[FieldTrip] coherence normalization

Mon Dec 5 19:56:02 CET 2011

Yes, Guido Nolte came up with that around the same time (2004).

I found this link by google, there might be a better one

http://keck.ucsf.edu/~houde/sensorimotor_jc/GNolte04a.pdf

Imaginary coherence is insensitive to volume conduction in EEG.

I think the interpretation is different for MEG, but you can certainly easily compute it; you might still want to contrast different conditions.

Tolga Özkurt wrote:
> Regarding the discussion here, I've gotten onto a recent paper (Sekihara 
> et al., 2011) talking about "imaginary coherence" to prevent the seed 
> region effects. 
> 
> Even though imaginary coherence does not contain total connectivity 
> information, it might at least be used to select the coherent regions 
> that you want to project on your brain image and ignore the rest.
> 
> Tolga
> 
> 
> ------------------------------------------------------------------------
> *From:* jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
> *To:* Email discussion list for the FieldTrip project 
> <fieldtrip at donders.ru.nl>
> *Sent:* Friday, December 2, 2011 8:49 PM
> *Subject:* Re: [FieldTrip] coherence normalization
> 
> Hi Jan, Tom and the rest,
> 
> I agree with Tom, but would like to strongly emphasize that differences 
> in power across conditions more often than not will affect the coherence 
> landscape in a non-trivial way. This does not only count for power 
> changes in the reference dipole, but also for changes in power for third 
> party dipoles (i.e. any potential other source). Therefore the 
> interpretation of the subtracted  coherence volumes should be done with 
> care.
> 
> BW,
> 
> JM
> 
> On Dec 2, 2011, at 6:52 PM, Tom Holroyd (NIH/NIMH) [E] wrote:
> 
>> The solution I have adopted is to always look at coherence contrasts. 
>> Make two volumes using the same reference dipole in two different 
>> conditions, then subtract the volumes. The self-coherence of the 
>> reference will disappear. Mostly. Then use stats, like a U-test.
>>
>> Jan.Hirschmann at med.uni-duesseldorf.de 
>> <mailto:Jan.Hirschmann at med.uni-duesseldorf.de> wrote:
>>> Hi community,
>>> Regarding this thread on suppressing the reference dipole from 2004, 
>>> what is the current status? Has anybody found and implemented a 
>>> recommendable way to project out activity from unwanted dipoles? 
>>> Thank you for any comments/opinions!
>>> Best,
>>> Jan Hirschmann
>>>   On 21 Oct 2004, at 17:23, Tom Holroyd wrote:
>>>
>>>> / When running a coherence volume using a reference dipole, one/
>>>> / naturally expects the coherence will be high around the reference/
>>>> / dipole./
>>>> / /
>>>> / This effect tends to dominate the images./
>>>> / /
>>>> / Is there a way to normalize the coherence volume to eliminate/
>>>> / this effect?  Perhaps by dividing by the coherence in a "control"/
>>>> / state?/
>>> Hi Tom,
>>> The dominating effect of the refdip is indeed very problematic. I just
>>> happened to have discussed this with Joachim Gross, and I have included
>>> our email exchange below. Please first read that ...
>>> Basically I agree with Joachim, and I don't trust the supdip that is
>>> implemented in FieldTrip's sourceanalysis function. Better test and map
>>> the significance of the difference in coherence between two conditions
>>> using randomization of the trials before the coherence is beamed (that
>>> is implemented in sourceanalysis + sourcestatistics).
>>> Robert
>>> --------------------------------------------------------------------
>>> my question to Joachim was
>>> ----------------------------------------------------------------------
>>> Begin forwarded message:
>>>
>>>> / From: Robert Oostenveld <//roberto at smi.auc.dk 
>>>> <http://smi.auc.dk> 
>>>> <http://mailman.science.ru.nl/mailman/listinfo/fieldtrip>//>/
>>>> / Date: 1 October 2004 10:26:02 GMT+02:00/
>>>> / To: Joachim Gross <//jgross at uni-duesseldorf.de 
>>>> <http://uni-duesseldorf.de> 
>>>> <http://mailman.science.ru.nl/mailman/listinfo/fieldtrip>//>/
>>>> / Subject: dipole suppression/
>>>> / /
>>>> / Hi Joachim,/
>>>> / /
>>>> / What I always still had to ask you is how you do supression of 
>>>> dipoles/
>>>> / in DICS, especially in the case of coherence imaging. I have thought/
>>>> / of two ways of projecting them out:/
>>>> / /
>>>> / 1) compute supdip leadfield and its projection on the COV/CSD matrix,/
>>>> / then project it out of the COV/CSD matrix (which looses 2 or 3 from/
>>>> / its rank)./
>>>> / /
>>>> / 2) compute supdip leadfield and add it to the leadfield of the dipole/
>>>> / with which is scanned (scandip). Subsequently compute the source/
>>>> / COV/CSD on those 6 leadfield components and select the 3x3 submatrix/
>>>> / that corresponds with the scandip to continue the computations with./
