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Hi Yawu, Please, see below: On 10 July 2015 at 08:38, Liu Y <[log in to unmask]> wrote: > Hi Anderson, > Again. Some questions concerning the results. > The study actually is a longitudinal study. Group A is the baseline FA > suntract followup FA of control group, and Group B is subtraction of > treatment group. Based on the design.mat and design.con, is my > understanding correct? The tbss_tfce_corrp_tstat1 indicates the FA subtract > of ctr group is larger than the one of treatment group, > tbss_tfce_corrp_tstat2 means FA subtract of ctr group is smaller than the > one of treatment group, right? > Yes. > What does the tbss_tfce_corrp_tstat3 and tbss_tfce_corrp_tstat4 mean? > The 3rd contrast tells about a positive change (along time) for group A, and the 4th contrast the same for group B. All the best. Anderson > Best regards, > Yawu > > On Wed, Jul 8, 2015 at 1:34 PM, Liu Y <[log in to unmask]> wrote: > >> Hi Anderson, >> Many thanks for such an awesome advice! >> Best regards, >> Yawu >> On 08/07/2015 1:00 pm, "Anderson M. Winkler" <[log in to unmask]> >> wrote: >> >>> Hi Yawu, >>> >>> Yes, in that case, then it's possible to compare. And even better if >>> there is an equal number of subjects of each group in each site. ITo get >>> around the warning message you have two mutually exclusive options: >>> >>> 1) Assume that the variances for both sites are the same. In that case, >>> simply ignore the warning, and run randomise making sure that the option >>> "-e" is *not* used, thus allowing all subjects to be permuted freely >>> across groups and sites. >>> >>> 2) Not assume that the variances for both sites are the same. In that >>> case, use the "group" column to define one such "group" per site (not per >>> experimental group, but actual scanning site). The warning message will >>> appear again: just ignore it. If the number of subjects in each site is >>> almost the same (you have 85 subjects overall, so if about 40-45 subjects >>> are in each site), then you can use randomise, now including the option "-e >>> design.grp". If, however, the number of subjects in each site is too >>> different (e.g., something like about 30 in one site and 50 in the other, >>> or anything more extreme than that) then randomise cannot be used. Instead, >>> use PALM, with the options "-eb design.grp" and also "-vg auto", so that >>> the different variances for each site are taken into account. >>> >>> For either of these cases, the design and contrasts as you have are fine. >>> >>> There could be other complicated cases (variances for each experimental >>> group being different, or both groups and sites with different variances, >>> being four variance groups overall). These can be dealt with in PALM if >>> needed, but other modifications would need to be made then. >>> >>> All the best, >>> >>> Anderson >>> >>> >>> On 8 July 2015 at 10:11, Liu Y <[log in to unmask]> wrote: >>> >>>> Hi Anderson, >>>> Maybe I did not say clearly in y previous emails. Our data are from two >>>> sites, the Group 1 contains two sites' data, and Group 2 also contains two >>>> sites' data. In this situation, we can compare the two groups, right? >>>> Thanks, >>>> Yawu >>>> >>>> On Wed, Jul 8, 2015 at 11:26 AM, Anderson M. Winkler < >>>> [log in to unmask]> wrote: >>>> >>>>> Hi Yawu, >>>>> >>>>> If each experimental group was acquired at a different site, it's not >>>>> possible to separate site effects from group effects. Any difference found >>>>> could be ascribed to scanner differences, and nothing can be said about the >>>>> groups. >>>>> >>>>> So, no analysis can be done comparing groups. >>>>> >>>>> This is unrelated to the warning message, but addressing the message >>>>> isn't relevant because of the issue above. >>>>> >>>>> All the best, >>>>> >>>>> Anderson >>>>> >>>>> >>>>> >>>>> >>>>> On 8 July 2015 at 08:20, Liu Y <[log in to unmask]> wrote: >>>>> >>>>>> Dear Anderson, >>>>>> Thanks for instant reply. I have read the link and followed the >>>>>> instruction, but when I saved the design in Glm, it warned me 'Problem >>>>>> with processing the model: Warning - design matrix uses different groups >>>>>> (for different variances), but these do not contain "separable" EVs for the >>>>>> different groups (...)' >>>>>> In our study, each group has different site data. >>>>>> Best regards, >>>>>> Yawu >>>>>> >>>>>> On Wed, Jul 8, 2015 at 9:59 AM, Anderson M. Winkler < >>>>>> [log in to unmask]> wrote: >>>>>> >>>>>>> Hi Yawu, >>>>>>> >>>>>>> Please, see this example in the GLM manual: >>>>>>> >>>>>>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM#Two-Group_Difference_Adjusted_for_Covariate >>>>>>> >>>>>>> Only note, though, that as shown, all subjects from one site seem to >>>>>>> be in one group, whereas all subjects from the other site seem to be in the >>>>>>> other group. If the design is entirely like that, it isn't possible to >>>>>>> disambiguate the effects of group vs site. >>>>>>> >>>>>>> All the best, >>>>>>> >>>>>>> Anderson >>>>>>> >>>>>>> >>>>>>> On 8 July 2015 at 07:54, Liu Y <[log in to unmask]> wrote: >>>>>>> >>>>>>>> Dear FSL experts, >>>>>>>> >>>>>>>> I would like to compare the FA difference between group 1 and group >>>>>>>> 2 with adjusting age, gender, study site, and education years (all >>>>>>>> demeaned). >>>>>>>> >>>>>>>> I wonder if my design.mat and design.con are correct? Thanks in >>>>>>>> advance. >>>>>>>> >>>>>>>> Mat: >>>>>>>> /NumWaves 6 >>>>>>>> /NumPoints 85 >>>>>>>> /PPheights 1 1 0 0 0 0 >>>>>>>> /Matrix >>>>>>>> group1 group2 site education sex age >>>>>>>> 1 0 -0.32 3.92 -0.44 4.66 >>>>>>>> 1 0 -0.32 -1.08 0.56 -3.17 >>>>>>>> 1 0 -0.32 2.92 0.56 1.52 >>>>>>>> . >>>>>>>> . >>>>>>>> . >>>>>>>> 0 1 0.68 1.92 -0.44 -1.82 >>>>>>>> 0 1 0.68 1.92 -0.44 -5.54 >>>>>>>> >>>>>>>> con: >>>>>>>> /ContrastName1 group A > group B /ContrastName2 group B > group A >>>>>>>> /ContrastName3 group A mean /ContrastName4 group B mean /NumWaves 6 >>>>>>>> /NumContrasts 4 /PPheights 1.000000e+00 1.000000e+00 1.000000e+00 >>>>>>>> 1.000000e+00 /RequiredEffect 0.848 0.848 0.650 0.544 /Matrix 1.000000e+00 >>>>>>>> -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>>>>>>> -1.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>>>>>>> 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 >>>>>>>> 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 >>>>>>>> 0.000000e+00 0.000000e+00 0.000000e+00 >>>>>>>> >>>>>>>> BR, >>>>>>>> Yawu >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >