permutation clustering test using TFCE

✉️ Mailing List Archive (read-only)
1

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)).
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")...

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?

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.

Hoping that it is useful for you,
Best,
Laetitia G.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140731/fc9ce509/attachment.html

2

Thanks Latitia,

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
step_down=0.05).

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!
Best,
Denis

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu
Mne_analysis Info Page

The information in this e-mail is intended only for the person to whom it

is

addressed. If you believe this e-mail was sent to you in error and the

e-mail

contains patient information, please contact the Partners Compliance

HelpLine at

MyComplianceReport.com: Compliance and Ethics Reporting . If the e-mail was sent to you in

error

but does not contain patient information, please contact the sender and

properly

dispose of the e-mail.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140731/0dd35b8e/attachment.html