Hi Paul
thank you for your reply. In my understanding dwi_corrected.bvec and bval are corrected after eddy. However, there is a second correction
line 95-97
#apply affine reg to bvec
/opt/HCPpipelines/global/scripts/Rotate_bvecs.sh dwi_corrected.bvec \
${nm}0GenericAffine_fsl.txt $outdir/dwi.bvecs
which applies the transformation matrix of the DWI to t1 registration to bvecs. It is unclear to me which subscript was used. I tried to use the rotate_bvecs script of the HCPpipeline
(https://github.com/Washington-University/HCPpipelines/blob/master/global/scripts/Rotate_bvecs.sh)
however the output consisted entirely of zeros.
Any further help would be greatly appreciated
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