Dear Mrtrix team,
Hope this message finds you well.
I am relatively new to the DWI/DTI field and really excited to pick up a new set of skills to look at the brain differently.
My question is regarding generating and using the basis functions to estimate the FOD. Based on the documentation and some of the messages, it seems that the common basis function is preferable when comparing different groups. Then, here are my two questions.
Should you use only control (presumed to be healthy subjects) to create the basis function and apply this to all the cohort that will be part of the analysis?
More specifically, I work with Alzheimer’s disease and we know that the white matter is damaged during the disease process. However, I am not sure whether or how the disease processes will affect the estimation of basis functions in different tissue classes. Then, would the use of a common response function introduce any bias in estimating the FOD, and subsequent connectomic, track density, etc analyses? My understanding is that the basis functions of the different tissues are used together with the DWI data to estimate the FOD, which is used subsequently to quantify all the metrics (connectome, density, tractography, etc), through deconvolution. Then, I can only imagine that the quality of basis functions (in other words, depending on how you estimate the basis functions) will affect your results.
Your expertise and guidance would be very much appreciated.