I think that would work. You would need to change the time stamps on the .mat file in the analysis folder. When you re-run selxavg3-sess, it will see that the .mat files are newer than the beta and regenerate the contrasts. But what are you planning to do the the beta file? It sounds like a potentially bad idea
doug
On 07/09/2013 10:26 PM, Joseph Dien wrote:
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 <jdien07@mac.com mailto:jdien07@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 1.0000The 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 <jdien07@mac.com mailto:jdien07@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 <greve@NMR.MGH.HARVARD.EDU mailto:greve@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:
- 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).
- 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
- 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
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E-mail: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
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E-mail: jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//