[FieldTrip] Attempt at cluster analysis on seed to whole brain coherency values

Paul Dhami pdhami06 at gmail.com
Mon Oct 15 04:37:52 CEST 2018

Dear Fieldtrip,

I have a dataset in which I'd like to compare, between controls and
patients, their imaginary coherency values in a seed to whole brain manner.
In other words, I would like to calculate the imaginary coherency between a
single seed electrode and the rest of the remaining electrodes, and *ultimately
use ft_freqstatistics' cluster analysis* to test for a significance
difference between the groups' seed-to-whole-scalp coherency maps.

>From my understanding, this would require a bit of hacking to implement
this. I attempted to do so and describe what I did below, with the goal to
eventually create something that would work with freqstatistics :

   - ran freq analysis with output as 'powandcsd' and method as 'mtmconvolv'
   - on the results of freqanalysis, ran ft_connectivityanalysis with
   cfg.method = 'coh' and cfg.complex = 'absimag'
   - with each subject's resulting structure from ft_connectivityanalysis,
   I first chose a seed of interest
   - I then found the indices of the 59 channel combinations in relation to
   the seed of interest in labelcmb
   - Using the indices, I then pruned/removed the remaining channel
   combinations of no interest from both the labelcmb and cohspctrm, reducing
   cohspctrm to a channel of interest (59) x frequency x time matrix (as in it
   only included values for the channel combinations of interest)
   - I rename the dimord as 'chan_freq_time'
   - create 'label' field with standard electrode labels
   - I then create powspctrm in my structure, which holds the exact same
   data as the cohspctrm (created powspctrm strictly for freqstatistics)
   - removed the fields of 'labelcmb' and 'cohspctrm'
   - because my powspctrm is missing the seed channel, I then inserted a
   matrix of ones with the appropriate dimensions into where it should be
   (e.g. if my seed of interest was channel FCZ, I would then insert into my
   matrix of ones into the 19th position of the powspctrm, thus shifting the
   latter matrices so now it becomes a matrix with 60 channels in the
   appropriate order)

>From my understanding, the resulting structure of each subject should
contain now the coherency values between the seed of interest and the rest
of the electrodes in 'powspctrm'.

I then used freq_statistics (in the standard way) with cluster correction
to compare the coherency between groups, and from what I can tell with no
errors popping up, it worked. I then interpreted the resulting clusters in
a similar fashion as you would do for a typical frequency chan-freq-time
analysis (instead of power, looking at coherency clusters now).

My questions are:
1) In regards to implementation (assuming something like this can even be
appropriately implemented), do things look okay?
2) Am I wrong in thinking that the cluster results of freq_statistics can
be interpreted in a similar fashion as to a typical frequency
chan-freq-time analsyis (just replacing power with coherency)?

Sorry for the long-winded email, but any help would be greatly appreciated.

Thank you,
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