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Hi Elena, Please, see below: On 21 August 2016 at 16:37, elena mazza <[log in to unmask]> wrote: > Good evening Anderson, > doing the different designs, some doubts come up. > > 1. Regarding the following design > > EV1: intercept > EV2: +1/-1 for group (+1 BP; -1 Controls) > EV3: age > EV4: sleep efficacy > EV5: EV2*EV3 (interaction group by age) > EV6: EV2*EV4 (interaction group by sleep efficacy) > EV7: EV3*EV4 (interaction age by sleep efficacy) > EV8: EV2*EV3*EV4 (interaction group by age by sleep efficacy) > > When I create the design.mat, is the order in which I enter the patients > that are part of group 1 and the ones that belong to group 2 important? > I mean EV2 has to include first all BP, and then all controls? > +1 > +1 > +1 > +1 > -1 > -1 > -1 > -1 > The order as the subjects are entered in the design has only to match the order as the images are entered in the 4D file used with randomise or PALM, or the same order as the COPEs or FEAT directories are entered in FEAT. That order is arbitrary and you can rearrange the rows at your convenience. > > 2. Regarding the intercept. i think I didn't understand exactly when I > have to use it in the designs. > > a) Why in the design above you suggested to inclued it, whereas in the > following design is not necessary? > > EV1: BP (coded as 0/1) > EV2: SCZ (coded as 0/1) > EV3: CON (coded as 0/1) > EV4: age BP (put zeros for the non-BP) > EV5: age SCZ (put zeros for the non-SCZ) > EV6: age CON (put zeros for the non-CON) > EV7: sleep efficacy BP (put zeros for the non-BP) > EV8: sleep efficacy SCZ (put zeros for the non-SCZ) > EV9: sleep efficacy CON (put zeros for the non-CON) > EV10: EV4*EV7 (that is, interaction age by sleep efficacy in BP) > EV11: EV5*EV8 (that is, interaction age by sleep efficacy in SCZ) > EV12: EV6*EV9 (that is, interaction age by sleep efficacy in CON) > > Note that there is no explicit EV for intercept in this case. > In this design, with 3 groups, the intercept is in fact there, but split across the three groups in EV1, EV2 and EV3. In the other design, with two groups, the intercept is shown explicitly. However, it is possible to reorganise both designs so that the opposite happens, i.e., it is possible to reorganise the design for 2 groups so that the intercept is split across, and it is also possible to reorganise the design with 3 groups so that there is a column full of ones for the intercept. These reorganised designs would lead to identical results. Choosing one or another is just a matter of readability. > > > b) I also read that demeaning can be skipped if an intercept is entered > in the design. So are they (demean-intercept) mutually exclusive? > For these designs that will use contrasts comparing groups there is no need for demeaning. Please have a look at Jeanette Mumford's page on this topic: http://mumford. fmripower.org/mean_centering/ > > > 3. Last question concern the randomise script: when do I have to add -D > option? > I read in the forum that if I demean by hand the values, in the design, i > don't have to add the -D option. If i don't demean by hand i have to add it. > Is that correct? > For these contrasts there is no need for -D as the intercept is in one way or another in the model and also because there are only group comparisons. Jeanette's page should clarify it. > > So, demeaning the values by hand AND adding in the script the -D option > is an error?! > Not an error. Randomise would demean again. Since the mean would already be zero, it would subtract zero, to no effect. All the best, Anderson > > Best, > Elena > > ________________________________ > Da: FSL - FMRIB's Software Library <[log in to unmask]> per conto di > Anderson M. Winkler <[log in to unmask]> > Inviato: martedì 14 giugno 2016 09.19.27 > A: [log in to unmask] > Oggetto: Re: [FSL] interaction design with two continuous variables in two > groups > > Hi Elena, > > With three groups, perhaps