimir

On Sat, Oct 24, 2009 at 7:39 AM, Hung Dang <hungptit at gmail.com> wrote:
> Dear all,
> Many researchers have been using Gaussian white noise as the additive
> noise for the  MEG/EEG signals to evaluate their inverse algorithm,
> however, this assumption may not true for the real MEG/EEG signals. I
> try to google for a while and have not find any good reference.
> So my question is how could we generate a more realistic MEG/EEG signal,
> interference, and noise to obtain a better judgment of how good are
> inverse solutions?
>
> Have a nice weekend
> Hung
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>
>

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


From hungptit at GMAIL.COM  Sat Oct 24 19:53:20 2009
From: hungptit at GMAIL.COM (Hung Dang)
Date: Sat, 24 Oct 2009 11:53:20 -0600
Subject: How to generate the EEG background noise and interference
In-Reply-To: <e1e7c57c0910240105r5d5b683fh6e3bb56cac175a8f@mail.gmail.com>
Message-ID: <SAT.24.OCT.2009.115320.0600.FIELDTRIP@NIC.SURFNET.NL>

Dear Vladimir,
Thanks a lot for an insightful and quick reply. That will definitely
help me a lot for my simulation studies.

Regards,
Hung



Vladimir Litvak wrote:
> Dear Hung,
>
> A simple and convincing thing to do would be to combine simulated data
> with real data. For instance if you are talking about ERP, you can add
> your simulated responses  to a real recording at times random with
> respect to the original triggers. Then you will get your simulated ERP
> with noise as real as it gets. By controlling the relative scaling of
> the real and simulated data you can test different SNRs.
>
> Best,
>
> Vladimir
>
> On Sat, Oct 24, 2009 at 7:39 AM, Hung Dang <hungptit at gmail.com> wrote:
>
>> Dear all,
>> Many researchers have been using Gaussian white noise as the additive
>> noise for the  MEG/EEG signals to evaluate their inverse algorithm,
>> however, this assumption may not true for the real MEG/EEG signals. I
>> try to google for a while and have not find any good reference.
>> So my question is how could we generate a more realistic MEG/EEG signal,
>> interference, and noise to obtain a better judgment of how good are
>> inverse solutions?
>>
>> Have a nice weekend
>> Hung
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>>
>>
>>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
>

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


From marco.rotonda at GMAIL.COM  Mon Oct 26 14:42:28 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Mon, 26 Oct 2009 14:42:28 +0100
Subject: importing raw data
Message-ID: <MON.26.OCT.2009.144228.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi there,
I'm trying to import a raw data file to perform artifacting.
The file I have is quite simple: 2 channels and only data sampled at 256.
I did the following operations:

FF = (csvread('FF.txt', 2, 0))';
data.trial{1} = FF;
data.time{1} = linspace(0,180,46080);
data.fsample=256;
data.label={'F3';'F4'};
data.cfg.trl=[1,46080,0];
cfg.continuous='yes';
cfg.trl=[1,46080,0];
cfg.channel={'F3';'F4'};
cfg2=artifact_eog(cfg,data);

but then I have the following message error:

??? Error using ==> artifact_zvalue at 202
no channels selected

Error in ==> artifact_eog at 179
   [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
   data);

What I miss?

in artifact_zvalue from 197:

cfg.artfctdef.zvalue.channel =
channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
sgnind        = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
numsgn        = length(sgnind);

if numsgn<1
 error('no channels selected');
else
 fprintf('searching for artifacts in %d channels\n', numsgn);
end


So I added:

cfg.artfctdef.zvalue.channel={'F3';'F4'};

but I get the same error
it seems that I need the header... but I have not.
is it?

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


From P.Toffanin at RUG.NL  Mon Oct 26 15:08:43 2009
From: P.Toffanin at RUG.NL (Paolo Toffanin)
Date: Mon, 26 Oct 2009 15:08:43 +0100
Subject: importing raw data
In-Reply-To: <LISTSERV%200910261442283870.8413@NIC.SURFNET.NL>
Message-ID: <MON.26.OCT.2009.150843.0100.FIELDTRIP@NIC.SURFNET.NL>

Did you try including also eye channels into the analysis?

