[Mne_analysis] t-test in source space?

[Graves, William]

Hi Alex,

Thanks for the reply. In addition to using the standard scipy.stats functions, it would be nice to be able to take advantage of some of the fancier tools you've developed in mne-python, like the permutation_t_test and permutation_cluster_test functions. The examples you give for their usage are in sensor space. I've tried simply feeding them stc data instead, with this kind of usage:

threshold = 2.1
T_obs, clusters, cluster_p_values, H0 = \
                permutation_cluster_test([cond1_stc.data, cond2_stc.data],
                            n_permutations=1000, threshold=threshold, tail=0,
                            n_jobs=7)

But when I do, shape(T_obs), I get the following:
(241,), which I suppose is the number of samples, but no information about the vertices. It's a similar story when I try using permutation_t_test.

Am I missing something obvious here, or do these functions simply not work for stc/source files? Perhaps I'm just calling them wrong or misunderstanding the output. Either way, I'd appreciate any help you could give.

Thanks again,
Will

________________________________________
From: Alexandre Gramfort [gramfort at nmr.mgh.harvard.edu]
Sent: Thursday, October 06, 2011 3:57 PM
To: Graves, William
Cc: mne_analysis at nmr.mgh.harvard.edu
Subject: Re: [Mne_analysis] t-test in source space?

Hi Will,

you can use scipy.stats.ttest_* functions to do analytical
t-tests from source estimates.

mne-python does not reimplement these standard stats functions.

I am personally curious to know more about what you do
precisely (how many subjects, mne vs dSPM etc.)

and glad that you found your way with mne-python !

Cheers,
Alex

On Thu, Oct 6, 2011 at 4:36 PM, Graves, William <wgraves at mcw.edu> wrote:
> Dear MNE Experts,
>
> The new mne-python tools look really nice to me and show lots of promise, especially for adding statistical functionality to MNE. Unfortunately, even after trying to go through the examples, I can't figure out a way to do a t-test between conditions in source space.
>
> I would greatly appreciate any help or advice I could get with this.
>
> Thanks in advance,
> Will
>
> ---
> William W. Graves, Ph.D.
> Instructor, Department of Neurology
> Medical College of Wisconsin
> Center for Imaging Research, MEB 4670
> 8701 Watertown Plank Road
> Milwaukee, WI  53226
> voice:  414.456.4653
> fax:  414.456.6335
> http://www.neuro.mcw.edu/~wgraves/
>
>
>
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