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Hi See below. Here's the outline: I have a sample of 50 subjects that have participated in a training study lasting for two months. Before and after the training, they were submitted to an MRI acquisition comprising T1 and DWI imaging. To test this hypothesis I plan to use the CAT12 toolbox for longitudinal segmentation and grey matter density, as well as the longitudinal pipeline in freesurfer for the cortical thickness. As for the DWI data, my idea is to calculate FA maps, perform probabilistic connectivity between my cortical ROIs and extract the FA from these regions (more specifically, from a delta maps of the FA at time 2 minus FA at time 1), all using FSL tools. For the DWI part, however, I have two important questions: 1) to avoid bias towards one of the time points, I should probably use an half-point registration between time 1 and time 2 to register the DW data onto the (half-point) T1. Is that true ? And if it is, how can I do it with flirt ? Yes. You can do this e.g. by registering 1 to 2 and 2 to 1, extracting the halfway matrix of both (with avscale), resampling 1 and 2 using halfway transforms and averaging, then re-flirting 1 and 2 to this halfway target (or directly to MNI if you combine with a transformation from the halfway target to MNI). 2) about the tractography: I think that overall the connectivity of my regions is unlikely to change in just 2 months, but I can also foresee some lovely reviewer claiming that if the tractography has been performed using only time 1 or time 2 there is a bias. How can I overcome this ? Is there a way to perform tractography from some sort of "half-point" DWI measure and then send back the results in the space of time 1 and time 2? Do you think I may be overkilling and that it would be enough to perform tractography using just time 1 ? I would still use both time points for tracking, no reason not to. You can simply run both in the same (halfway or MNI) space and average the results. Cheers Saad Thank in advance for any comment or answer on this questions Alain