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
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
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