Yes it would need to be rotated according to the rotations of the affine transformation:
https://github.com/Washington-University/HCPpipelines/blob/master/global/scripts/Rotate_bvecs.sh
Matt.
On 7/21/20, 8:20 AM, "FSL - FMRIB's Software Library on behalf of Samantha Baldi" <[log in to unmask] on behalf of [log in to unmask]> wrote:
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Dear FSL experts,
I have now a doubt about my processing pipeline, which I outline below:
- eddy for EC and motion correction
- registration of the average b0 volume to the T1 image to correct for EPI-induced distortions (given the lack of a field map or image with reversed phase encoding direction). Following the registration, the transform was applied to all DWI images. This step was performed outside the FSL environment, namely by using ANTS (antsRegistrationSyNQuick.sh and antsApplyTransform.sh).
- creation of binary mask (i.e. bet on the first b0 volume of the eddy-corrected, outlier free, registered to T1 diffusion image)
- bedpostx with following input: (1) eddy_corrected, outlier free, registered to T1 diffusion data, (2) binary mask, (3) bval, (4) eddy_rotated_bvecs file
- probtrackx2
Of note: (1) the input files for bedpostx and probtrackx2 were then in T1 space (and not diffusion space), (2) no operation on the bvec file was performed following eddy (so no change after registering the DWI data to T1).
I am now doubting whether some rotation of the bvec file should have been performed after registering to the T1 image? Is it a fundamental problem for bedpostx and the fiber tracking if I used the eddy_rotated_bvec file?
Thanks in advance for the help
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