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Hi Michiko, How about this model: EV1: Patient group 1 EV2: Patient group 2 EV3: Controls EV4: age EV5: sex EV6: Patient-specific nuisance variable. About mean-centering: if the contrasts will only compare groups (EV1, EV2 and EV3), such that all other variables are never tested on their own, then there is no need for any mean-centering. This should also address the template issue: use all subjects, or a balanced random composition of members from all three groups. All the best, Anderson On 20 May 2017 at 15:28, Michiko <[log in to unmask]> wrote: > Dear FSL experts, > > I am planning to run a 3 group analysis with TBSS on DTI data and have > some specific questions I hope to get some advice on: > > The aim is to compare if diffusion indices (e.g. FA) significantly differ > between the 3 groups - particularly between patient groups. Running a quick > t-test shows there is significant difference in disease duration, one of > the variables specific to the patient groups and which we have to account > for in the model. What is the best way to conduct the analysis? > > I am thinking of running 2 models as follows: > Model 1 - > subjects: everyone > regressors: mean ptgrp 1, mean ptgrp 2, mean HC, confounders available for > everyone (e.g. age, demeaned across everyone) > contrasts: ptgrp 1 vs HC, ptgrp 2 vs HC, ptgrp 1 vs ptgrp 2 > > Should this model test only ptgrp 1 vs HC and ptgrp 2 vs HC as opposed to > also including testing ptgrp 1 vs ptgrp 2? > With this model, is it OK to leave it as such and not include the other > pt-specific confounders since I am conducting model 2? Or is it better to > regress out within-pt group duration differences (by demeaning within > groups)? > > Model 2 - > subjects: ptgrp 1 and ptgrp 2 > regressors: mean ptgrp 1, mean ptgrp 2, all possible confounders (demeaned > across all pts, also including previous covariates in Model 1, but > re-demeaned to new mean calculated from pt-only groups???) > contrasts: ptgrp 1 vs ptgrp 2 > > I am also using the -n flag for tbss_2_reg (study-specific template). In > this case, because model 2 only includes the patient groups, would I have > to redo the step involving creating the study-specific template in order to > run model 2? i.e. having to generate a new template for this purpose. > > Thanks very much in advance! >