Hi.

1. I would suggest you use a feature in MRtrix3 called dwidenoise.

So, if your data is called dwi.nii, then you would need to first convert it to mrtrix3 format (.mif) using your bvec and bval:

mrconvert dwi.nii -fslgrad bvec.bvec bval.bval dwi_mif.mif

Then, denoise the data (to extract the noise):

dwidenoise dwi_mif.mif dwi_mif_denoised.mif -noise noise.mif

The noise.mif is your noise map which has the values you need to measure the noise. To convert it to .nii format:

mrconvert noise.mif noise_nii.nii

2. I would encourage you to register your T1 image to your diffusion space, rather than your diffusion space to your T1 image space.

3. Have a look at my Handbook (http://jeromemallershandbookofstructuralbrainmrianalysis.yolasite.com/?_sm_au_=iWHrSsBDn5JWbQVVML8tvK34L00HF ), Part 1, from page 61 which has step by step instructions for extracting FA, MD etc values for the CC (and many other WM tracts).

Jerome