External Email - Use Caution
Hi Freesurfer team,
My lab recently switched over from FS6 to FS7 and I think I've encountered a bug with recon-all. I'm running subjects stepwise and editing them, running recon-all with the -autorecon2 and -autorecon3 flags initially are no problem, they run fine. Trying to re-run them or use the -autorecon2-wm, -autorecon-pial etc. flags lead to crashing at certain parts of the program. The error message I get is "if: expression syntax". Digging into the code, it seems to crash when it hits a line of code "if($ud || $ForceUpdate)". The syntax superficially looks right (I don't know tcsh), checking the variables it seems like $ForceUpdate is never set, but removing it from recon-all doesn't fix the problem. It seems the $ud variable is for checking if updates are needed for a set of volumes passed to the program. I don't know why that would be a problematic argument, removing that part seems to fix it, but this also seems like an important variable and I don't know enough about tcsh to understand why it works after removing it. Can one of the folks who wrote the recon-all script help me out? I'm running the commands step-wise as a work-around, but that is much less convenient.
Best, Kody Zalewski