Hi
There is a critical piece missing, the command tensor2metric produces positive and negative values. Many MRI tools such as the popular ITKSnap will not display such FAC maps correctly, as they distinguish positive and negative.
I am actually not certain negative vector directions are meaningful in this context?
To correct this one would need to add a command such as fslmaths -abs, i.e. the total pipeline would be something like
dwi2tensor dwi.mif - | tensor2metric - -vec dec.nii
fslmaths dec.nii -abs fac.nii
I know it seems almost trivial, but believe me finding it out can be extremely frustrating and time consuming, and computing FAC maps seems like a common starting point when dipping one’s toe into the DWI world.
best
Mark