Reorientation of DWI data can indeed be an issue when bvecs are not correctly updated. I suggest you use one of the existing DWI tool datasets to process your data, as these tools know how to correctly adjust bvecs. Btw, if you have a re-orientation transform matrix and you apply it in Slicer via its resampling tool, the gradient vectors will get correctly updated if you have the DWI data as NRRD (I am not sure, but I doubt that Slicer is doing it correctly for nii/bvec/bval data).

Re eddy: Likely it does not matter, given you do not provide eddy with any information from topup.

Originally posted by tu ruilin:

Hi, Martin

Thanks for the reply! As I am kind of new in DWI analysis, I have some quetions about these data, and apologize in advance for the following questions.

1. I noticed  the orientation of the raw DWI data differs from the processed data, so I reoriented the raw data using 3D Slicer and fslswapdim before preprocessing. However, I'm not sure if this method alters the bvecs. If so, is there a better way to reorient the data (the same orientation with the processed T1 images) and output the corresponding bvecs?
2. When using FSL's eddy for Eddy Current Correction, is it reasonable to set the parameter of acqp.txt to -1 0 0 0.1 (since there is no phase encoding direction, I arbitrarily chose one direction).

Best,
Ruilin Tu