On 07/09/2013 04:11 PM, Joseph Dien wrote: > Hi, > I have a question about how mkcontrast-sess works. I ran an > analysis using the mkanalysis-sess option spmhrf 2 so there are three > regressors for each predictor, the primary, the latency, and the > dispersion. When specifying the contrast weights for mkcontrast-sess, > the documentation indicates that they are specified in terms of the > conditions as numbered in the paradigm file, not the individual > regressors. Furthermore there only appears to be one contrast value > output for each contrast, not three. > > How are the three regressors being handled? I can think of several > scenarios: > > 1) the contrast weights are not actually in terms of conditions (the > documentation is incorrect), they are actually in terms of the > regressors (so contrasting conditions 1 and 2 could be specified as -a > 1 -a 2 -a 3 -c 4 -c 5 -c 6). > > 2) the latency and dispersion regressors are being ignored (a common > practice). The contrast weights should therefore be specified as -a 1 > -c 2. This is what happens. If you want to use the derivatives, then you need to spec -setwdelay. When you run the command, it will prompt you for 3 values to use. If you spec 1 0 0, then it will be the same as the default. If you want to test only the first derivative, then you would spec 0 1 0. Note that the 3rd regressor is the 2nd derivative wrt time, not the first derivative wrt the dispersion parameter. You cannot get the Calhoun 2004 value using a contrast (it is non-linear). doug > > 3) The Calhoun et al (2004) approach is being used to combine the > three regressors into a "derivative boost" amplitude > measure. The contrast weights should therefore be specified as -a 1 -c 2. > > Thanks for any help you can give me! > > Joe > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdie...@mac.com <mailto:jdie...@mac.com> > Phone: 202-297-8117 > http://joedien.com// > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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