It's my first time using FreeSurfer and I'd like some guidance regarding some of my steps.

I'm attempting to perform myelin mapping as outlined in the paper by Righart (2017) Ann Neurol. Overall, I want to calculate myelin maps from each subject, sample them from the mid-cortical level to create cortical myelin surface maps, and perform vertexwise and ROI based analyses.

Here's what I've done so far:

1. recon-all for all the subjects

2. Used bbregister to register the native T2 scans to the conformed T1 scans using this command: bbregister --s C01 --mov C01_T2.nii --init-fsl --reg register.dat --t2 (my understanding here is that this generates the .dat file that has the transformation to register the T2 image to the conformed orig.mgz file from subject C01)

3. Applied the register.dat file to the native T2 using mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz --fstarg --reg register.dat (this registers the T2 to the orig.mgz file in the conformed space)

The next step for me is to perform mri_vol2surf. My question here is, which file should I select for the --srcreg flag and what should the --trgsubject input be? Secondly, am I on the right track to complete the analysis i.e., correct file types and my understanding of the steps? Clarifications regarding these questions and any suggestions for further directions will be very helpful!

Let me know. Thanks!