External Email - Use Caution
Hi, I am testing a new installation of freesurfer. Two errors occurred, and I'm hoping someone can help me troubleshoot:
First, recon-all exits with error indicating that it is unable to create a symbolic link:
[GHS\026278@vmcntdsktp10 fs_sample1]$ tail /neuro_images_isilon/026278/fs_sample1/sample001/scripts/recon-all.log 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 vmcntdsktp10 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sample001 exited with ERRORS at Sat Jun 22 17:10:41 EDT 2019
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
The error occurs in CentOS 7 running on a virtual machine environment, with the latest stable freesurfer release, 6.0.
The recon-all process was being run on the sample_001.mgz file to test the installation, and ran for about 7 hours.
Second, when I tried to use the -use-gpu flag, the process seems to be missing a library:
[GHS\026278@vmcntdsktp10 fs_sample1]$ recon-all -subject sample001 -i ./sample-001.mgz -use-gpu -all Testing for CUDA device: /usr/local/freesurfer/bin/mri_em_register_cuda: error while loading shared libraries: libcudart.so.5.0: cannot open shared object file: No such file or directory Linux vmcntdsktp10 3.10.0-957.21.3.el7.x86_64 #1 SMP Tue Jun 18 16:35:19 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sample001 exited with ERRORS at Sat Jun 22 10:05:12 EDT 2019
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[GHS\026278@vmcntdsktp10 fs_sample1]$
Can you suggest workarounds for one or both of these errors? Thanks,
John
Warm regards,
Please, note my new email address, john.absher@prismahealth.org
John R. Absher, MD, FAAN Division of Neurology, Department of Medicine
Prisma Health-Upstate 200 Patewood Drive, Suite 350B City, SC 29615 864-454-4500 (office) 864-350-6655 (mobile) 864-454-4505 (fax)
Inspire health. Serve with compassion. Be the difference.
---------------------------------------------------------------------- CONFIDENTIALITY NOTICE This message is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is strictly prohibited by law. If you have received this communication in error, please notify me immediately.