Paolo

On Monday 26 October 2009 02:42:28 pm Marco Rotonda wrote:
> Hi there,
> I'm trying to import a raw data file to perform artifacting.
> The file I have is quite simple: 2 channels and only data sampled at 256.
> I did the following operations:
>
> FF = (csvread('FF.txt', 2, 0))';
> data.trial{1} = FF;
> data.time{1} = linspace(0,180,46080);
> data.fsample=256;
> data.label={'F3';'F4'};
> data.cfg.trl=[1,46080,0];
> cfg.continuous='yes';
> cfg.trl=[1,46080,0];
> cfg.channel={'F3';'F4'};
> cfg2=artifact_eog(cfg,data);
>
> but then I have the following message error:
>
> ??? Error using ==> artifact_zvalue at 202
> no channels selected
>
> Error in ==> artifact_eog at 179
>    [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
>    data);
>
> What I miss?
>
> in artifact_zvalue from 197:
>
> cfg.artfctdef.zvalue.channel =
> channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
> sgnind        = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
> numsgn        = length(sgnind);
>
> if numsgn<1
>  error('no channels selected');
> else
>  fprintf('searching for artifacts in %d channels\n', numsgn);
> end
>
>
> So I added:
>
> cfg.artfctdef.zvalue.channel={'F3';'F4'};
>
> but I get the same error
> it seems that I need the header... but I have not.
> is it?
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/neuroimaging/fieldtrip.


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From marco.rotonda at GMAIL.COM  Mon Oct 26 15:15:26 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Mon, 26 Oct 2009 15:15:26 +0100
Subject: importing raw data
In-Reply-To: <200910261508.43870.p233228@rug.nl>
Message-ID: <MON.26.OCT.2009.151526.0100.FIELDTRIP@NIC.SURFNET.NL>

nope... only 2 channels...


On 26/ott/2009, at 15.08, Paolo Toffanin wrote:

> Did you try including also eye channels into the analysis?
>
> Paolo
>
> On Monday 26 October 2009 02:42:28 pm Marco Rotonda wrote:
> > Hi there,
> > I'm trying to import a raw data file to perform artifacting.
> > The file I have is quite simple: 2 channels and only data sampled
> at 256.
> > I did the following operations:
> >
> > FF = (csvread('FF.txt', 2, 0))';
> > data.trial{1} = FF;
> > data.time{1} = linspace(0,180,46080);
> > data.fsample=256;
> > data.label={'F3';'F4'};
> > data.cfg.trl=[1,46080,0];
> > cfg.continuous='yes';
> > cfg.trl=[1,46080,0];
> > cfg.channel={'F3';'F4'};
> > cfg2=artifact_eog(cfg,data);
> >
> > but then I have the following message error:
> >
> > ??? Error using ==> artifact_zvalue at 202
> > no channels selected
> >
> > Error in ==> artifact_eog at 179
> > [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
> > data);
> >
> > What I miss?
> >
> > in artifact_zvalue from 197:
> >
> > cfg.artfctdef.zvalue.channel =
> > channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
> > sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
> > numsgn = length(sgnind);
> >
> > if numsgn<1
> > error('no channels selected');
> > else
> > fprintf('searching for artifacts in %d channels\n', numsgn);
> > end
> >
> >
> > So I added:
> >
> > cfg.artfctdef.zvalue.channel={'F3';'F4'};
> >
> > but I get the same error
> > it seems that I need the header... but I have not.
> > is it?
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of the
> > FieldTrip toolbox, to share experiences and to discuss new ideas
> for MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/neuroimaging/fieldtrip.
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
>   http://listserv.surfnet.nl/archives/fieldtrip.html
>
>   http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From Nina.Kahlbrock at UNI-DUESSELDORF.DE  Mon Oct 26 15:18:42 2009
From: Nina.Kahlbrock at UNI-DUESSELDORF.DE (Nina)
Date: Mon, 26 Oct 2009 15:18:42 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <200910261508.43870.p233228@rug.nl>
Message-ID: <MON.26.OCT.2009.151842.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi Marco,

you might want to try:



cfg.artfctdef.eog.channel = {your EOG channel(s)};



Nina



  _____

Von: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag
von Paolo Toffanin
Gesendet: Montag, 26. Oktober 2009 15:09
An: FIELDTRIP at NIC.SURFNET.NL
Betreff: Re: [FIELDTRIP] importing raw data



Did you try including also eye channels into the analysis?





Paolo





On Monday 26 October 2009 02:42:28 pm Marco Rotonda wrote:
> Hi there,
> I'm trying to import a raw data file to perform artifacting.
> The file I have is quite simple: 2 channels and only data sampled at 256.
> I did the following operations:
>
> FF = (csvread('FF.txt', 2, 0))';
> data.trial{1} = FF;
> data.time{1} = linspace(0,180,46080);
> data.fsample=256;
> data.label={'F3';'F4'};
> data.cfg.trl=[1,46080,0];
> cfg.continuous='yes';
> cfg.trl=[1,46080,0];
> cfg.channel={'F3';'F4'};
> cfg2=artifact_eog(cfg,data);
>
> but then I have the following message error:
>
> ??? Error using ==> artifact_zvalue at 202
> no channels selected
>
> Error in ==> artifact_eog at 179
> [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
> data);
>
> What I miss?
>
> in artifact_zvalue from 197:
>
> cfg.artfctdef.zvalue.channel =
> channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
> sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
> numsgn = length(sgnind);
>
> if numsgn<1
> error('no channels selected');
> else
> fprintf('searching for artifacts in %d channels\n', numsgn);
> end
>
>
> So I added:
>
> cfg.artfctdef.zvalue.channel={'F3';'F4'};
>
> but I get the same error
> it seems that I need the header... but I have not.
> is it?
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/neuroimaging/fieldtrip.





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

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

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

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


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From marco.rotonda at GMAIL.COM  Mon Oct 26 17:20:12 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Mon, 26 Oct 2009 17:20:12 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <001a01ca5647$38b652a0$cd136386@VMED.UKD>
Message-ID: <MON.26.OCT.2009.172012.0100.FIELDTRIP@NIC.SURFNET.NL>

So I need eog channels other than the 2 I have?


On 26/ott/2009, at 15.18, Nina wrote:

> Hi Marco,
> you might want to try:
>
> cfg.artfctdef.eog.channel
> = {your EOG channel(s)};
>
> Nina
>
> Von: FieldTrip
> discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von
> Paolo Toffanin
>
> Gesendet: Montag, 26. Oktober 2009
> 15:09
>
> An: FIELDTRIP at NIC.SURFNET.NL
>
> Betreff: Re: [FIELDTRIP] importing
> raw data
>
> Did you try including also eye channels into the
> analysis?
>
>
>
>
> Paolo
>
>
>
>
> On Monday 26 October 2009 02:42:28 pm Marco Rotonda
> wrote:
>
> > Hi there,
>
> > I'm trying to import a raw data file to perform artifacting.
>
> > The file I have is quite simple: 2 channels and only data sampled
> at 256.
>
> > I did the following operations:
>
> >
>
> > FF = (csvread('FF.txt', 2, 0))';
>
> > data.trial{1} = FF;
>
> > data.time{1} = linspace(0,180,46080);
>
> > data.fsample=256;
>
> > data.label={'F3';'F4'};
>
> > data.cfg.trl=[1,46080,0];
>
> > cfg.continuous='yes';
>
> > cfg.trl=[1,46080,0];
>
> > cfg.channel={'F3';'F4'};
>
> > cfg2=artifact_eog(cfg,data);
>
> >
>
> > but then I have the following message error:
>
> >
>
> > ??? Error using ==> artifact_zvalue at 202
>
> > no channels selected
>
> >
>
> > Error in ==> artifact_eog at 179
>
> > [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
>
> > data);
>
> >
>
> > What I miss?
>
> >
>
> > in artifact_zvalue from 197:
>
> >
>
> > cfg.artfctdef.zvalue.channel =
>
> > channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
>
> > sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
>
> > numsgn = length(sgnind);
>
> >
>
> > if numsgn<1
>
> > error('no channels selected');
>
> > else
>
> > fprintf('searching for artifacts in %d channels\n', numsgn);
>
> > end
>
> >
>
> >
>
> > So I added:
>
> >
>
> > cfg.artfctdef.zvalue.channel={'F3';'F4'};
>
> >
>
> > but I get the same error
>
> > it seems that I need the header... but I have not.
>
> > is it?
>
> >
>
> > ----------------------------------
>
> > The aim of this list is to facilitate the discussion between users
> of the
>
> > FieldTrip toolbox, to share experiences and to discuss new ideas
> for MEG
>
> > and EEG analysis. See also
>
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
>
> > http://www.ru.nl/neuroimaging/fieldtrip.
>
>
>
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
>   http://listserv.surfnet.nl/archives/fieldtrip.html
>
>   http://www.ru.nl/fcdonders/fieldtrip/
>
> ----------------------------------
>
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis.
>
>   http://listserv.surfnet.nl/archives/fieldtrip.html
>
>   http://www.ru.nl/fcdonders/fieldtrip/
>


