Thanks for the quick response! So if I wanted to use the Calhoun 2004 approach, I should be able to use the Steffener 2010 correction to address the violation of the assumption that the regressors were standardized and generate a new beta.nii.gz file where the primary beta values have been replaced with the Calhoun 2004 measure. Can I assume the three regressors are more or less orthogonal? I got non-zero numbers when I tried to test the assumption in the Xtmp.X variable
sum(X(1:207,4).*X(1:207,5)) but not hugely non-zero so maybe just rounding errors? On Jul 9, 2013, at 4:16 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 202-297-8117 http://joedien.com//
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