[pymvpa] Help with map2nifti()

[Taku Ito]

Are all datasets supposed to have mappers?  My data set was loaded directly
from a NIFTI file, using mvpa2.datasets.mri.fmri_dataset, and when I loaded
it there was no mapper attached, though I attributed it target values and
chunks.  In other words, my original data set also does not have any
mappers.  Should I be manually attributing mappers to my data set (e.g.,
the searchlight call or the z-scoring call) and attach all those mappers as
a Chain?

Thanks!
Taku


On Sat, Nov 2, 2013 at 11:02 AM, Yaroslav Halchenko
<debian at onerussian.com>wrote:

> do in ipython
>
> map2nifti?
>
> and check out its doc:
>
> Definition: map2nifti(dataset, data=None, imghdr=None, imgtype=None)
> Docstring:
> Maps data(sets) into the original dataspace and wraps it into an Image.
>
> Parameters
> ----------
> dataset : Dataset
>   The mapper of this dataset is used to perform the reverse-mapping.
> data : ndarray or Dataset, optional
>   The data to be wrapped into NiftiImage. If None (default), it
>   would wrap samples of the provided dataset. If it is a Dataset
>   instance -- takes its samples for mapping.
>
>
> so if your res[1] doesn't have the mapper, just give as the first argument
> the
> original dataset which had it and which you gave to searchlight call
>
> On Fri, 01 Nov 2013, Taku Ito wrote:
>
> >    Hi again,
> >    I'm having issues with saving searchlight maps back to NIFTI format...
> >    I've been using the mvpa2.datasets.mri.map2nifti module and I've tried
> >    both
> >    map2nifti(res[1])�
> >    #and�
> >    map2nifti(res[1]).save('s1.nii.gz')
> >    But both come back with the
> >    AttributeError: 'DatasetAttributesCollection' object has no attribute
> >    'mapper'
> >    It seems that I have no mapper in my data set object - however, all
> I've
> >    done on the original data set is take out some samples, z-score them,
> and
> >    run an mvpa searchlight analysis with a NFoldPartitioner and Balancer
> >    (combined into a chainNode). �It seems that the dimensions of the
> output
> >    data set are essentially the same, minus the fact that the number of
> >    samples was reduced from 360 to 150 or so.
> >    I have, been able to use the h5save() command for hdf5 files, but
> would
> >    like to get it into NIFTI format so I can view the statistical maps in
> >    AFNI. �
> >    Please let me know if you have any insights! Your help is appreciated.
> >    Taku
> --
> 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
>
> _______________________________________________
> Pkg-ExpPsy-PyMVPA mailing list
> Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa




-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/attachments/20131104/8b8804d8/attachment.html>