Hello,
I'm trying to run recon-all after making manual edits with control points (command: recon-all -make all -subjid [sub]), but the recon-all is exiting with errors at the jacobian_white step:
------ Error below: ------
mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
reading surface from ../surf/lh.white.preaparc...
mrisReadTriangleFile(../surf/lh.sphere.reg): surface doesn't match ../surf/lh.white.preaparc
No such file or directory
mrisReadTriangleFile failed.
No such file or directory
mris_jacobian: could not read target surface ../surf/lh.sphere.reg
No such file or directory
-------------------------------
I was wondering if you have any thoughts on why this might be happening? I have attached the recon-all.log and recon-all-status.log files, and my FreeSurfer version is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.
A few things I noticed that I thought might be related: while the recon-all was running I only saw IsRunning.rh in the scripts directory, not IsRunning.lh+rh. Also, in the recon-all-status.log file, it looks like the lh
and rh parts of each step are not always occurring together (although maybe they don't necessarily have to?).
Thank you!
Anne