Dicom to mif vs dicom to nii then nii to mif


I tried 1) dicom to mif conversion using mrconvert and 2) dicom to nii and then nii (+bvec/bval) to mif on the same subject.

I ran a pipeline that includes denoising, gibbs removal and then concatenated them (2 acquisition directions) and then performed dwifslpreproc for both the above 1) and 2).

After that I got the output of both and ran DTIFIT, 2) produced a nice FA image, but 1) produced a very messy FA image. All methods after the first file conversion step are the same, so I was surprised to see that. I see this in the FA, MD, V1, etc, otherwise the images look very similar.

Any insight is much appreciated?
PS: I checked the bvacs files output after dwifslpreproc and they are different (in values and sign).

Dear Daveyin,

Without the exact commands and intermediate results, it is difficult to tell where things go wrong.

If you closely inspect the output and input of each command using mrinfo and mrview, you should be able to pinpoint exactly where and how both approaches deviate. If you post your findings here we can then help you get to the bottom of it.

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