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 <[email protected]> [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) >From just looking at it I have no clue what is wrong. Except for the dataset used this code is almost identical to the searchlight_dsm.py example. Does that one run for you? Did you inspect the dataset that it is somewhat "sane"? What does print blockavged_dataset.summary() say? Michael -- GPG key: 1024D/3144BE0F Michael Hanke http://mih.voxindeserto.de _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
