Hello,
I tried running the example for computing a dissimilarity matrix measure found
here: http://www.pymvpa.org/examples/searchlight_dsm.html (file is here:
https://github.com/PyMVPA/PyMVPA/blob/master/doc/examples/searchlight.py)
When trying to run the example file searchlight_dsm.py, I get an error at this
line:
# setup searchlight with 5 mm radius and measure configured above
sl = Searchlight(dsmetric, radius=5)
It says that Searchlight is expecting 3 arguments, but only received 2. Sifting
through the code for the Searchlight class, it seems that the missing argument
it is expecting "queryengine". I'm wondering whether the class was updated
after this example was posted. I'm unclear what the query engine is and how
exactly I pass that argument to Searchlight. I have been unable to find those
details in the documentation. I am somewhat of a newbie to both python and
PyMVPA.
Another example, searchlight_surf.py, uses Searchlight with the queryengine
argument:
qe = disc_surface_queryengine(radius, epi_fn,
white_surf_fn, pial_surf_fn,
source_surf_fn)
…
clf = LinearCSVMC()
cv = CrossValidation(clf, NFoldPartitioner(),
errorfx=lambda p, t: np.mean(p == t),
enable_ca=['stats'])
…
roi_ids = None
sl = Searchlight(cv, queryengine=qe, postproc=mean_sample(), roi_ids=roi_ids)
Also, what is the difference between using Searchlight and sphere_searchlight
(which is used in the other examples)?
I don't want to run cross validation or a classifier, I just need to compute
the similarity (e.g., pearson correlation) between voxels in 2 different
conditions at each searchlight position, then obtain a map of those results.
Thanks!
Jason
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