----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.
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From P.Toffanin at RUG.NL  Mon Oct 26 20:02:06 2009
From: P.Toffanin at RUG.NL (Paolo Toffanin)
Date: Mon, 26 Oct 2009 21:02:06 +0200
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <A75DF2B4-3129-41CE-9EB4-E4BBC1784BB0@gmail.com>
Message-ID: <MON.26.OCT.2009.210206.0200.FIELDTRIP@NIC.SURFNET.NL>

That's the idea.

Paolo

On Mon, 26 Oct 2009 17:20:12 +0100
  Marco Rotonda <marco.rotonda at GMAIL.COM> wrote:
> So I need eog channels other than the 2 I have?
>
>
> On 26/ott/2009, at 15.18, Nina wrote:
>
>> Hi Marco,
>> you might want to try:
>>
>> cfg.artfctdef.eog.channel
>> = {your EOG channel(s)};
>>
>> Nina
>>
>> Von: FieldTrip
>> discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von
>> Paolo Toffanin
>>
>> Gesendet: Montag, 26. Oktober 2009
>> 15:09
>>
>> An: FIELDTRIP at NIC.SURFNET.NL
>>
>> Betreff: Re: [FIELDTRIP] importing
>> raw data
>>
>> Did you try including also eye channels into the
>> analysis?
>>
>>
>>
>>
>> Paolo
>>
>>
>>
>>
>> On Monday 26 October 2009 02:42:28 pm Marco Rotonda
>> wrote:
>>
>> > Hi there,
>>
>> > I'm trying to import a raw data file to perform artifacting.
>>
>> > The file I have is quite simple: 2 channels and only data sampled
>>
>> at 256.
>>
>> > I did the following operations:
>>
>> >
>>
>> > FF = (csvread('FF.txt', 2, 0))';
>>
>> > data.trial{1} = FF;
>>
>> > data.time{1} = linspace(0,180,46080);
>>
>> > data.fsample=256;
>>
>> > data.label={'F3';'F4'};
>>
>> > data.cfg.trl=[1,46080,0];
>>
>> > cfg.continuous='yes';
>>
>> > cfg.trl=[1,46080,0];
>>
>> > cfg.channel={'F3';'F4'};
>>
>> > cfg2=artifact_eog(cfg,data);
>>
>> >
>>
>> > but then I have the following message error:
>>
>> >
>>
>> > ??? Error using ==> artifact_zvalue at 202
>>
>> > no channels selected
>>
>> >
>>
>> > Error in ==> artifact_eog at 179
>>
>> > [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
>>
>> > data);
>>
>> >
>>
>> > What I miss?
>>
>> >
>>
>> > in artifact_zvalue from 197:
>>
>> >
>>
>> > cfg.artfctdef.zvalue.channel =
>>
>> > channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
>>
>> > sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
>>
>> > numsgn = length(sgnind);
>>
>> >
>>
>> > if numsgn<1
>>
>> > error('no channels selected');
>>
>> > else
>>
>> > fprintf('searching for artifacts in %d channels\n', numsgn);
>>
>> > end
>>
>> >
>>
>> >
>>
>> > So I added:
>>
>> >
>>
>> > cfg.artfctdef.zvalue.channel={'F3';'F4'};
>>
>> >
>>
>> > but I get the same error
>>
>> > it seems that I need the header... but I have not.
>>
>> > is it?
>>
>> >
>>
>> > ----------------------------------
>>
>> > The aim of this list is to facilitate the discussion between users
>>
>> of the
>>
>> > FieldTrip toolbox, to share experiences and to discuss new ideas
>> for MEG
>>
>> > and EEG analysis. See also
>>
>> > http://listserv.surfnet.nl/archives/fieldtrip.html and
>>
>> > http://www.ru.nl/neuroimaging/fieldtrip.
>>
>>
>>
>>
>> ----------------------------------
>>
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis.
>>
>>   http://listserv.surfnet.nl/archives/fieldtrip.html
>>
>>   http://www.ru.nl/fcdonders/fieldtrip/
>>
>> ----------------------------------
>>
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis.
>>
>>   http://listserv.surfnet.nl/archives/fieldtrip.html
>>
>>   http://www.ru.nl/fcdonders/fieldtrip/
>>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
>of the FieldTrip  toolbox, to share experiences and to discuss new
>ideas for MEG and EEG analysis. See also
>http://listserv.surfnet.nl/archives/fieldtrip.html and
>http://www.ru.nl/neuroimaging/fieldtrip.

