Hi, I processed about 80 subjects with -prep stage and then checked the bbregister registrations with
tkregister2 --mov /study5/aa-scratch/TEENEMO/freesurfer_local/toot/057/dmri/dwi.nii.gz --reg /study5/aa-scratch/TEENEMO/freesurfer_local/toot/057/dmri/xfms/anatorig2diff.bbr.dat --surf
found 17 subjects with bad registrations, as always because the fsl registration initialization was bad.
so now i manually fix the registeration and use the manual fix for the initialization and rerun bbregister and get a good registration.
so now i need to rerun -prep phase but have it use the good registration instead of computing a new bbregister registration.
will trac-all -prep -nointra -c configfile accomplish this or do i need to get in and tinker with the scripts to make it run everything including computing new fsl and inverse registration matricies but using my bbregister good registration.
thanks
greg