[pymvpa] Help with map2nifti()

[Taku Ito]

Great!  Works like a charm. Thanks a lot.


On Mon, Nov 4, 2013 at 1:03 PM, Yaroslav Halchenko <debian at onerussian.com>wrote:

>
> On Mon, 04 Nov 2013, Taku Ito wrote:
>
> >    You're right, thank you, I was looking through the incorrect data set
> - My
> >    original data set (the one I wrote to right after fmri_dataset), has
> the
> >    following mappers:
> >    In [104]: data[1].a.mapper
> >    Out[104]: ChainMapper(nodes=[FlattenMapper(shape=(59, 69, 59),
> >    auto_train=True, space='voxel_indices'),
> >    StaticFeatureSelection(dshape=(240189,), slicearg=array([False, False,
> >    False, ..., False, False, False], dtype=bool))])
> >    However, after this data set, I constructed a sub-data set by just
> >    selecting certain samples with the target values I wanted, splitting
> the
> >    datasets accordingly, and then reconcatenating them into a new data
> set.
>
> that is where probably the mapper got "lost" ;-)
>
> >     (I then ran the ZScoreMapper() on this new data set, since I only
> wanted
> >    to Z score the samples I was going to use in the searchlight
> analysis.)
> >    In [105]: data_stack[1].a.mapper
> >    Out[105]: ZScoreMapper()
> >    Finally, I ran the searchlight analysis which resulted in:
> >    In [106]: res[1].a.mapper
> >    Out[106]: ZScoreMapper()
> >    Would it then be accurate for me to simply use the ChainMapper from
> the
> >    original data set (exclude the ZScoreMapper from the map2nifti
> function),
> >    like so:
> >    map2nifti(data[1], res[1].samples)
>
> yes -- should work
>
> >    Or would it be more accurate of me to construct a new ChainMapper
> which
> >    includes the ZScoreMapper, append it to the ChainMapper of the
> original
> >    data set, and then re-attribute it to the searchlight output data
> set?
>
> nah -- probably not needed/not worth the hassle.  If you did no action
> which would change 'features' origin, taking original dataset would be
> the easiest and most straightforward
>
> >    Thanks again!  This has been a huge hassle, and you've been a great
> help
> >    (though I realize that much of the troubles were my own carelessness
> >    now... Sorry!).
>
> well -- we should bear our portion of blame here too ;)  may be we
> should issue a warning whenever hstacking/etc datasets with the mappers
> so they do not get lost without notice (actually current master might
> keep them... I would need to check).
>
> Cheers,
> --
> Yaroslav O. Halchenko, Ph.D.
> http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
> Senior Research Associate,     Psychological and Brain Sciences Dept.
> 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
>
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>



-- 
Takuya Ito
Cognitive Control & Psychopathology Laboratory
Washington University in St. Louis

Cole Neuroscience Laboratory (http://www.mwcole.net/)
Center for Molecular and Behavioral Neuroscience (CMBN)
Rutgers-Newark University
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