[pymvpa] Zscore creates nan in dataset

[gal star]

Hello,
Unfortunately it did not remove the nan's vectors.

I've also tried to remove those specific scans from the samples list,
It still created nan vectors out of different scans.

Do you have any idea what can i do to remove/avoid those from the dataset?

My code looks like so:

attr =  SampleAttributes (os.path.join(source, map_name))
fds = fmri_dataset(samples=os.path.join(source,map_name),
targets=attr.targets, chunks=attr.chunks)
int = numpy.array([l in ['221','211','23'] for l in fds.sa.targets])
fds = fds[int]
zscore(fds, param_est=('targets',['23']), chunks_attr='chunks')

Thanks,
Gal Star





On Sun, Jan 18, 2015 at 7:40 PM, Yaroslav Halchenko <debian at onerussian.com>
wrote:

>
> On Sun, 18 Jan 2015, gal star wrote:
>
> >    Hello,
> >    Im using zscore, and i receive the following exception:
> >    " Some input data for predict is not finite (Nan or Inf)".
> >    I've checked my pre-processed nifti files - they don't include Nan
> values,
> >    and yet after using zscore i get that the dataset includes Nan values.
> >    How can i fix this situation so i could move forward withA
> >    the processing in my script?
> >    I've attached the script i'm using.A
>
> you must have some invariant (absent variance) features/voxels.  Use
> remove_invariant_features  to strip those away first
>
> --
> Yaroslav O. Halchenko, Ph.D.
> http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
> Research Scientist,            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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