[Mne_analysis] Group level sensor space permutation cluster t-test on n channels?

[Denis-Alexander Engemann]

Hi Peter,

On Sun, Jun 8, 2014 at 3:01 PM, Peter Goodin <pgoodin at swin.edu.au> wrote:

>  Hi MNE list,
>
>  I'm having a bit of trouble on getting group level sensor space stats
> going. I've run similar in Fieldtrip and just create an array (or matrix in
> matlab speak) consisting of participants x channels x samples, and looking
> through the examples it seems we need to work directly with the array data
> too. But none of the functions I've used seem to accept anything other than
> a 2d array (3d for TF) and all the examples seem to either be single
> channel or one sample t-tests.
>

you can use all  `mne.stats.permutation_cluster_XXX` functions. They accept
mutli-dimensional arrays as input. Irrespective of the cluster-forming stat
used (t-test, f-test) they will perform a cluster permutation test.
For sensor space data you first have to assemble a corresponding matrix /
array.

X = np.array([e.data for e in m_evoeds])

To yield meaningful results you need to specify a connectivity structure,
e.g., based on the fieldtrip neighbor definitions.
C.f. https://github.com/mne-tools/mne-python/pull/1306 which we recently
added.

The input matrix is then expected to be of size n_subjects, n_times,
n_channels.

HTH,
Denis

 Are group level stats available currently or does something need to be
> written / cobbled together to get them to work?
>
>  Thanks for any help,
>
>  Peter
>
>    __________________________
> Peter Goodin,
>  BSc (Hons), Ph.D Candidate.
>
>  Brain and Psychological Sciences Research Centre (BPsych)
> Swinburne University,
> Hawthorn, Vic, 3122
>
> http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profile&pid=4149
>
>  Monash Alfred Psychiatry Research Centre (MAPrc)
> Level 4, 607 St Kilda Road,
> Melbourne 3004
>
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