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


From marco.rotonda at GMAIL.COM  Mon Oct 26 20:04:20 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Mon, 26 Oct 2009 20:04:20 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <web-127111963@mail3.rug.nl>
Message-ID: <MON.26.OCT.2009.200420.0100.FIELDTRIP@NIC.SURFNET.NL>

so I could not do zvalue artifact on 2 channels only?

On 26/ott/2009, at 20.02, Paolo Toffanin wrote:

> That's the idea.
>
> Paolo
>
> On Mon, 26 Oct 2009 17:20:12 +0100
> Marco Rotonda <marco.rotonda at GMAIL.COM> wrote:
>> So I need eog channels other than the 2 I have?
>> On 26/ott/2009, at 15.18, Nina wrote:
>>> Hi Marco,
>>> you might want to try:
>>>
>>> cfg.artfctdef.eog.channel
>>> = {your EOG channel(s)};
>>>
>>> Nina
>>>
>>> Von: FieldTrip
>>> discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Im Auftrag von
>>> Paolo Toffanin
>>>
>>> Gesendet: Montag, 26. Oktober 2009
>>> 15:09
>>>
>>> An: FIELDTRIP at NIC.SURFNET.NL
>>>
>>> Betreff: Re: [FIELDTRIP] importing
>>> raw data
>>>
>>> Did you try including also eye channels into the
>>> analysis?
>>>
>>>
>>>
>>>
>>> Paolo
>>>
>>>
>>>
>>>
>>> On Monday 26 October 2009 02:42:28 pm Marco Rotonda
>>> wrote:
>>>
>>> > Hi there,
>>>
>>> > I'm trying to import a raw data file to perform artifacting.
>>>
>>> > The file I have is quite simple: 2 channels and only data
>>> sampled at 256.
>>>
>>> > I did the following operations:
>>>
>>> >
>>>
>>> > FF = (csvread('FF.txt', 2, 0))';
>>>
>>> > data.trial{1} = FF;
>>>
>>> > data.time{1} = linspace(0,180,46080);
>>>
>>> > data.fsample=256;
>>>
>>> > data.label={'F3';'F4'};
>>>
>>> > data.cfg.trl=[1,46080,0];
>>>
>>> > cfg.continuous='yes';
>>>
>>> > cfg.trl=[1,46080,0];
>>>
>>> > cfg.channel={'F3';'F4'};
>>>
>>> > cfg2=artifact_eog(cfg,data);
>>>
>>> >
>>>
>>> > but then I have the following message error:
>>>
>>> >
>>>
>>> > ??? Error using ==> artifact_zvalue at 202
>>>
>>> > no channels selected
>>>
>>> >
>>>
>>> > Error in ==> artifact_eog at 179
>>>
>>> > [tmpcfg, artifact] = artifact_zvalue(tmpcfg,
>>>
>>> > data);
>>>
>>> >
>>>
>>> > What I miss?
>>>
>>> >
>>>
>>> > in artifact_zvalue from 197:
>>>
>>> >
>>>
>>> > cfg.artfctdef.zvalue.channel =
>>>
>>> > channelselection(cfg.artfctdef.zvalue.channel, hdr.label);
>>>
>>> > sgnind = match_str(hdr.label, cfg.artfctdef.zvalue.channel);
>>>
>>> > numsgn = length(sgnind);
>>>
>>> >
>>>
>>> > if numsgn<1
>>>
>>> > error('no channels selected');
>>>
>>> > else
>>>
>>> > fprintf('searching for artifacts in %d channels\n', numsgn);
>>>
>>> > end
>>>
>>> >
>>>
>>> >
>>>
>>> > So I added:
>>>
>>> >
>>>
>>> > cfg.artfctdef.zvalue.channel={'F3';'F4'};
>>>
>>> >
>>>
>>> > but I get the same error
>>>
