[Eeglablist] Group level brain connectivity analyses in sourcelevel

[Makoto Miyakoshi]

Dear Avniel,

> One question: why not simply interpolate between sources on the brain and
then morph all of the individual source spaces into a common source space?

Yes, that's almost what Nima's Network Projection approach does. Instead of
interpolation, his approaches uses 3-D smoothing on equivalent dipole
points and made them into probabilistic distributions of EEG sources.
Simple interpolation would fail, for example, when one has only three ICs.

Makoto

On Thu, Jul 14, 2016 at 12:21 PM, Ghuman, Avniel <ghumana at upmc.edu> wrote:

> One question: why not simply interpolate between sources on the brain and
> then morph all of the individual source spaces into a common source space?
> This is what MNE does. I personally then build my connectivity matrices
> etc. in the common source space.
>
> From: Makoto Miyakoshi <mmiyakoshi at ucsd.edu<mailto:mmiyakoshi at ucsd.edu>>
> Reply-To: <mmiyakoshi at ucsd.edu<mailto:mmiyakoshi at ucsd.edu>>
> Date: Thursday, July 14, 2016 2:25 PM
> To: Aleksandra Vuckovic <Aleksandra.Vuckovic at glasgow.ac.uk<mailto:
> Aleksandra.Vuckovic at glasgow.ac.uk>>
> Cc: EEGLAB List <eeglablist at sccn.ucsd.edu<mailto:eeglablist at sccn.ucsd.edu>>,
> James Jones-Rounds <jj324 at cornell.edu<mailto:jj324 at cornell.edu>>
> Subject: Re: [Eeglablist] Group level brain connectivity analyses in
> sourcelevel
>
> Dear Alex,
>
> In theory yes, but instead of dipole density you need to have dipole pair
> density. All of this minor difference from Measure Projection is summarized
> as Network Projection which is unpublished but presented in Nima's PhD
> thesis.
>
> I chose, however, not to create domains. Creating 'domains' based on
> measure similarity smells like double dipping to me. Instead, I separate
> the dipole pair density cloud into anatomical regions (note that this was
> also prepared by Nima, so I'm still using his option). Using anatomical
> ROIs is as good as creating across-subject domains to prepare common data
> structure across subjects.
>
> It uses AAL (Tzourio-Mazoyer et al., 2002) that has 88 anatomical regions,
> but I merged upper and lower basal regions such as caudate, thalamus,
> amygdala, hippocampus, etc. Thus the current scheme uses 76 regions, and
> the connectivity matrix size is 76x76. Each of the graph edge has time x
> freq x subject data.
>
> Makoto
>
> On Thu, Jul 14, 2016 at 11:10 AM, Aleksandra Vuckovic <
> Aleksandra.Vuckovic at glasgow.ac.uk<mailto:Aleksandra.Vuckovic at glasgow.ac.uk>>
> wrote:
> Hi
> Does it mean that if you do MPT analysis and create domains you extend to
> group connectivity analysis between domains?
> Regards
> Alex
>
> Sent from my iPhone
>
> On 14 Jul 2016, at 18:49, Makoto Miyakoshi <mmiyakoshi at ucsd.edu<mailto:
> mmiyakoshi at ucsd.edu>> wrote:
>
> Dear James,
>
> I'm surprised you know a lot about development of the group-level SIFT.
> Let me tell you a little bit about the current development. When I started
> it, there were two possibilities for me.
> 1. Wes & Tim's 'Bayesian Hierarchical Modeling' with interpolating
> 'missing' ICs acorss subjects.
> 2. Nima's 'Network Projection' which blurs existing ICs and average across
> subjects.
> I chose the second plan since Bayesian Hierarchical Modeling was too
> fancy. Nima's concept of 'Network Projection', which is a variation of
> Measure Projection, was technically more straightforward and familiar to
> me. So I bothered Nima a lot to learn how to make it work.
>
> SCCN has been struggling with IC inconsistency across subjects, and the
> difficulty in the solution is actually only a variation of the same
> issue... it's always there as long as you use ICA on individual data, which
> is Scott's philosophy and I don't want to give it up.
>
> Thus, the solution I've been developing is not Tim's. What I do is Nima's
> 'blur, weight, and average' approach using his code. It would be
> interesting if we could compare the results from the two methods.
>
> Makoto
>
>
> On Thu, Jul 14, 2016 at 6:31 AM, James Jones-Rounds <jj324 at cornell.edu
> <mailto:jj324 at cornell.edu>> wrote:
> I have been struggling with this issue for a couple years, also, and have
> two responses to your questions, Iman.
>
> First, some of the (fomer) researchers at UCSD, including Tim Mullen (who
> developed the SIFT connectivity toolbox), were working hard on a
> group-level, source-space connectivity toolbox, that would use markov chain
> monte carlo estimations of posterior distribution densities to deal with
> the missing data problem that is inherent to multi-subject connectivity
> analyses. Here is a link to a poster they presented a couple years ago on
> it.
>
> http://sccn.ucsd.edu/~scott/pdf/Thompson_and_Mullen_Poster_ICONXI.pdf
>
> However, due to some extenuating circumstances, they were not able to
> complete it. I am so thankful Makoto has taken up the charge to address the
> issue with his own toolbox!
>
> Second, a work-around that I have been using has been to conduct k-means
> clustering (using the standard STUDY function in EEGLAB), with a heavy
> weight on "dipole location" in the pre-clustering step. Then, I use these
> across-subject clusters (choosing the clusters that have the highest
> recruitment, i.e. have IC's from as many subjects as possible) to determine
> which IC's I will measure connectivity between. In other words, if Cluster
> 5 and Cluster 9 both recruited IC's from >90% of my subjects, then for each
> subject that has IC's in both clusters, I will measure the connectivity
> between the components, for that subject, that are in both clusters.
>
> Then i average the connectivity values accordingly, and simply ignore any
> subjects that are not co-occurring in both clusters of interest.
>
