Hi Andy
I think the rh.white.H is generated by mris_curvature. Does that help?
Cheers,
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Andy Worth
Sent: Tuesday, January 19, 2021 5:29 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Cannot find rh.white.H
External Email - Use Caution
Hello,
We're seeing this error a lot: "Cannot find rh.white.H" which is generated
here<https://secure-web.cisco.com/1kFmpUflCYrLlkn0X825hErhILvuejPNzV2WrombAVtg_sM4GT1g_2GUF6a8ZpRLVYi6pkG1WL5R_6FXRwzi6naGRJeM7eDTmdEF-qJnBHyt5W5477N06HJUDcSZV4VKP4uEWN7jv5UaPYN359YbKBW5yzUfr9B0_s3qNTfysJplHplUIbwiqmCVwtIfKMz7yXNuZZXM4FoZcbX1-iJQn_WZ-OrPOy86L9-F_bHcRD-NMim4sO1ulpWfa_sOXqCEpXur17Xf6obk1monjfSBi3A/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Fscripts%2Frecon-all%23L3610>.
It does not occur if -parallel is turned off.
I see that reconbatchjobs does "exec" on the commands sequentially in the order
of the list, but it runs each in the background:
exec $JOB >> $LOG 2>&1 &
so I thought it might just be slightly possible that these two commands:
set cmd1 = (rm -f $hemi.white.$suffix)
set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix)
could end up in a race condition where the file is linked and then immediately
removed if somehow the ln command is executed before the rm command.
However, I tried reproducing this behavior with a test script but the rm always
happens before the ln.
Any help would be appreciated!
Thanks,
Andy Worth
Scientific Solutions Engineer
he, him, his
[https://secure-web.cisco.com/1YriYUvcgCSjRhC6yGeZ5vu_KysFv12VbE-P3WRYMut0v4dV5ZLR8MvWGUaa793niFj0dFyrx1Q6R_6ywkKWHzWY_c19RzETcRJS4x5y66xdtc1cDH235ZWSyN2zx3loPwx8XdLAC8gvP8QOO1Oj0gx4uxiXCDKC2wFY-tb4JgWLPrDrSNN-S6wN0WEom-ZfbujWPJrzylnmiuXFChuep6ROueyv5d-m6UBjUbry6P3gOXvc8RL-9ciCZHIFhaf3WWhYC3Zgn6ooOXcbz58SPcg/https%3A%2F%2Fdrive.google.com%2Fuc%3Fid%3D1oozBEoFHbBP_5xYyw59-9YNoEOsX6Ghd%26export%3Ddownload]<http://secure-web.cisco.com/1KxdUXSlflua-8jA7AL5CzR1vwNWqcPAt_z76LcUsPIdfrRmC2dUPKB5OQjPwfI_jJhAZe2cqlldgaNHGreNViKQUc8HWIh1UnI4eQW4PHcuCADZ_aF04n5OnjAwF_LEoRNv0nXMW3oxAUuH3CTQlGSfM9hl2zeEho-vAJ01wD1qhOrci0dfnp4FgfjX8QDdjl7x9By5VVtEj02Q5ED4l7TeC286ILTihn0s4abzLg_CLEKV4JUAvu6bDSQD7FMzVt_OR0Sr6Px4kg4nS-Be7NA/http%3A%2F%2Fwww.flywheel.io%2F>
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