In fact the method implemented in PyMVPA is not similar to what is used in the paper. The CDist Node will compute distances between all pairs of targets betas b (eg. i,j) between the 2 chunks (A/B), that is for squared euclidian: d(b_iA,b_jB) = (b_iA-b_jB).(b_iA-b_jB)T While the crossvalidated squared euclidian as described in this paper is: d_AB(b_i,b_j) = (b_iA-b_jA).(b_iB-b_jB)T . The first measures distance between patterns across chunks. The second measures between chunks "covariance" of intra-chunk multivariate distance which are then tested for ranks or ordinal stability across cross-validation chunks.
I will try to implement the latter in PyMVPA at some point. On Tue, Apr 25, 2017 at 4:23 PM, Matteo Visconti di Oleggio Castello < matteo.visco...@gmail.com> wrote: > Yes, you should be able to use it within searchlights as any other Measure > class. Unfortunately, I do not think that it can support a varying > covariance matrix at the moment, which makes it less ideal to work with > Mahalanobis distances. We should augment that to allow such option. > > On Tue, Apr 25, 2017 at 12:44 PM, basile pinsard <basile.pins...@gmail.com > > wrote: > >> Hi Matteo, >> >> thanks, that's great, I will give it a try. >> Also do you think this can be used in a Searchlight? >> Even with varying kwargs to give the spatial covariance matrix in case of >> mahalanobis? >> >> Thank you. >> >> Basile >> >> On Tue, Apr 25, 2017 at 12:13 PM, Matteo Visconti di Oleggio Castello < >> matteo.visco...@gmail.com> wrote: >> >>> Hi Basile, >>> >>> the new release of PyMVPA 2.6.1 introduces mvpa2.measures.rsa.CDist, >>> that allows you to compute cross-validated RSA ( >>> https://github.com/PyMVPA/PyMVPA/blob/master/mvpa2/measures/rsa.py#L27), >>> and you can specify which distance metric you want to use, with additional >>> kwargs. >>> >>> Matteo >>> >>> On Tue, Apr 25, 2017 at 11:14 AM, basile pinsard < >>> basile.pins...@gmail.com> wrote: >>> >>>> Hi PyMVPA developers and users. >>>> >>>> I was wondering if there was a way in PyMVPA to use the approaches >>>> described in this paper: >>>> "Reliability of dissimilarity measures for multi-voxel pattern analysis" >>>> were the use of cross-validated mahalanobis distance is advocated in >>>> favor of correlation based RSA measures. >>>> >>>> Thank you. >>>> >>>> -- >>>> Basile Pinsard >>>> >>>> *PhD candidate, * >>>> Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne >>>> Universités, UPMC, INSERM, CNRS >>>> *Brain-Cognition-Behaviour Doctoral School **, *ED3C*, *UPMC, Sorbonne >>>> Universités >>>> Biomedical Sciences Doctoral School, Faculty of Medicine, Université de >>>> Montréal >>>> CRIUGM, Université de Montréal >>>> >>>> _______________________________________________ >>>> Pkg-ExpPsy-PyMVPA mailing list >>>> Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org >>>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg- >>>> exppsy-pymvpa >>>> >>> >>> >>> >>> -- >>> Matteo Visconti di Oleggio Castello >>> Ph.D. Candidate in Cognitive Neuroscience >>> Dartmouth College >>> >>> +1 (603) 646-8665 <(603)%20646-8665> >>> mvdoc.me <http://www.mvdoc.me/> || linkedin.com/in/matteovisconti || >>> github.com/mvdoc >>> >>> _______________________________________________ >>> Pkg-ExpPsy-PyMVPA mailing list >>> Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org >>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg- >>> exppsy-pymvpa >>> >> >> >> >> -- >> Basile Pinsard >> >> *PhD candidate, * >> Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne >> Universités, UPMC, INSERM, CNRS >> *Brain-Cognition-Behaviour Doctoral School **, *ED3C*, *UPMC, Sorbonne >> Universités >> Biomedical Sciences Doctoral School, Faculty of Medicine, Université de >> Montréal >> CRIUGM, Université de Montréal >> >> _______________________________________________ >> Pkg-ExpPsy-PyMVPA mailing list >> Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org >> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa >> > > > > -- > Matteo Visconti di Oleggio Castello > Ph.D. Candidate in Cognitive Neuroscience > Dartmouth College > > +1 (603) 646-8665 <(603)%20646-8665> > mvdoc.me <http://www.mvdoc.me/> || linkedin.com/in/matteovisconti || > github.com/mvdoc > > _______________________________________________ > Pkg-ExpPsy-PyMVPA mailing list > Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa > -- Basile Pinsard *PhD candidate, * Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS *Brain-Cognition-Behaviour Doctoral School **, *ED3C*, *UPMC, Sorbonne Universités Biomedical Sciences Doctoral School, Faculty of Medicine, Université de Montréal CRIUGM, Université de Montréal
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