>>> > it seems that I need the header... but I have not.
>>>
>>> > is it?
>>>
>>> >
>>>
>>> > ----------------------------------
>>>
>>> > The aim of this list is to facilitate the discussion between
>>> users of the
>>>
>>> > FieldTrip toolbox, to share experiences and to discuss new
>>> ideas  for MEG
>>>
>>> > and EEG analysis. See also
>>>
>>> > http://listserv.surfnet.nl/archives/fieldtrip.html and
>>>
>>> > http://www.ru.nl/neuroimaging/fieldtrip.
>>>
>>>
>>>
>>>
>>> ----------------------------------
>>>
>>> The aim of this list is to facilitate the discussion between
>>> users  of the FieldTrip  toolbox, to share experiences and to
>>> discuss new  ideas for MEG and EEG analysis.
>>>
>>>  http://listserv.surfnet.nl/archives/fieldtrip.html
>>>
>>>  http://www.ru.nl/fcdonders/fieldtrip/
>>>
>>> ----------------------------------
>>>
>>> The aim of this list is to facilitate the discussion between
>>> users  of the FieldTrip  toolbox, to share experiences and to
>>> discuss new  ideas for MEG and EEG analysis.
>>>
>>>  http://listserv.surfnet.nl/archives/fieldtrip.html
>>>
>>>  http://www.ru.nl/fcdonders/fieldtrip/
>>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip  toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>>  and http://www.ru.nl/neuroimaging/fieldtrip.
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.

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


From nathanweisz at MAC.COM  Mon Oct 26 21:17:31 2009
From: nathanweisz at MAC.COM (Nathan Weisz)
Date: Mon, 26 Oct 2009 21:17:31 +0100
Subject: data.label wrong after componentanalysis?
Message-ID: <MON.26.OCT.2009.211731.0100.>

hi everyone,

for an analysis of EEG data i'm doing some ICA cleaning. since there
are many conditions / epochs, i do the ICA on a subset of trials and
then apply the calculated mixing matrix to the individual conditions.

i noticed (and i'm quite sure it's no user related error) that after
rejecting components and reconstructing the preprocessing data
structure, that the sequence in data.label has changed (apparently
into alphabetical order). however that rows in the 2-D matrices making
up data.trial(xy) have not changed, accordingly. i noticed because the
topography of the auditory N1 was a huge mess.

changing the labels solved the problem, i.e.:
ica_cleaned_data.label = data_before_ica_cleaning.label;

for those interested here the original code:

load([outdir '/dataB1F1.mat'], 'dataB1F1') %load data for one condition

cfg=[];
cfg.topo=comp.topo;
cfg.topolabel=comp.topolabel;

tmpcomp=componentanalysis(cfg,dataB1F1); %apply precomputed ICA to
condition

cfg=[];
cfg.component=ncmp;

dataB1F1=rejectcomponent(cfg, tmpcomp); %reject components obviously
representing artefacts

