Sorry all, I've off-line for a while. OK, @bthirion: In the demo, I
pseudo-randomly tweaked the threshold value from 2.5 to 2.3, loosely saying
to myself, "after all, one number is not as good as another". You're right,
'low'  thresholds will only lead to noisy figures. Here, the threshold is
for a z statistic map indeed.

Altogether, this is just a demo, and the user/caller will always be
responsible for deciding a value, --and a meaning-- for the threshold
parameter. At the moment, no assumption what soever is made about the
actual meaning of this threshold, beyond the natural understanding that
"image/map values (absolute ?) less than threshold should be taken as zero".


On Wed, Oct 9, 2013 at 8:04 PM, bthirion <notifications@github.com> wrote:

> In examples/labs/need_data/localizer_glm_ar.py:
>
> >               slicer='z',
> >               black_bg=True,  # looks much better thus
> >               figure=10,
> > -             threshold=2.5)
> > +             threshold=2.3)
>
> I agree that percentiles are very useful in general, for instance when
> you're dealing with independent components maps etc. However, I tend to
> disagree when it's about a z map that comes from a glm: the common use in
> the community is to threshold according a given type I error control. The
> defaults thresholds adpted e.g. in SPM are - p < 0.001 uncorrected (z
> >3.09). - or p < 0.05 corrected (z>4.8 approximately if you use 3mm
> voxels). I think that these are reasonable rules -- as long as we're
> dealing with a z map. Sorry for bringing such a mess in a quite unrelated
> PR.
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/nipy/nipy/pull/291/files#r6864257>
> .
>



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