Hi experts,

I am doing a longitudinal (2 time points) FBA following this pipeline (Fibre density and cross-section) and Genc et al. 2018.

Using TBSS, I found decreased FA from TP1 to TP2, which are also the common findings in the literatures. However, using the same data and FBA, I found the opposites, i.e. significant increased FD and logFC in some tracts.

My question is which step I could have done wrong in FBA? For my data, I have low b-value and single shell (b=1000 and 0). I used single-shell 3-tissue CSD to model the FOD. The inter-subjects FOD template and mask look fine. The number of fixels is also quite reasonable. For the statistical analysis, I calculated the changes TP1 - TP2, and used the one-sample t-test. The matrix includes 1s and 2 covariates:

1 2 1.2

1 1 0.5

1 1 -2.1

The contrasts are 1 0 0 for decrease and -1 0 0 for increase.

I noticed a reply in another topic:

How could I found the massive false temporal changes? Is there any other confounders that I am not aware of?

Thanks in advance!