 >> [comp.cfg.channel(1:5) tmpcomp.cfg.channel(1:5)] %demonstrate
channel label mismatch

ans =

     'Lm'     'L1'
     'LE1'    'L10'
     'LE2'    'L11'
     'LE3'    'L12'
     'LD2'    'L13'

the crucial line appears to be in componentanalysis line 220:
cfg.channel = intersect(cfg.channel, cfg.topolabel);

intersect sorts the outcome:
 >> a=randperm(10)

a =

      7     1     9     3     6     2     5     4    10     8

 >> b=randperm(10)

b =

      6     3     5     1     8     2    10     4     9     7

 >> intersect(a,b)

ans =

      1     2     3     4     5     6     7     8     9    10

since i use all channels, simply replacing the label-field with the
original label-field works for me.

best,
nathan

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


From r.oostenveld at FCDONDERS.RU.NL  Wed Oct 28 14:11:35 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Wed, 28 Oct 2009 14:11:35 +0100
Subject: data.label wrong after componentanalysis?
In-Reply-To: <2B0C43B0-93FD-455C-BE01-D7B8002A7425@mac.com>
Message-ID: <WED.28.OCT.2009.141135.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Nathan,

thanks for the notification. It sounds like a potentially nasty bug,
so we'll look into it.

best,
Robert


On 26 Oct 2009, at 21:17, Nathan Weisz wrote:

> hi everyone,
>
> for an analysis of EEG data i'm doing some ICA cleaning. since there
> are many conditions / epochs, i do the ICA on a subset of trials and
> then apply the calculated mixing matrix to the individual conditions.
>
> i noticed (and i'm quite sure it's no user related error) that after
> rejecting components and reconstructing the preprocessing data
> structure, that the sequence in data.label has changed (apparently
> into alphabetical order). however that rows in the 2-D matrices
> making up data.trial(xy) have not changed, accordingly. i noticed
> because the topography of the auditory N1 was a huge mess.
>
> changing the labels solved the problem, i.e.:
> ica_cleaned_data.label = data_before_ica_cleaning.label;
>
> for those interested here the original code:
>
> load([outdir '/dataB1F1.mat'], 'dataB1F1') %load data for one
> condition
>
> cfg=[];
> cfg.topo=comp.topo;
> cfg.topolabel=comp.topolabel;
>
> tmpcomp=componentanalysis(cfg,dataB1F1); %apply precomputed ICA to
> condition
>
> cfg=[];
> cfg.component=ncmp;
>
> dataB1F1=rejectcomponent(cfg, tmpcomp); %reject components obviously
> representing artefacts
>
> >> [comp.cfg.channel(1:5) tmpcomp.cfg.channel(1:5)] %demonstrate
> channel label mismatch
>
> ans =
>
>    'Lm'     'L1'
>    'LE1'    'L10'
>    'LE2'    'L11'
>    'LE3'    'L12'
>    'LD2'    'L13'
>
> the crucial line appears to be in componentanalysis line 220:
> cfg.channel = intersect(cfg.channel, cfg.topolabel);
>
> intersect sorts the outcome:
> >> a=randperm(10)
>
> a =
>
>     7     1     9     3     6     2     5     4    10     8
>
> >> b=randperm(10)
>
> b =
>
>     6     3     5     1     8     2    10     4     9     7
>
> >> intersect(a,b)
>
> ans =
>
>     1     2     3     4     5     6     7     8     9    10
>
> since i use all channels, simply replacing the label-field with the
> original label-field works for me.
>
> best,
> nathan
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.
>

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


From r.oostenveld at FCDONDERS.RU.NL  Wed Oct 28 14:17:33 2009
From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld)
Date: Wed, 28 Oct 2009 14:17:33 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <2173B9D8-114C-476C-9759-0D042CD2A9A7@gmail.com>
Message-ID: <WED.28.OCT.2009.141733.0100.FIELDTRIP@NIC.SURFNET.NL>

Hi Marco

On 26 Oct 2009, at 20:04, Marco Rotonda wrote:
> so I could not do zvalue artifact on 2 channels only?

you can in principle compute the z-value, but I don't think that that
will help you much. If it were only a single channel, it would just be
a scaling of the data in that channel with the standard deviation.
Since you have two, it is also the accumulation of the z-value over
teh two channels.

