[FieldTrip] coherence normalization

Fri Dec 2 18:52:07 CET 2011

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 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://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://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://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://mailman.science.ru.nl/mailman/listinfo/fieldtrip>//"/
> 
>>/ <//robert.oostenveld at 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
> 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