[pymvpa] searchlight on ER data

Anna Manelis anna.manelis at gmail.com
Wed Dec 29 19:07:11 UTC 2010

```Thanks for the prompt response. I guess a hidden message was "Don't use the
0.4.5 version. If you want to do searchlight on ER data, download the 0.6
version " :) Am I right?   Will 0.5  also do a trick?

On Wed, Dec 29, 2010 at 1:58 PM, Yaroslav Halchenko
<debian at onerussian.com>wrote:

> Hi Anna,
>
> Sorry for the delay with replies.
>
> The main issue is that 0.4 is not ready to provide adequate
> support for doing spatio-temporal searchlight analysis "properly" out of
> the box.  That was one of the reason for initiating development of
> 0.5.
>
> What I meant by "properly":
>
>  that in voxels?  seconds? mm?
>
>  could we add distances in time and space together?
>
> so we wanted to have a clean way to specify radii per each dimension (i.e.
> space/time) without hassle, so that they (time and space) do not
> "interfere" with each other.
>
> in 0.4 you could probably craft some custom metric and distance function
> which would have proper separation between the two "dimension"
> (time/space), but we do not have it built-in.
>
> What you probably could do (but once again -- we haven't tested that
> much in 0.4) -- assign a metric where you disregard difference between
> time and space and just ask for neighboring voxels in space and time,
> but once again, it would make voxel  (1,1,1) at time 0 as distant from
> (0,0,0) at time 0, as (1,1,0) at time 1, and depending on the radii
> might not take any other voxel at time 1; so it litterally becomes some
> kind of spatio-temporal ellipsoid ;)
>
> to accomplish that you just assign the metric to both chainmapper of the
> ds and its trailing mapper (which has a metric with correct dimensions
> actually, but adding actual mm^2 to sec^2 has even less sense ;)):
>
> ds.mapper._mappers[1].metric = \
> ds.mapper.metric = DescreteMetric(elementsize=[1.0, 1.0, 1.0, 1.0],
>                                  distance_function=cartesianDistance)
>
> That might work (at least it doesn't crash ;))
>
> But, once again, even if it works, its interpretation and validity are at
> question ;)
>
> For doing "correct" Spatio-temporal searchlight in upcoming 0.6, see
> http://dev.pymvpa.org/tutorial_eventrelated.html#if-that-was-easy where
> search
> "radii" can be specified directly per each dimension (space/time).
>
> On Wed, 29 Dec 2010, Anna Manelis wrote:
>
> >    I am trying to use searchlight on event-related fMRI data. The error
> >    message suggests that there is a problem with assigning metrics to
> >    MappedDataset.
> --
> =------------------------------------------------------------------=
> Keep in touch                                     www.onerussian.com
> Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic
>
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