I am currently going through the dt_recon tutorial on your website and I just have a quick question regarding the recon-all and dt_recon commands on freesurfer. 

For me to process dt_recon, my understanding is that I must process recon-all first. 

But where my confusion lies is:

- do I perform recon-all on the actual dwi.nii.gz image, then dt_recon with the same dti files (including the bval and bvec of the same dwi.nii.gz file) 

OR

- should I have two separate sets of data, one T1 and one DTI, and perform recon-all on T1 images and take DWI images from the same subject to perform dt_recon?

My understanding was that the second bullet is the right way to go since the dt_recon uses the outputs from T1 recon-all to register properly. 

Please let me know which one is correct, and if I am missing something. 

Thank you so much for your help, I really appreciate your time. 

M