Dear FSL experts:
I am new fsl users, I have some questions.
I generated FA image by following the following steps
1: eddy_correct
2: Bet, threshod 0.5
3: dtifit
In the generated FA image, there are very high intensity in the brain boundary, and there are some voxels FA > 1, see the attached figure. The FA image seems to look unclear.
I used DWIs of the 32 directions to generate FA. I converted decom to .img (.hdr) by MRIConvert. There are 34 volumes in this 4D image, and I checked bvecs and bvals (see the attached file) and found:
the last gradient direction in bvecs is 0 0 0, and the last value in bvals is 800, I am not sure that these files are correct.
But I delete the last volume in 4D image, remove the last gradient direction (0 0 0 ) in bvecs and the last b = 800 in bvals, but I got errors in ditfit:
Errors: bvecs and bvals don't have the same number of entries.
why? I removed the last gradient direction in bvecs and b value in bvals, respectively.
I saw many old archives that we can use rotate_bvecs to rotate the bvecs after eddy_correct. Is it necessary?
I didn't find such command in fsl ( I uses v4.10 version) . If rotate_bvecs is necessary, how should I do?
Any comments, Thank you in advance
Best
Shugao