Hi MRtrix3 experts,
I’m comparing two acquisition schemes to evaluate the quality of the reconstructed FA maps between these two schemes.
case 1) DWI_15 (2b0 + 15 diffusion-weighted images) repeat 4 times.
For TopUp correction, additional reversed phase encoding b0 image is acquired.
case 2) DWI (7b0 + 60 diffusion-weighted images).
For TopUp correction, additional reversed phase encoding b0 image is acquired
For 1), I planned to run dwipreproc for four individual DWI_15 scans individually. FA will be reconstructed from the DWI images averaged over all four scans. The idea behind this is that: to fit the DTI model, DWI volumes of 1) (higher SNR, fewer DW directions) might generate a more accurate FA than using the DWI volumes of 2) ( lower SNR but more DW directions). However, I need to take care of the motion between scan sets for case1.
To take care of the motion between four sets of DWI_15, should I run rigid registration? (If so, should I Run registration before dwipreproc or after dwipreproc?) Or should I try to combine four sets of DWI_15 into one matrix (2b0 + 15DW) x4 and run dwipreproc on this combined matrix?
Thank you for your help in advance.