>>>> / /
>>>> / Both methods don't really gave me very convincing results. A third/
>>>> / approach would be to add the supdip leadfield to the (identity) noise/
>>>> / matrix and project it through the filters. Then nai=pow/noise is/
>>>> / corrected for the presence of the supdip, but that does not result in/
>>>> / a supressed source coherence distribution. What is your idea or/
>>>> / approach for this?/
>>>> / /
>>>> / best regards/
>>>> / Robert/
>>>> / /
>>> ----------------------------------------------------------------------
>>> and his answer (Joachim, I hope you don't mind me sharing this on the
>>> list)
>>> ----------------------------------------------------------------------
>>> Begin forwarded message:
>>>
>>>> / From: Joachim Gross <//jgross at uni-duesseldorf.de 
>>>> <http://uni-duesseldorf.de> 
>>>> <http://mailman.science.ru.nl/mailman/listinfo/fieldtrip>//>/
>>>> / Date: 14 October 2004 17:20:45 GMT+02:00/
>>>> / To: "//robert.oostenveld at fcdonders.kun.nl 
>>>> <http://fcdonders.kun.nl> 
>>>> <http://mailman.science.ru.nl/mailman/listinfo/fieldtrip>//"/
>>>> / <//robert.oostenveld at fcdonders.kun.nl <http://fcdonders.kun.nl> 
>>>> <http://mailman.science.ru.nl/mailman/listinfo/fieldtrip>//>/
>>>> / Subject: dipole suppression/
>>>> / /
>>>> / Hi Robert,/
>>>> / /
>>>> / sorry for the delay./
>>>> / /
>>>> / The dipole suppression is indeed a complex issue./
>>>> / We first implemented it because it facilitates visualization and the/
>>>> / exact identification of the first/
>>>> / strongest local maxima./
>>>> / Nevertheless, it is quite dangerous because the map is (locally)/
>>>> / distorted in a non-trivial way./
>>>> / We are now trying to move away from suppressing the sources. I think/
>>>> / it would be better to identify the/
>>>> / significant local maxima (significance based on/
>>>> / randomization/permutation)./
>>>> / But what we are doing at the moment is your approach 3./
>>>> / So we add the supdip leadfield to the noise covariance matrix and 
>>>> look/
>>>> / at pow/noise./
>>>> / /
>>>> / For coherence we are basically doing the same thing./
>>>> / So we divide the coherence map (or actually the map of cross spectral/
>>>> / densities) by a noise map/
>>>> / that peaks at the locations of the "unwanted" dipoles./
>>>> / With this procedure we loose absolute coherence values./
>>>> / This is not so important for us since we get the absolute values from/
>>>> / the coherence and partial coherence spectra/
>>>> / that are computed afterwards./
>>>> / It works surprisingly well but should be used with care./
>>>> / /
>>>> / A better approach would be to map partial coherence (with the 
>>>> unwanted/
>>>> / dipoles removed). But we have not implemented/
>>>> / this so far./
>>>> / /
>>>> / Again, I think it is better to have regions of interest identified by/
>>>> / their significance./
>>>> / /
>>>> / Joachim/
>>>  ----------------------------------------------------------------------
>>> Robert Oostenveld, PhD
>>> Center for Sensory-Motor Interaction (SMI)
>>> Aalborg University, Denmark
>>> and
>>> F.C. Donders Centre for Cognitive Neuroimaging
>>> University Nijmegen
>>> P.O. Box 9101
>>> NL-6500 AH Nijmegen
>>> The Netherlands
>>> Tel: +31 (0)24 3619695
>>> Fax: +31 (0)24 3610989
>>> ----------------------------------------------------------------------
>>> N.B. Starting from 1 September 2004, the University of Nijmegen has
>>> changed its name to Radboud University Nijmegen. All web- and
>>> email-addresses ending in ".kun.nl" should therefore be changed into
>>> ".ru.nl". Please update your address book and links.
>>>  Jan Hirschmann
>>> MSc. Neuroscience
>>> Insititute of Clinical Neuroscience and Medical Psychology
>>> Heinrich Heine University Duesseldorf
>>> Universitaetsstr.  1
>>> 40225  Duesseldorf
>>> Tel: 0049 - (0)211 - 81 - 18415
>>> ------------------------------------------------------------------------
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> -- 
>> "The test of a first-rate intelligence is the ability to hold two
>> opposed ideas in the mind at the same time, and still retain the
>> ability to function." — F. Scott Fitzgerald
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> 
> Jan-Mathijs Schoffelen, MD PhD 
> 
> Donders Institute for Brain, Cognition and Behaviour, 
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> 
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
> 
> J.Schoffelen at donders.ru.nl <mailto:J.Schoffelen at donders.ru.nl>
> Telephone: +31-24-3614793
> 
> 
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> 
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-- 
"The test of a first-rate intelligence is the ability to hold two
opposed ideas in the mind at the same time, and still retain the
ability to function." — F. Scott Fitzgerald