[Mne_analysis] spatiotemporal cluster tests in EEG sensor space

[Maryam Zolfaghar]

        External Email - Use Caution        

Hi all,

I am new to using cluster analysis for my time-frequency EEG data. I am
still a bit confused of how exactly "
*mne.stats.spatio_temporal_cluster_test*" works. I first wanted to try
setting all parameters according to the following fieldtrip page (The
configuration settings of  ft_timelockstatistics ):
http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/

However, I could not find any parameters for some of them, for example:

cfg.clusteralpha    = 0.05;            % alpha level of the sample-specific
test statistic
cfg.clusterstatistic = 'maxsum';    % test statistic that will be evaluated
under the                               permutation distribution.
cfg.minnbchan       = 2;                 % minimum number of neighborhood
channels
cfg.clustertail         = 0;
cfg.alpha                = 0.025;          % alpha level of the permutation
test

If I set *connectivity* to its default (None), MNE statistical function's
outputs gave me the followings: (my input '*X*' is [cond1, cond2], each
cond is averaged over a frequency range and with the shape: n_subj X n_time
X n_chann)
*t_obs* with the shape (n_times X n_chann),
*cluster_p_value* as an one-dimensional (n_times*n_chann) array, and
*cluster* as a connection between t_obs and cluster_p_value to find
corresponding indices.

It seems it does all pixel-wise statistics and not any cluster-based
correction. So
1. Is the "threshold" the alpha level of the sample-specific test statistic
(similar to cfg.clusteralpha in fieldtrip ft_timelockstatistics)?
2. How to set connectivity matrix to consider both time and spatial
correlation? to have clusters instead of pixel-by-pixel statistical values
(t_val)?
3. In fieldtrip, cfg.clusterstatistic could be set to 'maxsum', how should
I set this in MNE?
4. How to get the threshold value of TFCE?
5. To plot the result (shape n_times X n_chann) with topoplot, it got the
average of statistics over one channel and all time points, so when I
create a topoplot of a boolean matrix (True for significant channels and
False for non-significant ones), it does not give me a topoplot map with
only two colors (e.g., red for significant channels and blue for
non-significant ones). Is there any function to show only significant
channels on topoplot map in a better way?

Thank you,
-Mary
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