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!