Why not just create a new volume and then compute contrasts from the new volume? What you are suggesting will work I think, but it leaves me a little nervous. The p-values will be meaningless.
As for the 2nd derivative, I think it must be a numerical issue (it is not computed analytically). Why do you need the 2nd derivative?
doug
On 07/10/2013 12:47 PM, Joseph Dien wrote:
I'm thinking of generating a modified beta.nii.gz file where the primary betas have been replaced with the Calhoun et al (2004) derivative boost measure. What do you think? Also, please note my question below about the second derivative as it is causing me concern about my analysis. Thanks!
Joe
On Jul 10, 2013, at 12:39 PM, Douglas N Greve <greve@NMR.MGH.HARVARD.EDU mailto:greve@NMR.MGH.HARVARD.EDU> wrote:
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 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 1.0000
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 <jdien07@mac.com mailto: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 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: > > 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: jdien07@mac.com mailto:jdien07@mac.com > mailto:jdien07@mac.com > mailto:jdien07@mac.com > Phone: 202-297-8117 > http://joedien.com// > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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: jdien07@mac.com mailto:jdien07@mac.com mailto:jdien07@mac.com Phone: 202-297-8117 http://joedien.com//
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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/
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Joseph Dien, Senior Research Scientist University of Maryland
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