[pymvpa] Error running dissimilarity analysis
Michael Hanke
michael.hanke at gmail.com
Wed Dec 16 22:15:03 UTC 2009
Hey,
[ sorry for the delay ]
On Wed, Dec 16, 2009 at 12:04:28PM +0100, Valentin Haenel wrote:
> Would anyone of the senior developers like to comment on this, please.
You're senior too -- no? ;-)
> * Michael W. Cole <mwcole at gmail.com> [091214]:
> > 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)
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