Hello Freesurfer, I was trying to run recon-all in stages (autorecon1, autorecon-2 and autorecon3) with T2. First, I ran autorecon1 with T2 (recon-all -autorecon1 -i input_volume -T2 /T2_volume -T2pial -s ) and i got an error (MRISread (........./surf/lh.white): could not open file Loading mov Projecting LH Surfs Loading lh.white surf No such file or directory.
When can I use the -T2 -T2pial command? Also, which set of recon-all scripts is correct?
recon-all -autorecon1 -i /input_volume -s recon-all -autorecon2 -T2 /T2_volume T2pial -s recon-all -autorecon3 -T2 /T2_volume T2pial -s
OR
recon-all -autorecon1 -i /input_volume -s recon-all -autorecon2 -s recon-all -autorecon3 -T2 /T2_volume T2pial -s
Thank you
Best, Paul