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Hi Kim, The test statistic will be the same, although the p-values may be different. To have identical p-values, for designs 2 and 3, would need to drop the -within, leaving -whole only. However, the p-values would still differ a bit, even if using the same seed, as with designs of different sizes, the random permutations will rarely be equivalent. All the best, Anderson On 10 June 2016 at 13:50, Kim TRAN <[log in to unmask]> wrote: > Hi Anderson, > > As one timepoint is knocked out from each subject in design 2 and 3, if I > enter in model only the data of timepoint 1 or 2, the design 2/3 and this > one should give the same results? > > EB EV1 EV2 > 1 1 0 > 1 1 0 > 1 1 0 > 1 1 0 > 1 1 0 > 1 0 1 > 1 0 1 > 1 0 1 > > Thanks a lots, > > Best regard, > > Kim TD > > On Wed, 20 Jan 2016 08:58:10 +0000, Anderson M. Winkler < > [log in to unmask]> wrote: > > >Hi Kim, > > > >Design 1 tests within-subject effects (if there is a difference between > >timepoints, for instance, and interactions). Design 4 tests > between-subject > >effects (if there is a group difference across both timepoints). > > > >In design 1, the subject-specific intercepts are entered as additional, > >confound EVs. In design 4, the subject-specific slopes are entered as > >additional, confound EVs. > > > >Designs 2 and 3 do something else: for these designs either of the two > >timepoints is knocked out from each subject, such that it's as if these > >marked timepoints didn't exist. Design 2 causes t2 to be ignored, such > that > >comparisons are between groups on what concerns timepoint 1 only. Design 3 > >causes t1 to be ignored, such that comparisons are between groups on what > >concerns timepoint 2 only. > > > >So, please note that for designs 2 and 3, it's the opposite than what you > >wrote below, i.e., design 2 tests timepoint 1, whereas design 3 tests > >timepoint 2. > > > >All the best, > > > >Anderson > > > > > >On 19 January 2016 at 13:07, Kim TRAN <[log in to unmask]> wrote: > > > >> Hi Anderson, > >> > >> I have a small question, what is the difference between design1 et > design4 > >> in the file that you showed me? I think they're kind of similar. > Design2 is > >> used for testing 2nd scan because values for EV3-Ev22 are in the 2nd > scan, > >> and design3 is used for the 1st scan, isn't it? Could you check this for > >> me? Thank you very much, > >> > >> Best regard, > >> > >> Kim > >> > >> On Sat, 14 Nov 2015 07:44:22 +0000, Anderson M. Winkler < > >> [log in to unmask]> wrote: > >> > >> >Hi Kim, > >> > > >> >These tests need to go in separate designs. You can still correct > across > >> >all with -corrcon in PALM. Or prune your hypotheses to what is more > >> >relevant (presumably the effect of the treatment, which is in design > 1), > >> >and run that in randomise or FEAT. > >> > > >> >All the best, > >> > > >> >Anderson > >> > > >> >On 13 November 2015 at 09:20, Kim TRAN <[log in to unmask]> wrote: > >> > > >> >> Hi Anderson, > >> >> > >> >> I am so sorry for having bothered you. I've found the response in > others > >> >> sheets of your file. It's all that I want, but I cannot make it just > >> with > >> >> one design? > >> >> > >> >> Thanks a lots, > >> >> Kim > >> >> > >> >> On Fri, 13 Nov 2015 08:58:05 +0000, Kim TRAN <[log in to unmask]> > >> >> wrote: > >> >> > >> >> >Hi Anderson, > >> >> > > >> >> >Thank you very much for your reply. The contrasts C1 and C2 in your > >> >> attached file are the differences (t1-t2) for each group? Because I > >> want to > >> >> run a one side t-test, could I add these 2 more contrasts for a > complete > >> >> approach: > >> >> >C5: -1 0 0 0 0 ... (t2-t1 in group 1) > >> >> >C6: 0 -1 0 0 0 ... (t2-t1 in group 2) > >> >> > > >> >> >Might they change the interpretation of C3 and C4? > >> >> > > >> >> >Thanks a lots, > >> >> > > >> >> >Kim > >> >> > > >> >> > > >> >> >On Fri, 13 Nov 2015 07:46:47 +0000, Anderson M. Winkler < > >> >> [log in to unmask]> wrote: > >> >> > > >> >> >>Hi Kim, > >> >> >> > >> >> >>Design is fine, but the contrasts need to be changed. Please, > delete > >> all > >> >> of > >> >> >>them and instead use: > >> >> >> > >> >> >>C1: 1 -1 0 0 0 0 .... > >> >> >>C2: -1 1 0 0 0 0 .... > >> >> >> > >> >> >>These will test the effect of the treatment, and can be used in > FEAT, > >> >> >>randomise, or PALM. > >> >> >> > >> >> >>However, it seems you also want to compare groups in the 1st and > 2nd > >> >> scans, > >> >> >>is this correct? If yes, please see at this link > >> >> >>< > >> >> > >> > https://dl.dropboxusercontent.com/u/2785709/outbox/mailinglist/design_kimtran.ods > >> >> > > >> >> >>the relevant designs. You'd need to use PALM, in which case you can > >> also > >> >> >>correct across all of them in the same run (option -corrcon). > Include > >> the > >> >> >>options -whole and -within (both) if you take this route. > >> >> >> > >> >> >>All the best, > >> >> >> > >> >> >>Anderson > >> >> >> > >> >> >> > >> >> >> > >> >> >>On 12 November 2015 at 16:24, Kim TRAN <[log in to unmask]> > wrote: > >> >> >> > >> >> >>> Dear FSL experts, > >> >> >>> > >> >> >>> I have 8 subjects, each scanned 2 times at 2 times point. The > fisrt > >> 5 > >> >> >>> subjects are in drug group, and another 3 are in placebo group. I > >> want > >> >> to > >> >> >>> compare results of those 2 groups. Are the design and contrasts > >> below > >> >> >>> correct? > >> >> >>> > >> >> >>> EB EV1 EV2 EV3 EV4 EV5 EV6 EV7 > EV8 > >> >> >>> EV9 EV10 > >> >> >>> 1 1 0 1 0 0 0 0 0 > >> >> 0 > >> >> >>> 0 > >> >> >>> 1 -1 0 1 0 0 0 0 0 > >> >> 0 > >> >> >>> 0 > >> >> >>> 2 1 0 0 1 0 0 0 0 > >> >> 0 > >> >> >>> 0 > >> >> >>> 2 -1 0 0 1 0 0 0 0 > >> >> 0 > >> >> >>> 0 > >> >> >>> 3 1 0 0 0 1 0 0 0 > >> >> 0 > >> >> >>> 0 > >> >> >>> 3 -1 0 0 0 1 0 0 0 > >> >> 0 > >> >> >>> 0 > >> >> >>> 4 1 0 0 0 0 1 0 0 > >> >> 0 > >> >> >>> 0 > >> >> >>> 4 -1 0 0 0 0 1 0 0 > >> >> 0 > >> >> >>> 0 > >> >> >>> 5 1 0 0 0 0 0 1 0 > >> >> 0 > >> >> >>> 0 > >> >> >>> 5 -1 0 0 0 0 0 1 0 > >> >> 0 > >> >> >>> 0 > >> >> >>> 6 0 1 0 0 0 0 0 1 > >> >> 0 > >> >> >>> 0 > >> >> >>> 6 0 -1 0 0 0 0 0 1 > >> >> 0 > >> >> >>> 0 > >> >> >>> 7 0 1 0 0 0 0 0 0 > >> >> 1 > >> >> >>> 0 > >> >> >>> 7 0 -1 0 0 0 0 0 0 > >> >> 1 > >> >> >>> 0 > >> >> >>> 8 0 1 0 0 0 0 0 0 > >> >> 0 > >> >> >>> 1 > >> >> >>> 8 0 -1 0 0 0 0 0 0 > >> >> 0 > >> >> >>> 1 > >> >> >>> > >> >> >>> Contrast: > >> >> >>> mean G1, 1st scan 5 0 1 1 1 1 > >> >> 1 > >> >> >>> 0 0 0 > >> >> >>> mean G1, 2nd scan -5 0 1 1 1 1 > >> >> 1 > >> >> >>> 0 0 0 > >> >> >>> mean G2, 1st scan 0 3 0 0 0 0 > >> >> 0 > >> >> >>> 1 1 1 > >> >> >>> mean G2, 2nd scan 0 -3 0 0 0 0 > >> >> 0 > >> >> >>> 1 1 1 > >> >> >>> G1 > G2, 1st scan 5 -3 1 1 1 1 > >> >> 1 > >> >> >>> -1 -1 -1 > >> >> >>> G1 > G2, 2nd scan -5 3 1 1 1 1 > >> >> 1 > >> >> >>> -1 -1 -1 > >> >> >>> > >> >> >>> Any help you can provide will be greatly appreciated. > >> >> >>> Best regard, > >> >> >>> Kim > >> >> >>> > >> >> >> > >> >> > >> > > >> > > >