Run it with -debug as the first option, capture the output, and send it
to us.
On 4/1/2021 8:29 PM, zalewk 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 list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
