Dear all, I am trying to run a very simple searchlight on fMRI data via PyLab (on Mac Leopard).
My code is as follows: from mvpa.suite import * import os from matplotlib.pyplot import figure, show from mvpa.misc.io.base import SampleAttributes from mvpa.datasets.nifti import NiftiDataset if __debug__: debug.active += ["SLC"] attr = SampleAttributes(os.path.join(pymvpa_dataroot, 'attributes_test.txt')) dataset = NiftiDataset(samples=os.path.join(pymvpa_dataroot, 'time_series_original_run_all.nii.gz'), labels=attr.labels, chunks=attr.chunks, mask=os.path.join(pymvpa_dataroot, 'anatomy_mask.nii.gz')) detrend(dataset, perchunk=True, model='linear') zscore(dataset, perchunk=True, baselinelabels=[1], targetdtype='float32') # choose classifier clf = LinearCSVMC() # setup measure to be computed by Searchlight # cross-validated mean transfer using an Odd-Even dataset splitter cv = CrossValidatedTransferError(TransferError(clf), OddEvenSplitter()) cv = CrossValidatedTransferError( transfer_error=TransferError(LinearCSVMC(), splitter=OddEvenSplitter()) s1 = Searchlight(cv, radius=5) s1_map = s1(dataset) dataset.map2Nifti(s1_map).save('searchlight_5mm.nii.gz') --- this runs fine for a while and then it crashes and gives me the following errors which I am not sure what they mean. optimization finished, #iter = 59 nu = 0.775000 obj = -0.000003, rho = -0.999986 nSV = 67, nBSV = 57 Total nSV = 414 --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/<ipython console> in <module>() /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/mvpa/measures/base.pyc in __call__(self, dataset) 103 container applying transformer if such is defined 104 """ --> 105 result = self._call(dataset) 106 result = self._postcall(dataset, result) 107 return result /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/mvpa/measures/searchlight.pyc in _call(self, dataset) 106 107 # compute the datameasure and store in results --> 108 measure = self.__datameasure(sphere) 109 results.append(measure) 110 /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/mvpa/measures/base.pyc in __call__(self, dataset) 103 container applying transformer if such is defined 104 """ --> 105 result = self._call(dataset) 106 result = self._postcall(dataset, result) 107 return result /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/mvpa/algorithms/cvtranserror.pyc in _call(self, dataset) 171 172 # run the beast --> 173 result = transerror(split[1], split[0]) 174 175 # unbind the testdataset from the classifier /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/mvpa/clfs/transerror.pyc in __call__(self, testdataset, trainingdataset) 1300 Returns a scalar value of the transfer error. 1301 """ -> 1302 self._precall(testdataset, trainingdataset) 1303 error = self._call(testdataset, trainingdataset) 1304 self._postcall(testdataset, trainingdataset, error) /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/mvpa/clfs/transerror.pyc in _precall(self, testdataset, trainingdataset) 1256 self.__clf.states._changeTemporarily( 1257 enable_states=['training_confusion']) -> 1258 self.__clf.train(trainingdataset) 1259 if self.states.isEnabled('training_confusion'): 1260 self.training_confusion = self.__clf.training_confusion /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/mvpa/clfs/base.pyc in train(self, dataset) 366 367 if dataset.nfeatures > 0: --> 368 result = self._train(dataset) 369 else: 370 warning("Trying to train on dataset with no features present") /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/mvpa/clfs/libsvmc/svm.pyc in _train(self, dataset) 185 libsvm_param._setParameter('weight', weight) 186 --> 187 self.__model = svm.SVMModel(svmprob, libsvm_param) 188 189 /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/mvpa/clfs/libsvmc/_svm.pyc in __init__(self, arg1, arg2) 267 msg = svmc.svm_check_parameter(prob.prob, param.param) 268 if msg: --> 269 raise ValueError, msg 270 self.model = svmc.svm_train(prob.prob, param.param) 271 ValueError: C <= 0 ------- Your input would be greatly appreciated. Thanks a lot, J
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