Dear MRtrix3 community,
I am posting a message because I would have some questions regarding eddy preprocessing, particularly the slice-to-volume correction. I noticed zig-zag artifacts in several raw images of the database, so I wanted to add this option to the preprocessing. After correction, these zig-zag artifacts were well corrected in all the images, but I realized that, in some other images, eddy introduced some small motion (rotations) between slices. I was therefore wondering if someone has encountered this situation before and what would be your advise: should I not use the slice to volume correction?
I also noticed that eddy added some high intensity voxels at the very edges of the FOV, outside the brain, despite using a brain mask. I am not sure it is a big issue since it is outside the brain, but I still find it strange.
Thank you so much for your help!