However, I think that for your 2-channel data it is much more robust
to manually (i.e. visually) identify the artifact time-windows. You
can use the new DATABROWSER function for that.

best,
Robert

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


From marco.rotonda at GMAIL.COM  Wed Oct 28 14:21:36 2009
From: marco.rotonda at GMAIL.COM (Marco Rotonda)
Date: Wed, 28 Oct 2009 14:21:36 +0100
Subject: AW: [FIELDTRIP] importing raw data
In-Reply-To: <B50DE1AF-891D-4935-BF73-161C1D1C2A22@fcdonders.ru.nl>
Message-ID: <WED.28.OCT.2009.142136.0100.FIELDTRIP@NIC.SURFNET.NL>

thank you very much! I'll try...



On 28/ott/2009, at 14.17, Robert Oostenveld wrote:

> Hi Marco
>
> On 26 Oct 2009, at 20:04, Marco Rotonda wrote:
>> so I could not do zvalue artifact on 2 channels only?
>
> you can in principle compute the z-value, but I don't think that
> that will help you much. If it were only a single channel, it would
> just be a scaling of the data in that channel with the standard
> deviation. Since you have two, it is also the accumulation of the z-
> value over teh two channels.
>
> However, I think that for your 2-channel data it is much more robust
> to manually (i.e. visually) identify the artifact time-windows. You
> can use the new DATABROWSER function for that.
>
> best,
> Robert
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip  toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html
>  and http://www.ru.nl/neuroimaging/fieldtrip.

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


From wibral at BIC.UNI-FRANKFURT.DE  Fri Oct 30 10:36:05 2009
From: wibral at BIC.UNI-FRANKFURT.DE (Michael Wibral)
Date: Fri, 30 Oct 2009 10:36:05 +0100
Subject: PhD position in the areas of cognitive neuroscience an d
 neuroimaging
Message-ID: <FRI.30.OCT.2009.103605.0100.FIELDTRIP@NIC.SURFNET.NL>

Dear Fieldtrip users,

the Institute for Medical Psychology in Frankfurt (Prof. Jochen Kaiser) is offering a PhD position in the areas of cognitive neuroscience and neuroimaging (see below). Please also feel free to forward this message to interested colleagues.

Best Regards,
Michael Wibral

Job offer: PhD Student in Cognitive Neuroscience
The Institute of Medical Psychology at the University of Frankfurt/Germany invites applications for a PhD student position in the areas of cognitive neuroscience and neuroimaging. Employment duration will initially be limited to 2 years but can be extended*.
The work focuses on investigating auditory and visual memory processing employing magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI). The successful candidate will plan and conduct MEG, fMRI and behavioral experiments, perform data analyses, and publish the results.
The Institute of Medical Psychology provides access to state of the art research facilities of the Frankfurt Brain Imaging Center including two 3-Tesla research scanners, a 275-channel MEG system, and a 128-channel EEG system. We offer excellent supervision by experienced researchers and possibilities for participation in training courses and international scientific conferences. Last but not least, we provide a positive and highly productive working atmosphere!
Candidates should have a background and hold a Masters Degree in neuroscience, psychology, biology, or a related field. The candidate should enjoy experimental neuroscience, interdisciplinary collaboration and should be motivated to acquire new skills and knowledge. Furthermore, the candidate should be fluent in English both orally and written. Experience with fMRI or EEG/MEG, and good knowledge of statistics and programming skills are highly desirable.
Applications of women are specifically invited. In case of similar qualifications, competence, and specific achievements, women will be considered on preferential terms within the framework of the legal possibilities. Disabled candidates with equivalent qualifications will be given preference.
Please send your application (deadline: 30th November, 2009) to: 
Prof. Jochen Kaiser
Institut für Medizinische Psychologie
Goethe-Universität
Heinrich-Hoffmann-Straße 10
D-60528 Frankfurt am Main
Germany
j.kaiser at med.uni-frankfurt.de
URL: http://www.imp.uni-frankfurt.de

*The limitation of the contract is based upon the regulations of the "Wissenschaftszeitvertragsgesetz" in conjunction with the "Hessisches Hochschulgesetz". The salary will be based on BAT or the tariffs for German civil service employees.


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