[pymvpa] Connecitvity Hyperalignment and SeedQuerryEngine

[Feilong Ma]

Hi Vincent,

The main query engine for searchlight connectivity hyperalignment should be
similar to that used for searchlight response hyperalignment, and we
usually use a 20 mm radius, which is the same one used in Swaroop's 2016
searchlight hyperalignment paper.  Sometimes I use a slightly smaller
radius (e.g., 15 mm, 10 mm) to speed up the computations, but in general 20
mm radius usually works well.

The other query engine (SeedQueryEngine) is specific for connectivity
hyperalignment, and is used to compute connectivity targets (sometimes also
called connectivity seeds) by averaging responses in each searchlight.  In
the connectivity hyperalignment paper we used connectivity seeds from a
low-resolution surface (AFNI's ico8), and that in combination with a 13 mm
radius can make sure the entire cortical surface is covered by the
searchlights.

If you want to perform a quick analysis with data in volume, you can use a
query engine that will generate searchlights in volume space.  Below is an
example usage
https://github.com/PyMVPA/PyMVPA/blob/5b01da5529c8653da948e9e03c9361168d954482/mvpa2/algorithms/searchlight_hyperalignment.py#L683-L685

Best,
Feilong

On Fri, Oct 12, 2018 at 11:39 AM Yaroslav Halchenko <debian at onerussian.com>
wrote:

>
> On Fri, 12 Oct 2018, Vincent Taschereau-Dumouchel wrote:
>
> > Hi everyone,
>
> > First of, thanks a lot for sharing the connectivity hyperalignment code.
> You guys are doing awesome work.
> > I am starting to play around with it and was wondering about 2 things:
>
> > - Do you have an example of the arguments that needs to be provided? One
> of them is the SeedQueryEngine. I went through the code a little and I am
> having a hard time determining what this is exactly.
>
> seed_queryengines  are needed for figuring out neighborhood to average
> for estimating connectivity to it.  I am not quite sure (CCing the
> original author Swaroop and Feilong who might know better) why your
> "main" queryengine could/shouldn't be used (the test uses the
> same) if you are working in the same "domain" (e.g. in the volume for
> both the searchlight and then the seeds).  If so, may be code could be
> adjusted to avoid demanding specification of the seed_queryengines?
>
> > - Also, can we use it not with surfaces but with typical volume data? I
> understand the problems associated with running a searchlight on volume
> data but I was just trying to take a quick peak at the function before
> processing surfaces and all.
>
> AFAIK, due to all those "query engines" flexibility, it could be used in
> a variety of scenarios:
>
> - everything in the volume
> - everything (projected) on the surface
> - having surface guiding selection of the voxels in the volume
>
>
> --
> Yaroslav O. Halchenko
> Center for Open Neuroscience     http://centerforopenneuroscience.org
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
> WWW:   http://www.linkedin.com/in/yarik
>
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