 |
 |
Hi Arsene, Please see below: On 7 June 2017 at 07:00, Henri Longin <[log in to unmask]> wrote: > Hi Anderson, > > > Thank you for your prompt answer. > > >> I think the topic in that thread is exactly what you need. I have just > posted an example design there, please have a look. > >> There are 3 groups for that one, whereas yours have 2, so you only have > to simplify it a bit. > > Finally I found the thread dealing with groups and 4 time points. I > changed the design to adapt it to my experiment involving 2 groups and 4 > repeated measures (find it attached). > > Could you please tell me: > > 1) if the attached design is correct for my case > Design and contrasts look fine to me. > > 2) On associated contrasts you mention *linear increase* and *linear > decrease*. > But the changes that may occur throughout the 4 measures should not > necessarily have to be linear. I wonder if this design still hold. > The design holds, only the fit will be poorer, with a higher (less significant) p-value. > > 3) Also, how could I set contrasts on this design matrix for example to > test: > > - t2 > t1 in G1 > - t4 > t2 in G2 > - G2 > G1 for t1 > - ... > > > Yes, you can. Only note that, the more contrasts, the higher is the chance of error type I. To correct for multiple contrasts, use the option -corrcon in PALM. All the best, Anderson > > Arsene > > > > ------------------------------ > *Von:* FSL - FMRIB's Software Library <[log in to unmask]> im Auftrag von > Anderson M. Winkler <[log in to unmask]> > *Gesendet:* Dienstag, 6. Juni 2017 02:36 > *An:* [log in to unmask] > *Betreff:* Re: [FSL] Design for an experiment of 2 groups and 4 repeated > measures... PALM? > > Hi Arsene, > > I think the topic in that thread is exactly what you need. I have just > posted an example design there, please have a look. There are 3 groups for > that one, whereas yours have 2, so you only have to simplify it a bit. > > All the best, > > Anderson > > > On 2 June 2017 at 08:32, Henri Longin <[log in to unmask]> wrote: > >> Hi Anderson.. >> >> >> Sorry about returning to you with non relevant questions 😞 >> >> But... concerning my experiment which was performed on 2 groups and 4 >> repeated measures (t1, t2, t3 and t4)... >> Typically, I would like to compare >> >> - time points on each group >> - same time points between the 2 groups >> >> >> >> You advised me the link https://www.jiscmail.ac.uk/cgi >> -bin/webadmin?A2=FSL;271bf4c3.1705... >> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;271bf4c3.1705> >> I installed PALM, but: >> 1) I still don't see how to design this kind of experiment with FEAT >> 2) How could be a typical command example in PALM... >> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;271bf4c3.1705> >> >> >> Best regards, >> >> >> Arsene >> >> >> ------------------------------ >> *Von:* FSL - FMRIB's Software Library <[log in to unmask]> im Auftrag >> von Anderson M. Winkler <[log in to unmask]> >> *Gesendet:* Donnerstag, 1. Juni 2017 02:06 >> *An:* [log in to unmask] >> *Betreff:* Re: [FSL] Trouble with Two-Sample Paired T-test results using >> randomise TFCE >> >> Hi Arsene, >> >> In that case, please see the reply I've sent to the other ongoing topic >> in the list: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;271 >> bf4c3.1705 >> >> It seems an identical problem. >> >> All the best, >> >> Anderson >> >> >> On 31 May 2017 at 12:50, Henri Longin <[log in to unmask]> wrote: >> >>> Hi Anderson, >>> >>> >>> Thank for answer >>> >>> About the example design in the spreadsheet, it seems like you did it >>> for 2 groups and 2 repeated measures (t1 and t2)... >>> >>> Unfortunately, my experiment was done on 2 groups and 4 repeated >>> measures (t1, t2, t3 and t4)... >>> >>> >>> Best regards, >>> >>> >>> Arsene >>> >>> ------------------------------ >>> *Von:* FSL - FMRIB's Software Library <[log in to unmask]> im Auftrag >>> von Anderson M. Winkler <[log in to unmask]> >>> *Gesendet:* Mittwoch, 31. Mai 2017 12:20 >>> >>> *An:* [log in to unmask] >>> *Betreff:* Re: [FSL] Trouble with Two-Sample Paired T-test results >>> using randomise TFCE >>> >>> Hi Henri, >>> >>> TFCE will not give results that are one the opposite of another. >>> >>> For the design, please see at this spreadsheet an example (it's the >>> design1): https://dl.dropboxusercontent.com/u/2785709/outbox >>> /mailinglist/design_arsene.ods >>> >>> Note it's necessary one exchangeability block per subject. >>> >>> All the best, >>> >>> Anderson >>> >>> >>> On 31 May 2017 at 06:14, Henri Longin <[log in to unmask]> >>> wrote: >>> >>>> >>>> Hi Anderson, >>>> >>>> >>>> >>>> Thanks for the answer.... >>>> >>>> >>>> For the question 1) you said: >>>> >>>> >> It can happen: TFCE uses not only the height (that is symmetric >>>> around zero for both contrasts) but also the spatial distribution (that is >>>> not symmetric). So, it differs. >>>> >>>> So, what could be the signification of this for the results I obtained? >>>> >>>> Also: I performed an experience with 4 repeated measures (condition 1, condition >>>> 2, condition 3, condition 4) over 2 groups (control and test). >>>> So I want to examine: >>>> 1) the *time* effect in the *control* group >>>> 2) the *time* effect in the *test* group >>>> 3) the *timeXgroup* interaction... >>>> >>>> How could I build my design matrix in FSL. I have look at the >>>> *FEAT-UserGuide* and *GLM-FslWiki* but all examples deal with 2 or 3 >>>> measures >>>> >>>> Thanks in advance >>>> >>>> >>>> Arsene >>>> >>>> >>>> ------------------------------ >>>> *Von:* FSL - FMRIB's Software Library <[log in to unmask]> im Auftrag >>>> von Anderson M. Winkler <[log in to unmask]> >>>> *Gesendet:* Mittwoch, 31. Mai 2017 02:23 >>>> *An:* [log in to unmask] >>>> *Betreff:* Re: [FSL] Trouble with Two-Sample Paired T-test results >>>> using randomise TFCE >>>> >>>> Hi Arsene, >>>> >>>> Please see below: >>>> >>>> >>>> On 29 May 2017 at 19:14, Henri Longin <[log in to unmask]> >>>> wrote: >>>> >>>>> Dear all, >>>>> >>>>> I'm performing a two-Sample Paired T-test VBM using a statistical >>>>> analysis with randomise TFCE. >>>>> >>>>> 1) Results obtained by estimating the 2 paired differences A-B and >>>>> B-A showed to be different from each other (what was expected) but one was >>>>> not the opposite of the other: why? >>>>> >>>> >>>> It can happen: TFCE uses not only the height (that is symmetric around >>>> zero for both contrasts) but also the spatial distribution (that is not >>>> symmetric). So, it differs. >>>> >>>> >>>>> >>>>> >>>>> 2) More generally, how can one optimally choose the number of >>>>> permutations in randomise TFCE? >>>>> >>>> >>>> There is no rule for this. More permutations make the p-values more >>>> reliable. The default in randomise is 5000 and it's ok to stay with that. >>>> >>>> All the best, >>>> >>>> Anderson >>>> >>>> >>>> >>>>> >>>>> Thanks in advance >>>>> >>>>> >>>>> Arsene >>>>> >>>> >>>> >>> >> >