[Mne_analysis] permutation clustering test using TFCE

Denis-Alexander Engemann denis.engemann at gmail.com
Thu Jul 31 09:14:01 EDT 2014
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Thanks Latitia,

On Thu, Jul 31, 2014 at 10:03 AM, Laetitia Grabot <laetitia.grabot at gmail.com>
> Hi Denis,
> I tried the spatio-temporal clustering with TFCE
(spatio_temporal_cluster_1samp_test) on alpha power data (size of epoch :
2s; decimation = 4 (so 501 time points)) with n_jobs = 6 and the default
TFCE parameter (dict(start = 0, step = 0.2)).

I think we need to improve the documentation on TFCE a bit. A good default
range is probably

dict(start=2, step=0.2)

> According to script output, 48 thresholds were used from 0 to 9.4.
> After 5h (!!), 10262484 clusters were found and finally after some others
hours the script crashed before the end ("cannot allocate memory")...

For TFCE N clusters equals N features. Howver if you do not scan the enitre
range of the test statistic you wont have to wait thast long.

> I tried on shorter data (1s so 250 time points) but it was also too long
and too memory-demanding. Then I tried to change the step parameter to
decrease the number of thresholds to test. I took step =0.5. 17 thresholds
were used from 0 to 8. 5121000 clusters were found and my script also ended
up crashing. So... what do you suggest to get acceptable computation time?

See above. Btw for roughtly 10.000 clusters with 15-20 thresholds I'm
waiting for roughly 15-20 minutes per iteration (multiple iterations with

> By the way, with p_threshold =0.001, I got no cluster; with  p_threshold
=0.01, I got one occipito-parietal cluster (pvalue = 0.026) lasting around
500ms, after something about 10min of computation.

I'm not sure what you refer to by `p_threshold`. Either you pass a dict or
a float. The latter will be a classical cluster permuation analysis, the
former TFCE.
You can howver use the p_threhold as start value for TFCE.

> Hoping that it is useful for you,
> Best,
> Laetitia G.

Yes, thanks!

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