[pymvpa] searchlight on ER data
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
> What I meant by "properly":
> you are specifying "radius" for your searchlight (e.g. 1), is
> 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.metric = \
> ds.mapper.metric = DescreteMetric(elementsize=[1.0, 1.0, 1.0, 1.0],
> 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
> "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
> Pkg-ExpPsy-PyMVPA mailing list
> Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
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