Dear experts,

I am potentially also interested in correct using of -T2pial feature with longitudinal stream.

The first (standard cross-sectional) and third step (-long ) was already elaborated here, but I am, however, not sure how to process by T2pial in the second step ( -base), which creates the unbiased template and process it by (almost) standard cross-sectional stream. I did not find creation of unbiased template of T2 in the recon-all code.

Therefore, in order to use -T2pial on -base run, I would probably need to create my T2 template by calling mri_robust_template on my T2's first, and then pass the created T2 template as input to recon-all -base run, like:

recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all -T2pial -T2 path_to_T2_template

I am correct?

Regards,

Antonin