Hi Anne,

Unfortunately, the “-make all” flag contains a bug in the stable6.0 release. However, this has been fixed in the dev version. This can be quickly fixed if you download this script - ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/centos6_x86_64/recon-all.makefile - and overwrite the current $FREESURFER_HOME/bin/recon-all.makefile

mv -f recon-all.makefile ${FREESURFER_HOME}/bin/recon-all.makefile # (sudo might be required)

Let me know if you still have issues

best, Andrew

On Oct 31, 2017, at 10:48 PM, Anne Park <annepark@sas.upenn.edumailto:annepark@sas.upenn.edu> wrote:

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 <recon-all-status.log><recon-all.log>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer