[FieldTrip] disconnected cluster

[Schoffelen, J.M. (Jan Mathijs)]

Hi Roy,

The inadvertent alphabetization of channels should not occur. This issue has popped up in the past on several occasions (and on several locations in the code) and it has been a really tricky issue to deal with once and for all. Thanks for all the detective work so far. From what you write, it seems that the cfg.channel that goes into channelconnectivity is already in alphabetical order. Would it be possible to track down where this happens? Do you explicitly add the alphabetical list to cfg.channel in your call to ft_timelockanalysis? Does the problem persist if you define cfg.channel = data.label, i.e. the list in the order as it occurs in the data. (I would assume that the order of the channels is the same across all input data structures).

Best,
Jan-Mathijs

On Nov 5, 2015, at 8:58 PM, Roy Cox <roycox.roycox at gmail.com<mailto:roycox.roycox at gmail.com>> wrote:

hi all,

I'm worried that something is not quite right with how the channel neighborhood configuration is used in the formation of spatial clusters.

I first noticed it when I got a significant cluster like below. Plotted are t statistics for a between-group comparison, with the significant "cluster" indicated with white electrodes. Notice F5 and P8 here which are disconnected from the rest. I should also mention that I have only one "time point" (and no frequencies), so it's not possible that these channels are somehow connected via a "time bridge" (if that would even be possible).<cluster.jpg>

I've inspected my channel layout and that looks good:

<2D_layout.jpg>
I've looked at my neighborhood plot and that looks good too, although I notice that frontal channels are plotted to the right here (not sure if that's simply by default):

<neighboorhood.jpg>

Looking into the disconnected channel F5, the neighborhood structure seems in order:

cfg.neighbours(15)

ans =

          label: 'F5'
    neighblabel: {'Af7'  'F3'  'F7'  'Fc5'}


I call ft_timelockstatistics, which then calls ft_statistics_montecarlo, which, on line 165 calls

cfg.connectivity = channelconnectivity(cfg);

Stepping into this function, on line 20 it says:

chans=cfg.channel;

Checking what this variable contains, it has all my channels in alphabetical order, but my electrode location order is most definitely not. I've tried to force the orders to be the same by setting cfg.channel = cfg.label before calling ft_timelockstatistics, but somewhere down the line my channel order is made alphabetical again.

So I suspect that the neighborhood structure, reflecting my actual channel order, is applied to the alphabetical channel order. That would explain why a cluster could be scattered across the brain (and also why there's still some spatial continuity given that alphabetically close channels are usually close together in space).

Has anyone ever seen this? Any suggestions how to solve this (other than making my entire channel location file alphabetical)? I'm also posting this because it may be of relevance to others.

Roy


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