Hi, Yaroslav, Thanks for the two ideas. I will certainly put #2 to task and get back to you. Another naive (but somewhat related) question: If I ran a searchlight analysis like the one I proposed, what would be the best way to save the peak performing (or other voxels of interest) voxel's coordinate/index and the index for the searchlight's neighboring voxels? I could then, I suppose, rerun the classifier on that searchlight ROI (without using the searchlight function) and harvest other properties (e.g., weights and confusion matrix) that I want. Again, many thanks for this, I am trying to learn quickly! Best, John
On Tue, Aug 18, 2009 at 11:08 PM, Yaroslav Halchenko<[email protected]> wrote: > >> I am new to PyMVPA, but so far I am really enjoying it. > Glad to hear it! Especially since you are coming with concrete questions > on somewhat novel usecases, not with bug reports that something crashed > upon you ;) > >> (2) Construct confusion matrix for each searchlight and save them all. >> (3) Save averaged (across the folds) SVM weights for all of the searchlights. > I could only wonder what you would do with those ;) but yeah -- we don't > have such functionality available "out of the box". > > But there are 2 possible ways "to accomplish the mission" > > #1 with our intervention: adjust searchlight's __call__ to provide > callbacks to your custom function or similar harvest_attribs, > which would simply collect anything you like from results of running cv > on each sphere > > #2 without our intervention: just look at the code of searchlight -- it > is very very short and self-explanatory. So, you could craft that loop > yourself by simply copy/pasting it and extending the way you like (can't > resist giving a pride to benefits of scripting and open-source) > > I guess, in the long run, #1 is preferable, but #2 could be the faster > track for you just to get the job done. > > P.S. to look at the code of searchlight, if you use ipython, the > simplest way is to call > > Searchlight?? > > Let us know if we should proceed with #1 ;) > > -- > .-. > =------------------------------ /v\ ----------------------------= > Keep in touch // \\ (yoh@|www.)onerussian.com > Yaroslav Halchenko /( )\ ICQ#: 60653192 > Linux User ^^-^^ [175555] > > > > _______________________________________________ > 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
