It looks as though selxavg3-sess generates the contrast analyses at the same time as the beta weights. Would it be possible to run selxavg3-sess once to obtain the beta weights, modify the beta.nii.gz file, and then rerun selxavg3-sess to obtain the contrast statistics using the modified beta weights?
Joe On Jul 9, 2013, at 5:08 PM, Joseph Dien <jdie...@mac.com> wrote: > I tried correlations and the 2nd derivative is definitely not orthogonal. > > >> corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)]) > > ans = > > 1.0000 -0.0000 -0.5427 > -0.0000 1.0000 -0.0298 > -0.5427 -0.0298 1.0000 > > I looked at the regressors that SPM generates for the same data: > > ans = > > 1.0000 0.0436 0.1740 > 0.0436 1.0000 -0.0226 > 0.1740 -0.0226 1.0000 > > The first derivative is not as orthogonal but the second derivative was much > more orthogonal. > Does this have to do with what you noted below about how the second > derivative is being calculated? > So does this mean I should avoid the spmhrf 2 option entirely to avoid loss > of statistical power? > > Thanks for the help! > > Joe > > > On Jul 9, 2013, at 4:34 PM, Joseph Dien <jdie...@mac.com> wrote: > >> 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// >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> 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// > > > > > > > > > > > > > _______________________________________________ > 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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