I have a question related to DWI data registration and FOD-based information that we want to incorporate into our subsequent analysis steps.
We are working with a data set of patients and we have two sessions for each patient with DTI measures - at two different time-points following a stroke. We want to look at white matter differences within subjects between the two time-points.
We, therefore, have two separate data sets for each time measurement (time point session 1 and time point session 2) after stroke. We have already completed the independent initial pre-processing steps (denoising, motion correction, edi current-correction). However, after that we want to estimate a response function for each subject twice - we want to compare the FOD results between sessions on a voxel-by-voxel basis. We need some advice on the pipeline to use for this purpose: shall we do the analysis first with the two data sets and then register the FOD images? Or should we perform the DWI registration after the pre-processing and then estimate the FOD images?
Our concern is that we are comparing data acquired at two-time points that we cannot merge into a single set, so we are not sure whether we can perform this if the data is not aligned in advance, and whether this would mean that we will be using two different response functions for the two sessions for each subject?
Your advice on how to solve this would be much appreciated.