Sorry, not following what you are suggesting? I want the second derivative for calculating the Calhoun et al 2004 derivative boost measure. My understanding is that to the extent that the BOLD signal deviates from the canonical hrf, the amplitude of the primary regressor will be attenuated and the variance will instead end up in the first and second derivatives (to the extent that they are able to accommodate the divergence). By using a Calhoun measure that incorporates both the first and second derivatives, in principle I'll have a BOLD measure that is more robust to deviations from the canonical hrf.
However, if the way FSFAST is calculating the second derivative regressor is resulting in loss of statistical power due to shared variance with the primary regressor, then it would be best to just not include it at all in the estimation step. On Jul 10, 2013, at 1:21 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > 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 >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 <jdie...@mac.com >>>> <mailto:jdie...@mac.com> >>>> <mailto: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 >>>>> <mailto:jdie...@mac.com> >>>>> <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >>>>>> <mailto: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> >>>>>>>> <mailto:jdie...@mac.com> >>>>>>>> <mailto:jdie...@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 >>>>>>> >>>>>>> -- >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Center >>>>>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>>>>> <mailto: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 >>>>>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>>>>>> <http://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 >>>>>>> <mailto: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 <mailto:jdie...@mac.com> >>>>>> <mailto:jdie...@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 >>>>>> >>>>>> >>>>>> 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 <mailto:jdie...@mac.com> >>>>> <mailto:jdie...@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 >>>>> >>>>> >>>>> 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 <mailto:jdie...@mac.com> >>>> <mailto:jdie...@mac.com> >>>> Phone: 202-297-8117 >>>> http://joedien.com// >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu <mailto: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 >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdie...@mac.com <mailto:jdie...@mac.com> >> Phone: 202-297-8117 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> > > -- > 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 -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 202-297-8117 http://joedien.com//
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