Sounds good! Regarding creating a new volume and computing contrasts from it, what do you mean? I didn't follow that.
Thanks! Joe On Jul 10, 2013, at 1:33 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > On 07/10/2013 01:29 PM, Joseph Dien wrote: >> 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. > Sorry, it had been a while since I read that paper. I did not know that > they had a formulation that included the 2nd derivative. >> >> 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. > I don't know how much it will hurt the power. You'd have to look at the > efficiency. > doug > >> >> >> On Jul 10, 2013, at 1:21 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu <mailto: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> >>>> <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> >>>>>> <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> >>>>>>> <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> >>>>>>>> <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> >>>>>>>>>> <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> >>>>>>>>> <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> >>>>>>>>> <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> >>>>>>>> <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> >>>>>>> <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> >>>>>> <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> >>>>> <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> >>>>> 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> >>>> <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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