Hi Amy
can you please send us the full command line and screen output? Otherwise
we can't help you.
thanks
Bruce
On Fri, 22 Jan 2016, AMY LIN wrote:
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!
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