As I mentioned in an earlier post, I am very new to diffusion imaging, and trying to explore this area. I am working through the BATMAN pipeline and just restarted because I think my input (either B0 or B1000) are incorrect. The following are the commands I ran as well as the output for residuals, noise, b0, and b1000:
dwidenoise dwi.b1000.mif dwi_den.mif –noise noise.mif
mrcalc dwi.b1000.mif dwi_den.mif –subtract residual.mif
mrview noise.mif residual.mif
Also in my previous iteration, my unringed image had revered colors compared to the image on the guide (namely, CSF was black compared to white). Any guidance on what I may be doing incorrectly?