[pymvpa] AttributePermutator: Permute within chunks (& subjects) but only training labels
Michael Bannert
mbannert at tuebingen.mpg.de
Mon May 22 16:28:21 UTC 2017
Hi Richard,
Thanks for your email. Unfortunately, this is not exactly the answer
that I'm looking for:
In the section you refer to, the only limiting condition is that the
test set labels should remain unpermuted. This solves only 50 % of my
problem. It has already been explained very well in the worked examples
- so no problem there.
However, I also want to permute only within runs (and subjects) and do
not see how this can be achieved with AttributePermutator (or any other
method).
Best,
Michael
On 22/05/17 17:32, Richard Dinga wrote:
> Hi,
> Does this answer your question?
> http://www.pymvpa.org/tutorial_significance.html#avoiding-the-trap-or-advanced-magic-101
>
>
> On Fri, May 19, 2017 at 8:18 PM, Michael Bannert
> <mbannert at tuebingen.mpg.de <mailto:mbannert at tuebingen.mpg.de>> wrote:
>
> Dear all,
>
> I would like to use permutation testing for spatially aligned
> across-subject decoding. I have one vector of beta estimates per run
> (aka chunks) and per subject. Hence I figured it would be wise to
> permute within subjects and runs.
>
> I can achieve this (I think) if I use AttributePermutator in this way:
>
> permutator = AttributePermutator(attr='targets', limit=['subject',
> 'chunks'], count=n_perm)
>
> According to the debugging information provided when setting the 'APERM'
> option, the permutations that are produced look reasonable.
>
> However, I would also like to permute only the training data. How can I
> accomplish this?
>
> I tried something like this:
>
> permutator = AttributePermutator(attr='targets', limit={
> 'partitions': 1, 'subject': range(n_subj), 'chunks':
> ['run%02.f' % j for j in range(1, n_runs + 1)]},
> count=1)
>
> ... but it doesn't work.
>
> I guess I am not very clear on what the documentation of
> AttributePermutator has to say about the limit argument.
>
> Could anyone help?
>
> Thanks & best,
> Michael
>
>
>
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