I have processed my DTI data and got whole brain tractography using Tract_Det algorithm. I have tried two times by using WM_mask and b0_mask as a seed image. The results are not the same obviously, but both are fine to me. However, some tract properties(FA, MD etc) are changed. I was wondering which option would be more acceptable?
It is unclear from your description how either of your whole-brain tractography masks - “WM_mask” and “b0_mask” - were derived. Without knowing exactly the nature of these masks and how they were generated, it is impossible to make a reasonable assessment about which is preferable given only the information that their outcomes differ.
Also bear in mind that deriving a mask for whole-brain tractography, and deriving the masks within which quantitative metrics are extracted, are two separate processes. So for instance, you may want to use a more lenient mask for tractography, but try to constrain extraction of tract properties to only the white matter.