Would anyone of the senior developers like to comment on this, please. V-
* 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) > > > > > Thank you, > Michael > > > On Sun, Dec 13, 2009 at 3:43 PM, Valentin Haenel > <[email protected]>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 <[email protected]> [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 > > > [email protected] > > > http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa > > > > > > _______________________________________________ > > Pkg-ExpPsy-PyMVPA mailing list > > [email protected] > > http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa > > > > > > -- > Michael W. Cole, Ph.D. > Post-doctoral researcher > Cognitive Control & Psychopathology Lab > Washington University in St. Louis > _______________________________________________ > Pkg-ExpPsy-PyMVPA mailing list > [email protected] > http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
