Thanks Peter again for the helpful reply!

We're still at the beginning of data collection for this study, so I'll look at adding a T2 for our next subjects!

If you'll indulge one more question on this line of thought: the axialization step for the structural.

I've noted in the new Tortoise instructions and in your post, the use of axialization to bring the structural into roughly AC-PC space. Where would this fit in the pipeline? Would it be better to ACPC the input to recon-all by hand and then reconstruct from there and use the outputs as the base for both tortoise and AFNI, or feed the raw structural into recon-all and ACPC/axialize the output for future processing?

Thanks again for all the insight. Linking these functional/structural pipelines has been a real goal for me, and this has really helped actualize that.

~Jared