[pymvpa] Why to standardize (z-score) a time course?

[Vadim Axel]

Thanks for the answer, Yaroslav.
To be on the safe side, what is the equation for " z-scoring against
baseline" you mentioned? I guess that you subtract the baseline condition
instead of the average. But how you calculate the std?

Do you mind name some "reasonable scaling approaches"? In one of your papers
you also tested " scaled percentage change relative to baseline".

Thanks,
Vadim



On Sat, Jul 31, 2010 at 4:10 AM, Yaroslav Halchenko
<debian at onerussian.com>wrote:

> primary reason for zscoring is usually to bring data into a reasonable
> range of values for a classifier to be sensitive...  usually it implies
> that values are primarily around 0 with values from -10 to 10 or so with
> the bulk from -2 to 2... z-scoring against baseline also has direct
> interpretation of cause
>
> in your case, if they are already betas from GLM -- they might be fine
> already... iirc betas are though not scaled by the level of unexplained
> variance (i.e. noise) so their values might be somewhat wild, so for
> classification it might still be worth z-scoring or any other reasonable
> scaling approach
>
> for correlation analysis situation is quite different though, especially
> if doing gross z-scoring (instead of z-scoring against baseline).  e.g. if
> you within your patterns have some prominent preference, for instance,
> anterior higher than posterior for one category,  z-scoring might
> damage that effect heavily or obliterate it entirely.
>
> Summary: z-score or not depends on what you want from your analysis and
> what is your hypothesis ;-)
>
> On Fri, 30 Jul 2010, Vadim Axel wrote:
>
> >    Hi,
> >    When I run classification on raw fMRI data I always make a z-score
> >    (subtract the mean and divide by std) for each voxel / scan.
> >    Now I tried some sort of correlation analysis, while I run a
> >    correlation for beta images (similar to Haxby 2001). So, the z-score
> is
> >    going to be across beta_per_condition values (several values only).
> The
> >    question is: does is make sense to zcore the beta results?
> >    I ran some simulations while I add a noise to each voxel. So, I know
> >    that there is a real correlation in my data. Whereas without zscore
> the
> >    results indeed show high correlation, after zscoring procedure the
> >    correlation is virtually disappeared. I also tried just to subtract
> the
> >    mean across conditions, but the correlations still do not look good.
> >    What is the correct way to do run this analysis?
> --
>                                  .-.
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