Hi Ryan,
Can you provide more information about your data? Such as number of diffusion directions, some demographic details like the species, age and whether it’s a clinical population or typical healthy individual? Also, what type of scanner was used - magnetic strength and manufacturer. When you look through the raw data in dtiprep, do you notice any inherent or consistent artifacts such as some cropped brain slices if the field of view cut off, for example, a few slices of the occipital lobe or do you see that the whole brain was included? Feel free to attach your xml of the setting you are using when you load the raw image and click “default” for the protocol. This will give me some info about the input data.

Thank you!

Rachel