THe last command run is
ln -s lh.white.preaparc.H lh.white.H
So I'm guessing that the error comes when the symbolic link is created (and it would not be captured in recon-all). That link is the first created in the stream, so it would not necessarily have shown itself before then. Try this:
cd /mnt/hgfs/ShareFolder/output/sample01/surf
ln -s lh.white.preaparc.H lh.white.H
Is there an error? If so, sent the error msg

On 8/2/2019 9:57 PM, Kuo Li wrote:

External Email - Use Caution

Dear FreeSurfer Developers,

I'm attempting to do cortical reconstruction, but for some of my subjects I get the following error when I run the recon-all command:

#--------------------------------------------

#@# Curv .H and .K lh Wed Jul 17 04:03:21 PDT 2019

/mnt/hgfs/ShareFolder/output/sample01/surf

mris_curvature -w lh.white.preaparc

total integrated curvature = 0.838*4pi (10.527) --> 0 handles

ICI = 216.7, FI = 1989.1, variation=32373.324

writing Gaussian curvature to ./lh.white.preaparc.K...done.

writing mean curvature to ./lh.white.preaparc.H...done.

rm -f lh.white.H

ln -s lh.white.preaparc.H lh.white.H

Linux ubuntu 4.18.0-25-generic #26~18.04.1-Ubuntu SMP Thu Jun 27 07:28:31 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sample01 exited with ERRORS at Wed Jul 17 04:03:23 PDT 2019

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

I've searched google and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached the recon-all.log in case it's of any use.

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2) Platform: Ubuntu 18.04.2 LTS

3) recon-all -i sample-001.nii.gz -s sample01 -all

4) recon-all.log: see attached
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer