I've noticed that each time I loaded my bvecs manually after loading my nii.gz, the bvecs y-direction is automatically flipped in dsistudio (i compared it with the bvec.txt i have). I'd like to understand/check if this is correct.
Some background about the dataset - we used in-house scripts to correct the data for motion and artifacts, the data's bvecs has only been x-flipped by us for FSL processing, and the image is in a typical DTI space, but not native DTI space. They are rigid-body registered relative to the T1, but with 2 mm voxels.
I did not turn on check b-table during QSDR and had done QC check. After I obtained the tractography results, I checked the direction for some regions and it seemed correct to me. However, I still get some weird tracks on the surface for the two participants i've tested (attached, sub2 is more problematic). Thus, I'm not sure if it's a bvecs flipping issue or some other issues that I overlooked.