I restrained the intensity values from 0 to 0.003. and check the values (lower left corner of the window). Values change a lot from -0.003 to +0.003.
I was expecting diff.mif at zero.
Not sure if I will be helpful here at all and whether you are struggling mostly with just obtaining the actual adc files but what I did was simply to:
dwi2tensor dwi_Exampledirectory.mif /home/Desktop/tensor_sub01.mif > just as an example at the end I specified the directory where I want the file to be saved to
Using the file derived from the first command to extract the mean diffusivity information from it and saving the final output file in NIFTI format as this is the format I want to use. So it was pretty straightforward to obtain those files. Then I actually used an fsl command to compute the mean of all the adc files I had per subject where at the end I could specify to obtain a txt. file and see the actual numbers.
You may want to look into the -lt and -gt functions as using them within mrcalc can help you specify a threshold lesser than/larger than a certain numerical value, but since I am a beginner myself, I research the MRTrix help page for these functions and then see what I can do with them.