[Mne_analysis] permutation clustering test using TFCE
laetitia.grabot at gmail.com
Mon Aug 4 08:33:29 EDT 2014
> Message: 2
> Date: Thu, 31 Jul 2014 15:14:01 +0200
> From: Denis-Alexander Engemann <denis.engemann at gmail.com>
> Subject: Re: [Mne_analysis] permutation clustering test using TFCE
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> CA+MN3OtGzf02SVJkYNsFgwjh8-306VC7nmW8S0uc7szDq-Tr5A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 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 dict(start=2, step=0.2) and dict(start=2, step=0.5), but I still
had 5 120 000 clusters (15 threshold for step =0.5). How can I not scan the
entire range of the test, as you suggested ? I didn't understand what you
mean by "features"...
> > 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.
Yes I was talking about classical permutation cluster analysis.
> > Hoping that it is useful for you,
> > Best,
> > Laetitia G.
> Yes, thanks!
Thanks a lot for your advice!
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