Hi!
In recon-all, I am launching the pipeline step by step (autorecon1, autorecon2, etc.), because I want to add my own skullstripped mask. At each step, I see this in the log:
Adding options -fix-ento-wm -transfer-base-bfs -fix-vsinus -fix-mca-dura -fix-ga -fix-acj -synthstrip -synthseg -synthmorph
So the options synthstrip, synthseg and synthmorph are run every time, which takes a long time for no reason. But options -nosynthmorph, -nosynthstrip, etc. do not seem to exist. Can we control these?
Also, as a side question, when I run the whole pipeline and check the synthstrip output, the result is very bad, with a lot of dura. But when I run synthstrip manually, the result is perfect. What’s happening?