Dear FSL experts,
I have a dataset of DWI images acquired only in one direction and few weeks ago I asked about EPI distortion correction in this forum using a T1-weighted image with ANTs.
I finally ended using BrainSuite with, which I think, pretty good results (I attached a jpeg for comparision)
However, since I haven't two datasets in opposite directions, I only can apply eddy_correct instead of "eddy" which I believe it rotates bvecs automatically. After that I need to rotate my bvecs with the Mark Jenkinson's script (fdt_rotate_bvecs).
I'm confused about bvecs rotation because BrainSuite gives already as an output an bvec rotated file after align the DWI to the T1 sequence.
Therefore I have the (1) the original bvec file (CA043_DTI.bvecs), (2) the rotated bvec after eddy_correct (rotated.bvecs) and (3) the rotated bvecs from BrainSuite (CA043_3D.dwi.RAS.bvec). I attached an example of the outputs, since BrainSuite changes the sign of all axis and I'm kind of insecure about this.
My pipeline for preprocessing was (1) eddy_correct (2) rotate_bvecs (3) skull-strip and bias field correction (BET, FAST) of the T1 (4) BrainSuite (bdp.sh -T1.bfc.nii.gz --nii dwi_eddy.nii.gz -b rotated_bvec -g bvals) and (4) BET b0 and (5) DTIFIT using the bvecs from BrainSuite.
I'm having different results in TBSS since I've done this type of preprocessing.
I appreciate any kind of suggestions/commentaries. I'm really interested in running a TBSS analysis with the EPI distortions solved and the bvecs reoriented.
Thank you very much,
Jonatan
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