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 <[email protected]>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": > > 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[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 > > _______________________________________________ > Pkg-ExpPsy-PyMVPA mailing list > [email protected] > http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa >
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