Thanks a lot for your help!
It seems that for now we have to specify a seed_queryEngine because of this in
the connectivity_hyperalignment script:
if params.seed_queryengines is None:
raise NotImplementedError("For now, we need seed queryengines.”)
But if we define an empty seed_queryEngine and use a seed_radius of 20 it seems
to work. Just like Feilong suggested it will be defined in
get_trained_queryengines.
One last question if I may: it seems that I always run out of RAM when I try to
run the script. Even if I use only 10 resting state dataset of 10 minutes (~
1GB) it will end up crashing after 24 hours because it ran out of the ~50GB I
allocated for the analysis.
Is that normal and do you guys have a rule of thumbs to determine how many RAM
the analysis will require? I might have to find another environment to run my
analyses as a function of what this requires.
Thanks a lot!
Vincent
> On Oct 12, 2018, at 3:52 PM, Feilong Ma <mafeil...@gmail.com> wrote:
>
> 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
>
> <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 <deb...@onerussian.com
> <mailto:deb...@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
> <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 <http://www.linkedin.com/in/yarik>
>
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