Hi all,
I'm trying to re-run subjects through recon-all for version 5.3.0 on a Mac 10.10.5 using Centos 6 but am not getting the normal output. There seems to be several strange things happening. The process ends almost instantaneously and says that it finished without error, so I don't get any errors or warnings. The correct subject directory folders are created (mri, bem, scripts, etc), but most of them are empty. The only folder that has anything in them are the scripts folder and the mri folder, which has the orig and transforms folders and are pretty much empty.
It seems that the program is only running the mri_convert command on the 001.mgz file, writing the output to the folder that I've specified and then finishes without error.
I've tried to run the commands on both local and remote servers to rule out an issue with the server and from different user accounts to rule out permission issues as I am a new lab member. I've also tried several different subjects to rule out problems with the scans. Also, these subjects have been run previously on an older version of FS, so the problem is likely not with the scans themselves.
Any help at all would be much appreciated!