[divarada]

BDP does not support saving the diffusion data in T1 space mainly due to memory requirements and since the corresponding data is not saved it does not save the rotated bvecs/bmats either.

However, we do have additional tools to perform the rigid registration.

Here is the link to the rigid registration source code: http://neuroimage.usc.edu/~chitresh/BDPinternal/BDP_addons/register_files_affine_v12.zip

You can run this to perform rigid registration and get diffusion files in T1 space.

However, to be able to obtain the rotated bvecs, you will need to make changes to BDPs code and rebuild it. Please refer to estimate_tensors_mprage.m file in BDP’s source code. There you can see how BDP internally rotates the bmatrices. Basically, you will have to save the rotated bvecs/bmats there and rebuild BDP or replicate that code in your current setup.

[micaceous]

Thank you for the detailed response and materials.

If you don’t mind, more remaining thing to clarify..so does this mean that the only provided bval (fileprefix.dwi.bval) and bvec (fileprefix.dwi.RAS.bvec) files in the regular output are technically incorrect for the distortion corrected diffusion data (fileprefix.dwi.RAS.correct.nii.gz) in native diffusion space? (not T1 space). Or are they correct, and they would only be incorrect if tried to apply to diffusion data in T1 space?

[Author]

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