Reply-To: | | [log in to unmask][log in to unmask]> >>>> wrote: >>>>> Hi Donald, >>>>> As far as I can tell, spm_regions filters and whitens the VOI time series, >>>>> and adjusts for the null space of the contrast if an adjustment is >>>>> specified >>>>> in xY.Ic. It defines the confound matrix, X0, but does not correct for it. >>>>> The following line in spm_peb_ppi corrects for the confounds. >>>>> >>>>> Yc = Y - X0*inv(X0'*X0)*X0'*Y; >>>>> PPI.Y = Yc(:,1); >>>>> >>>>> So the above correction does seem to be doing something different to >>>>> spm_regions. I'm wondering why the uncorrected data, Y, is used when >>>>> generating the ppi interaction term, while the corrected data Yc is to be >>>>> used as a covariate of no interest in the PPI model. I would has thought >>>>> that Yc should be used to generate the ppi interaction term as well. >>>>> >>>>> In my data, my X0 is a 195 x 7 matrix (I have 195 volumes per session). >>>>> >>>>> Regards, >>>>> Alex >>>>> >>>>> >>>>> On 30/04/2011 02:22, "MCLAREN, Donald" <[log in to unmask]> wrote: >>>>> >>>>>> I'm actually travelling at the moment. However, I know Y has already >>>>>> been adjusted as part of the VOI processing. >>>>>> >>>>>> Can you check what X0 looks like? >>>>>> >>>>>> Best Regards, Donald McLaren >>>>>> ================= >>>>>> D.G. McLaren, Ph.D. >>>>>> Postdoctoral Research Fellow, GRECC, Bedford VA >>>>>> Research Fellow, Department of Neurology, Massachusetts General >>>>>> Hospital and Harvard Medical School >>>>>> Office: (773) 406-2464 >>>>>> ===================== >>>>>> This e-mail contains CONFIDENTIAL INFORMATION which may contain >>>>>> PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED >>>>>> and which is intended only for the use of the individual or entity >>>>>> named above. If the reader of the e-mail is not the intended recipient >>>>>> or the employee or agent responsible for delivering it to the intended >>>>>> recipient, you are hereby notified that you are in possession of >>>>>> confidential and privileged information. Any unauthorized use, >>>>>> disclosure, copying or the taking of any action in reliance on the >>>>>> contents of this information is strictly prohibited and may be >>>>>> unlawful. If you have received this e-mail unintentionally, please >>>>>> immediately notify the sender via telephone at (773) 406-2464 or >>>>>> email. >>>>>> >>>>>> >>>>>> >>>>>> On Fri, Apr 29, 2011 at 2:55 AM, Alex Fornito <[log in to unmask]> >>>>>> wrote: >>>>>>> Hi all, >>>>>>> I have a question concerning the code used to implement a PPI analysis. >>>>>>> >>>>>>> In the spm_peb_ppi.m function packaged with SPM8, lines 329-332 remove >>>>>>> confounds from the input seed regions time course: >>>>>>> >>>>>>> % Remove confounds and save Y in ouput structure >>>>>>> %------------------------------------------------------------------------ >>>>>>> -- >>>>>>> Yc = Y - X0*inv(X0'*X0)*X0'*Y; >>>>>>> PPI.Y = Yc(:,1); >>>>>>> >>>>>>> PPI.Y is then to be used as a covariate of no interest when building the >>>>>>> PPI >>>>>>> regression model. However, on line 488, it is the uncorrected seed time >>>>>>> course, Y, that is input to the deconvolution routine and used to >>>>>>> generate >>>>>>> the ppi term: >>>>>>> >>>>>>> C = spm_PEB(Y,P); >>>>>>> xn = xb*C{2}.E(1:N); >>>>>>> xn = spm_detrend(xn); >>>>>>> >>>>>>> % Setup psychological variable from inputs and contast weights >>>>>>> %---------------------------------------------------------------------- >>>>>>> PSY = zeros(N*NT,1); >>>>>>> for i = 1:size(U.u,2) >>>>>>> PSY = PSY + full(U.u(:,i)*U.w(:,i)); >>>>>>> end >>>>>>> % PSY = spm_detrend(PSY); <- removed centering of psych variable >>>>>>> % prior to multiplication with xn. Based on discussion with Karl >>>>>>> % and Donald McLaren. >>>>>>> >>>>>>> % Multiply psychological variable by neural signal >>>>>>> >>>>>>> %---------------------------------------------------------------------- >>>>>>> PSYxn = PSY.*xn; >>>>>>> >>>>>>> Is there any specific reason why Y, rather than Yc(:,1), is used to >>>>>>> compute >>>>>>> PSYxn? I thought Yc might be more appropriate (?). >>>>>>> Thanks for your help, >>>>>>> Alex >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ------------------------------------------ >>>>>>> >>>>>>> Alex Fornito >>>>>>> Research Fellow >>>>>>> Melbourne Neuropsychiatry Centre >>>>>>> University of Melbourne >>>>>>> National Neuroscience Facility >>>>>>> Levels 1 & 2, Alan Gilbert Building >>>>>>> 161 Barry St >>>>>>> Carlton South 3053 >>>>>>> Victoria, Australia >>>>>>> >>>>>>> Email: [log in to unmask] >>>>>>> Phone: +61 3 8344 1876 >>>>>&gc |