[pymvpa] Help needed untangling searchlight accuracy bias

[Yaroslav Halchenko]

On Thu, 20 Oct 2011, Mike E. Klein wrote:
> Thanks for the quick response. I actually don't know how to crossplot…

should be as easy as

    import pylab as pl # not needed if you did import from mvpa.suite
    pl.plot(np.ravel(s1_map), np.ravel(s2_map), '.')
    pl.show() # your might not even need this one

alternatively -- here is a helper I hacked up/use -- probably should
place it under PyMVPA (see attached) -- just give it two nifti files ;-)

> histrograms are output from MRICron. 

    pl.hist

should become your friend

> I've tried to follow the plotting
> from the searchlight example from the manual, but haven't figured out
> to get my searchlight data in there (from nifti) without running the
> entire multi-hour script first.

just load using fmri_dataset with the original mask ;)

> As far as ds.summary, I've pasted below. It has been run averaged, but
> not detrended or zscored.

if I were you I would have detrended, zscored and only then averaged!

if averaging was done across multiple conditions spread through the
'run' detrending might be detremental

and I think I might know where other catch could be -- if you
zscore such a dataset as you have (2 samples total per chunk) with
zscoring per chunk -- do you know what values would you get? ;)

so -- how was zscoring done?

what about ds.summary() right before you fed it into searchlight?

-- 
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Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic
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