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Hi,
Running recon-all on sag T1 post-contrast MRI (for archival study) on virtualBox with centOS7 and freesurfer 6. The virtual box runs on a windows server and is allocated 8 processors and 16 GB memory by the windows server on which it resides. A citrix share provides the bulk of our filesystem storage space (/cifs). This filesystem appears not to allow symbolic links, such as these:
rh.white.H rh.white.K lh.white.H lh.white.K
These are symbolic links to [lr]h.white.preaparc.[HK], and recon-all stalls at the step during which these symbolic links are created. If we run the process in our /home directories on a linux filesystem, all is well, and recon-all runs correctly. However, only 8 GB of disc storage space there, and we have ~100 subjects to process. We thought we'd just run ~10 subjects or so, then move their data to the /cifs filesystem, but those 4 symbolic links won't copy.
Questions:
1. If we ignore this error and copy everything else to the /cifs filesystem, is that OK, since the recon-all is complete?
2. If we try to run a GLM contrast on all the subjects (e.g., compare 50 to the other 50) in the /cifs filesystem, where we have space to keep all the data in one place, will the inability to create a symbolic link in that filesystem crash our analysis?
3. One post suggested copying the linked files into the SUBJECTS_DIR directory, but that won't work on /cifs and isn't necessary on the linux filesystem; is there another workaround?
Thank you so much for you any guidance you can provide, and forgive me if there's some easy solution I've overlooked.
John
John R. Absher, MD, FAAN GHS Neurosciences jabsher@ghs.orgmailto:jabsher@ghs.org 864-350-6655 (mobile)