Dear Yaroslav, thanks for your quick reply. Just to have things clear: the definition of TransferError refers to the accuracy of the classifier's predictions on a novel dataset (first alinea of chapter 5.2 Error calculation). So the CrossvalidatedTransferError is the mean of the transfererrors (i.e., accuracies) over the validations. From your reply I understand that the outcomes of the analysis in the example (the Searchlight on fMRI data) are not the accuracies but the inverse (i.e., 1 - accuracy). Would you please confirm if this is right? Thanks for the example with the conversion to Nifti, that helped me a lot! Best regards, Nynke
On Mon, 21 Feb 2011, Nynke van der Laan wrote: > First, what do the values in the sl_map refer to? According to the > documentation, these are the TransferErrors of the > n-foldclassification. yeap or extended: output of Searchlight corresponds to the measure you provide, in this case it is CrossValidatedTransferError, which in turn aggregates TransferErrors with default argument errorfx=MeanMismatchErrorFx(); thus values are indeed errors in your case > Later on it is called an sensitivitymap. But > does this mean that it are the accuracies? (true pos + true neg/ > total) or are it sensitivities? (true positive/all positives) sorry for not-clear variable naming I guess -- there is no magic conversion happening from above errors into accuracies happening -- it remains the same error(s) (i.e. 1.0 - accuracy = 1.0 - (TP+TN)/total) > Second, I read that it is possible to map the values from the sl_map > back to the original dataspace. In the example the variable > masked_orig_sl_map is the sensitivity map that is mapped back into the > original dataspace. How can I save this variable as a nifti file in > order to be able to use it as an 3d-overlay for in, for example, > MRIcron or another imageviewer? please look at another example, which haven't made into the compiled manual: https://github.com/PyMVPA/PyMVPA/blob/maint%2F0.4/doc/examples/searchlight.py#L112 the critical function for that is map2Nifti hope this helps -- =------------------------------------------------------------------= Keep in touch www.onerussian.com Yaroslav Halchenko www.ohloh.net/accounts/yarikoptic _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