the most intuitive way is this: > > EV1: BP (coded as 0/1) > EV2: SCZ (coded as 0/1) > EV3: CON (coded as 0/1) > EV4: age BP (put zeros for the non-BP) > EV5: age SCZ (put zeros for the non-SCZ) > EV6: age CON (put zeros for the non-CON) > EV7: sleep efficacy BP (put zeros for the non-BP) > EV8: sleep efficacy SCZ (put zeros for the non-SCZ) > EV9: sleep efficacy CON (put zeros for the non-CON) > EV10: EV4*EV7 (that is, interaction age by sleep efficacy in BP) > EV11: EV5*EV8 (that is, interaction age by sleep efficacy in SCZ) > EV12: EV6*EV9 (that is, interaction age by sleep efficacy in CON) > > Note that there is no explicit EV for intercept in this case. > > The contrasts are then: > > Differences between groups: > C1: 1 -1 0 0 0 0 0 0 0 0 0 0 F1 > C2: 1 0 -1 0 0 0 0 0 0 0 0 0 F1 > C3: 0 1 -1 0 0 0 0 0 0 0 0 0 > > Interaction age by group: > C4: 0 0 0 1 -1 0 0 0 0 0 0 0 F2 > C5: 0 0 0 1 0 -1 0 0 0 0 0 0 F2 > C6: 0 0 0 0 1 -1 0 0 0 0 0 0 > > Interaction sleep efficacy by group: > C7: 0 0 0 0 0 0 1 -1 0 0 0 0 F3 > C8: 0 0 0 0 0 0 1 0 -1 0 0 0 F3 > C9: 0 0 0 0 0 0 0 1 -1 0 0 0 > > Interaction age by sleep efficacy by group: > C10: 0 0 0 0 0 0 0 0 0 1 -1 0 F4 > C11: 0 0 0 0 0 0 0 0 0 1 0 -1 F4 > C12: 0 0 0 0 0 0 0 0 0 0 1 -1 > > The t-contrasts (C1-C12) can all be repeated with the signs flipped, for a > total of 24 tests. The F-tests, however, remain the same for already being > bidirectional (two-tailed), i.e., no need to duplicate them up to F8. > > All the best, > > Anderson > > > On 13 June 2016 at 14:30, elena mazza <[log in to unmask]<mailto: > [log in to unmask]>> wrote: > Hello Anderson, > Thank you very much for your reply! > I have another question: what if I have three groups (such as > bipolar-schizophrenia-controls)? > > Thank you in advance. > > All the best, > Elena > ________________________________ > Da: FSL - FMRIB's Software Library <[log in to unmask]<mailto:FSL > @JISCMAIL.AC.UK>> per conto di Anderson M. Winkler <[log in to unmask] > <mailto:[log in to unmask]>> > Inviato: sabato 11 giugno 2016 08.56.03 > A: [log in to unmask]<mailto:[log in to unmask]> > Oggetto: Re: [FSL] interaction design with two continuous variables in two > groups > > Hi Elena, > > This would be a three-way interaction. The design is almost fine, only > need to replace the intercept (last EV) for two new EVs one for each group. > Instead, how about coding as this: > > EV1: intercept > EV2: +1/-1 for group > EV3: age > EV4: sleep efficacy > EV5: EV2*EV3 (interaction group by age) > EV6: EV2*EV4 (interaction group by sleep efficacy) > EV7: EV3*EV4 (interaction age by sleep efficacy) > EV8: EV2*EV3*EV4 (interaction group by age by sleep efficacy) > > The contrasts are then: > C1: [0 0 0 0 0 0 0 1] > C2: [0 0 0 0 0 0 0 -1] > > All the best, > > Anderson > > > On 10 June 2016 at 15:22, Elena Mazza <[log in to unmask]<mailto: > [log in to unmask]>> wrote: > Dear FSL users, > I had a question about how to set up a design. > I want to see if there is an interaction effect between age and sleep > efficacy on white matter integrity, and if this interaction differs in the > two groups that I considered (Healthy subjects VS Patients). > > I know that considering just ONE sample the design will be as follows: > > EV1: age > EV2: sleep efficacy > EV3: product EV1*EV2. > EV4: intercept > > where the interaction is tested with: > > C1: [0 0 1 0] > > C2: [0 0 -1 0] > > - Considering TWO groups (Healthy control->first group Vs Patients -> > second group), do I have to split each variables in two columns as follows? > > EV1: age of Healthy controls > EV2: age of Patients > EV3: sleep efficacy of Healthy controls > EV4: sleep efficacy of Patients > EV5: product EV1*EV3 > EV6: product EV2*EV4 > EV7: intercept > > where the difference between groups in the interaction is tested with: > > C1: [0 0 0 0 1 -1 0] > > C2: [0 0 0 0 -1 1 0] > > Is it correct? > how about the intercept? > > > Thank you in advance! > > Best, > Elena Mazza >