External Email - Use Caution
Hello Kody, One thing you could try to get more information printed about what is going on is to edit the very first line in the recon-all script to be: #! /bin/tcsh -xf … instead of #! /bin/tcsh -f Adding the x option will echo each line in the script as it’s run with the variable values expanded, and seeing that output could help with debugging.
- R.
On Apr 1, 2021, at 20:29, zalewk <zalewk@uw.edu> wrote: 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_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%E2%80%8B