[pymvpa] Error running dissimilarity analysis

[Michael W. Cole]

Hello Valentin,

Thanks for the reply.

I'm including the requested info:
PyMVPA 0.4.3 on Fedora 10 x86_64.

Here is the relevant part of the script:

    blockavged_dataset = NiftiDataset(samples=niftiFile,
>         labels=attrs.labels, chunks=attrs.chunks, labels_map={'cat1': 0,
> 'cat2': 1, 'cat3': 2, 'cat4': 3, 'cat5': 4},
>         mask=maskFile)
>
>     # remove first category from dataset
>     blockavged_dataset = blockavged_dataset.selectSamples(N.array([l != 0
> for l in blockavged_dataset.labels],
>                                             dtype='bool'))
>
>     """Create a dissimilarity matrix based on the labels of the data points
>     in our test dataset.  This will allow us to see if there is a
> correlation
>     between any given searchlight sphere and the experimental
> conditions."""
>
>     # create dissimilarity matrix using the 'confusion' distance
>     # metric
>     dsm = DSMatrix(blockavged_dataset.labels, 'confusion')


    #
>     # Run Searchlight
>     #
>
>     # choose classifier
>     dsmetric = DSMDatasetMeasure(dsm, 'pearson', 'pearson')
>
>     for radius in [6.4,9.6]:
>
>         # tell which one we are doing
>         print "Running searchlight with radius: %.2fmm..." % (radius)
>
>         # setup Searchlight with a custom radius
>         # radius has to be in the same unit as the nifti file's pixdim
>         # property.
>         sl = Searchlight(dsmetric, radius=radius)
>
>         # run searchlight on example dataset and retrieve error map
>         sl_map = sl(blockavged_dataset)
>


Thank you,
Michael


On Sun, Dec 13, 2009 at 3:43 PM, Valentin Haenel <valentin.haenel at gmx.de>wrote:

> Dear Micheal,
>
> could you please post pymvpa version, operating system, and the script you
> are
> using (if possible).
>
> The sphere size might not be the issue, since the searchlight will have
> less
> features at the edges of the brain, but its hard to tell from the error
> message alone.
>
> thanks.
>
> V-
>
> * Michael W. Cole <mwcole at gmail.com> [091213]:
> > I am trying to run a searchlight analysis based on the searchlight_dsm.py
> > example. I'm doing a 4-way classification with 2-voxel radius spheres.
> >
> > It will run for a few spheres, then crash with this error:
> >
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in <module>
> >   File "pymvpa_script1.py", line 154, in <module>
> >     sl_map = sl(blockavged_dataset)
> >   File "/usr/lib64/python2.5/site-packages/mvpa/measures/base.py", line
> 105,
> > in __call__
> >     result = self._call(dataset)
> >   File "/usr/lib64/python2.5/site-packages/mvpa/measures/searchlight.py",
> > line 108, in _call
> >     measure = self.__datameasure(sphere)
> >   File "/usr/lib64/python2.5/site-packages/mvpa/measures/ds.py", line 47,
> in
> > __call__
> >     test_mat = N.asarray([in_vec, dset_vec])
> >   File "/usr/lib64/python2.5/site-packages/numpy/core/numeric.py", line
> 230,
> > in asarray
> >     return array(a, dtype, copy=False, order=order)
> > ValueError: setting an array element with a sequence.
> >
> > I've found that the spheres that work have 1830 values each in in_vec and
> > dset_vec, but the sphere it crashes on only has 1540 values. I'm not sure
> if
> > this is related to the crash or not.
> >
> > Any ideas on how to get around this error?
> >
> > Thanks in advance!
> >
> > Michael
> >
> >
> > --
> > Michael W. Cole, Ph.D.
> > Post-doctoral researcher
> > Cognitive Control & Psychopathology Lab
> > Washington University in St. Louis
>
> > _______________________________________________
> > Pkg-ExpPsy-PyMVPA mailing list
> > Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> > http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
>
>
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>



-- 
Michael W. Cole, Ph.D.
Post-doctoral researcher
Cognitive Control & Psychopathology Lab
Washington University in St. Louis
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