> This is not ideal but does generate plausible results.
>
> I'm so glad you brought this issue back onto the front burner, Iman!
>
> James
>
> From: Makoto Miyakoshi<mailto:mmiyakoshi at ucsd.edu>
> Sent: Wednesday, July 13, 2016 12:00 AM
> To: Iman Mohammad-Rezazadeh<mailto:irezazadeh at ucdavis.edu>
> Cc: EEGLAB List<mailto:eeglablist at sccn.ucsd.edu>; Scott Makeig<mailto:
> smakeig at ucsd.edu>; s.sanei at surrey.ac.uk<mailto:s.sanei at surrey.ac.uk>
> Subject: Re: [Eeglablist] Group level brain connectivity analyses in
> sourcelevel
>
> Dear Iman,
>
> I have an alpha version. I'll present it in SfN this year (see below for
> poster info). I'm currently working on ULCA data sets using it. I plan to
> release a beta version of the tool this summer (of course, it's a pluging
> for EEGLAB). I'll meet my colleagues in Qusp soon to report finalization of
> it and discuss publication.
>
> Makoto
>
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Your abstract, "Group-level statistics on EEG effective source
> connectivity," has been accepted into the program as a traditional poster
> presentation
>
> Session Type: Poster
> Session Number: 851
> Session Title: Computational Tools for Human Data II
> Date and Time: Wednesday Nov 16, 2016 1:00 PM - 5:00 PM
> Location: San Diego Convention Center: Halls B-H
> Abstract Control Number: 9417
>
> Multivariate connectivity measures in EEG have been gathering attention to
> investigate causal information flow in dynamics across signals. There are
> known issues in applying this method on scalp-recorded channel EEG data,
> such as volume conductance and scalp mixing, which makes the original scalp
> channel data highly correlated. To address these issues, applying
> independent component analysis (ICA) as preprocess is effective. It finds a
> linear transform to obtain effective source signals that are temporally
> maximally independent to each other. Thanks to this, the issues raising
> from volume conductance and scalp mixing are both addressed cleverly
> without estimating any parameters in electrophysiological forward model.
> However, because ICA reveals individual differences, it creates problems in
> the group-level statistics. For example, in the conventional EEG analysis,
> group-level statistics was straightforward; selecting a channel e.g. Cz
> from all the subjects was regarded to be sufficient. But after ICA
> preprocessing, there is no exact common independent comonent across all the
> subjects. Hence we developed a following statistical framework: 1.
> Preprocess individual data with ICA, estimate equivalent current dipoles,
> and apply multivariate connectivity measures across all pairs of ICs; 2.
> Compute dipole density that distributes within MNI brain space by applying
> 3-D Gaussian kernel; 3. Segment dipole density into anatomical regions; 4.
> Compute region-to-region pairwise dipole density that is weighted by
> connectivity measures; 5, Repeat above process for all subjects; 6, Perform
> statistics between conditions using variance across subjects. We developed
> a free, open-source source toolbox that plugs into EEGLAB. With this
> solution, effective EEG source connectivity can be evaluated in
> time-frequency domain at the group-level statistics with multiple
> comparison corrections. It is also generate a movie to visualize
> information flow. We expect it will also impact MEG, ECoG, and other
> electrophysiological data analysis.
>
>
> On Tue, Jul 12, 2016 at 4:11 PM, Iman Mohammad-Rezazadeh <
> irezazadeh at ucdavis.edu<mailto:irezazadeh at ucdavis.edu>> wrote:
> Hi EEGLABers,
>
> My concern is because in any experiment subjects don’t necessarily share
> common EEG sources  ( nodes in the network) in terms of their locations,
> number of sources , etc.
>
>
> 1-      Does anyone has experience on doing group level connectivity
> analyses on source  ( not channel level).
>
> 2-      In a single subject design ( pre-/ post-treatment , for example)
> how can we compare the brain connectivity in source level by considering
> the above concern?
>
> I would greatly appreciate any input and also please share any resources
> that you might think it is helpful.
>
> Thanks
> Iman
> -------------------------------------------------------------
> Iman Rezazadeh, Ph.D
> Project Scientist  | Semel Intitute, UCLA , Los Angeles, CA
> Adjunct Researcher | Center for Mind and Brain, Davis, CA
>
>
>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>
> --
> James Jones-Rounds
> Laboratory Manager
> Human Development EEG and Psychophysiology (HEP) Laboratory,
> Department of Human Development,
> --------------------------------------------
> Cornell University | Ithaca, NY
> 607-255-9883<tel:607-255-9883>
> eeg at cornell.edu<mailto:eeg at cornell.edu>
>
> _______________________________________________
> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
> To unsubscribe, send an empty email to
> eeglablist-unsubscribe at sccn.ucsd.edu<mailto:
> eeglablist-unsubscribe at sccn.ucsd.edu>
> For digest mode, send an email with the subject "set digest mime" to
> eeglablist-request at sccn.ucsd.edu<mailto:eeglablist-request at sccn.ucsd.edu>
>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
> _______________________________________________
> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
> To unsubscribe, send an empty email to
> eeglablist-unsubscribe at sccn.ucsd.edu<mailto:
> eeglablist-unsubscribe at sccn.ucsd.edu>
> For digest mode, send an email with the subject "set digest mime" to
> eeglablist-request at sccn.ucsd.edu<mailto:eeglablist-request at sccn.ucsd.edu>
>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>



-- 
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://sccn.ucsd.edu/pipermail/eeglablist/attachments/20160714/7018aa9a/attachment.html>