[FieldTrip] coherence normalization

Mon Dec 5 21:38:55 CET 2011

Yes. Nolte mentions that although one often computes coherency relative to a baseline, one must be careful because of this and random flips of pi making hash of it if you just blindly subtract. Same thing for any relative phase calculation.

Also, I was misunderstanding things below; the interpretation is the same for MEG as it is for EEG, any source affects multiple sensors simultaneously. It is this spatial correlation that allows us to see it as a source after all, and what makes the imaginary part positive. If there were no spatial correlations there would be no imaginary part in the coherence.

heh, yes, it took me that long to understand this paper ... :-)

jan-mathijs schoffelen wrote:
> Hi all,
> 
> I would not venture to interpret a conditional difference in the 
> imaginary part of the coherency. When this quantity changes, it could 
> either be due to a change in the phase or to a change of the magnitude 
> of the coherency (or of any combination of the two). 
> 
> BW,
> 
> JM
> 
> 
> On Dec 5, 2011, at 7:56 PM, Tom Holroyd (NIH/NIMH) [E] wrote:
> 
>> 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
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>> 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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>>
>> -- 
>> "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
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 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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-- 
"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