I am trying to follow the steps in the FDT user guide: 

In the processing pipeline, they mention using BET first (to get nodif_brain_mask and nodif_brain)

In the DTIFit step, they say the Input Diffusion weighted data to be data.nii.gz. Do I use the Non skull stripped data here? 

Are we not going to use the skull stripped data? 

Thanks. 

- Anita.