Questions about dtiInit parameters

[Luie Wang]

Hi AFQ Community, 

I'm using dtiInit function to align my DWI (obtained from Siemens scanner) to ac-pc aligned T1 and create dt6.mat file. My images have already been corrected for eddy current and motion using FSL. However, I was not aware of the special handling with Siemens data and didn't set the parameter rotateBvecsWithCanXform to 1. When creating FOD (fibre orientation distribution) and generating tractography using MRtrix3, I realized the fiber orientation is wrong because bvecs is flipped over the x-axis. I have already fixed the bvecs (flip it over x-axis) and got very good tractography results. My FOD and tractography look fine after fixing the bvecs.  

My question is that, is it necessary for me to redo the dtiInit step with rotateBvecsWithCanXform =1? or has my manual correction (flipping bvecs over x-axis) already implement the function that should be done by this parameter? I have calculated FA and MD maps using in house developed software but I'm using the volume measures calculated by AFQ. Would the missing parameter influence the calculation of volume for the major white matter tracts? (I imported whole brain tractography generated by MRtrix3 and segment it in AFQ). 

Thank you so much in advance!

Best,

Luie