[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,
Paul
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