March 9, 2018 at 3:03 pm #1162
For a particular analysis/project I’m doing, I would like to run FSL’s bedpost and probtrack on BDP’s corrected diffusion data in T1 space.
I notice that the correct diffusion data (with b0 and all DWIs, fileprefix.dwi.RAS.correct.nii.gz) are only in native diffusion space. How can I get this into T1 space for input into bedpost? (I must have the full data, not just the tensors)
And what would be the correct bvals/bvecs for this diffusion data in T1 space?
Also, for a separate analysis/project I’m doing, I’m running bedpost/probtrack on the corrected diffusion data in native diffusion space (so using fileprefix.dwi.RAS.correct.nii.gz). Am I’m wondering what would be the correct bvals/bvecs (in native diffusion space) that have been adjusted for the distortion correction? (My original thought is that it would be fileprefix.dwi.bval and fileprefix.dwi.RAS.bvec, but are these adjusted for the distortion correction?)
Thank you so much,
March 16, 2018 at 3:51 pm #1168
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.
March 20, 2018 at 9:52 pm #1172
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?
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