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Hi David and Torben, Thank you both for your very helpful points! Perfect - this is exactly what I needed to know! :) Joelle On Thu, Oct 1, 2015 at 3:44 AM, Torben Lund <[log in to unmask]> wrote: > Dear all > > Starting from SPM12 you can now also write the “filtered” (=thresholded) > images directly form the Results Report section of the batch manager, > choose “thresholded SPM under “Wtite filtered images” and you will get the > thresholded spmT and spmF images. If you would like to write out both > uncorrected, FDR and FWE, you should make three “Results Report”. > > Best > Torben > > > > > Torben Ellegaard Lund > Associate Professor, PhD > Center of Functionally Integrative Neuroscience (CFIN) > Aarhus University > Aarhus University Hospital > Building 10G, 5th floor, room 31 > Noerrebrogade 44 > 8000 Aarhus C > Denmark > Phone: +45 7846 4380 > Fax: +45 7846 4400 > http://www.cfin.au.dk > [log in to unmask] (for official stuff) > [log in to unmask] (for faster response) > > > > > > Den 01/10/2015 kl. 09.18 skrev David Vállez Garcia < > [log in to unmask]>: > > Hi, > > The contrast manager uses the smpT.nii for the T-contrast and the spmF.nii > for the F-contrast. If you want to save the thresholded image according to > your p-value, k value (min number of voxel per cluster) and decision about > correction for multiple comparisons (FDR, FWE or uncorrected) you have to > save the file in the option "save thresholded image" located close to the > plot button. > > Hope this clarifies a bit more. > > David > > > -------- Original Message -------- > From: Joelle Zimmermann <[log in to unmask]> > Sent: Wednesday, September 30, 2015 11:18 PM > To: [log in to unmask] > Subject: Re: [SPM] SPM_T versus Con > > 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 >>>> >>> >>> >>> >> > > >