for my study I do different measurements but all with the same person. Due to the fact that the measurement is about 6 hours I record the data in 2 sessions.
Because I am not very familiar with all necessary processing steps and their order I would like to ask some questions.
First I was thinking to do the DWI denoising followed by the preproc script. After that I am not sure if I have to run a kind of registration, thus all my images are in the same space? When I do it (mrregister) do I have to register them all to a T1 image or to the first non diffusion image (b0)? I also read (Leemans, Jones Paper b-matrix rotation) so I was wondering if I have to reorientate my b files after registration?
So my questions are:
- Do I need to run a registration
- If yes…how will be the order of my pre-processing pipeline?
- On which image should the registration refer to and do I need to reorientate my b matrix?
- Do I have to do more preprocessing steps? (I want to estimate the directional information, so calculate fod’s and peaks, single shell and multi shell approach)
Thank you for any kind of help!