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Thanks for your help Chris. Could you clarify my question?: So when I select the contrast from the contrast manager that I want to look at, and load up the glass brain image, is this the spmT.nii or the con.nii? It looks more like the spmT.nii. On Wed, Sep 30, 2015 at 5:14 PM, Rita Elena Loiotile <[log in to unmask]> wrote: > oh oops. thanks for the clarification. sorry about that > > On Wed, Sep 30, 2015 at 5:12 PM, Christophe Phillips <[log in to unmask] > > wrote: > >> >> Dear Rita and Joelle, >> >> actually the p-values are not saved in any image but derived from the >> spmT (and degrees of freedom). >> The con image contain the estimated contrast, i.e. the linear combination >> of (beta) parameters you're interested in (e.g. a difference between 2 >> conditions). >> And yes, only con images should be passed to the 2nd level analysis. >> >> HTH, >> Chris >> >> - >> >> ------------------------------ >> *De: *"Rita Elena Loiotile" <[log in to unmask]> >> *À: *[log in to unmask] >> *Envoyé: *Mercredi 30 Septembre 2015 21:40:39 >> *Objet: *Re: [SPM] SPM_T versus Con >> >> >> Hi Joelle, >> Neither image is "thresholded." If you load and view either the con or >> spmT .nii files, you will see that there is a value at each voxel. >> The difference between the images is that the con image gives you the >> p-value at each voxel, while the spmT image gives you the t-statistic at >> each voxel. The functionality is the same as in regular null hypothesis >> significance testing. The t-statistic accounts for the difference in >> observed Beta relative to standard error of the Betas. The p-value tells >> you the statistical significance at each voxel; therefore, it accounts for >> the t-statistic at each voxel as well as the degrees of freedom of the data. >> P.S. when you do a second-level analysis, you should always use the con >> files, not the spmT's. >> >> On Wed, Sep 30, 2015 at 3:15 PM, Joelle Zimmermann < >> [log in to unmask]> wrote: >> >>> Hi SPMers, >>> >>> Am I correct that the spmT_0001.nii image is the same glass brain image >>> that I would see when I pick a particular contrast to visualize under >>> results and get the glass brain with the results table under it. Ie - the >>> regions that significantly stand out (based on the t-test) for that >>> particular contrast? >>> >>> Alternatively, what is actually the con_0001.nii image? Is this the same >>> image just not thresholded for significance? >>> >>> Thanks, >>> Joelle >>> >> >> >> >