Hi Max,
thank you for your help.
I have read both tutorials and already did the “Beginner DWI Tutorial”. But now I would like to do the Multi-tissue constrained spherical deconvolution approach. After reading the documentation I still have some questions:
1.The documentation says that I need to do a rigid-body registration between a T1 and the DWI images. Because there is no information how to do it I guess I just have to do the mrregister command with the rigid option?
2. Do I have to use the T1 image as template or as moving option? I guess as moving option?
3. Do I have to preprocess the DWI’s and the T1 before coregister?
4. I read that Eddy already includes the b-matrix reorientation but when I do a registration afterwards, do I need to reorientate again my b-matrix or is it just necessary for subject motion correction? I guess when I coregister just the T1 to the DWI’s I do not have to reorientate the b-matrix?
5. You suggested me the dwibiascorrect option. Is it also a necessary step cause I could not find it in the pre processing section on the documentation website?
6. I also try to find a solution by searching in the forum, but this confused me even more. In both i.) ii.) questions they were talking about freesurfer and flirt?
So I am just wondering if I have to do additional steps in my pipeline? Otherwise I would do it the way it is suggested on the documentation website?
- Do dwi denoising, dwipreproc, dwibiascorrect
- Registration of T1 with DWI (mrregister)
- Do 5ttgen, dwi2response
- Do dwi2fod msmt_csd
Sorry for all my questions but its my first time processing such data.
Thank you
Best
Max