Dear Freesurfer Group
I have found a problem in running my subjects. With "recon-all -autorecon1 -autorecon2 -autorecon3 -subjid N?" I ran several subjects after making corrections, but suddenly I received error message as following, and I can not run rest of the subjects. It is saying the subject is already running but I am running the subject elsewhere. Can you please help me to face this issue. Thanks a lot in advance.
INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /Users/christine/CorrectedOnes Actual FREESURFER_HOME /Applications/freesurfer -rw-r--r-- 1 christine staff 469592 Nov 4 12:46 /Users/christine/CorrectedOnes/N3237c/scripts/recon-all.log Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386
ERROR: it appears that recon-all is already running for N3237c based on the presence of /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh. It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type:
rm /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh
and re-run. Or you can add -no-isrunning to the recon-all command-line. The contents of this file are: ---------------------------------------------------------- ------------------------------ SUBJECT N3237c HEMI lh rh DATE Wed Nov 2 12:03:39 EDT 2011 USER christine HOST administrators-mac-pro.local PROCESSID 40999 PROCESSOR i386 OS Darwin Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ ----------------------------------------------------------
Best Regards --------------------------------------------------- Nooshin N. Zadeh Graduate Assistant
Departments of Electrical Engineering and Neurology University of Miami ** * * * *
Hi Nooshin,
you can jsut add -no-isrunning to the command line if you are sure the process has finished. This happens when it was killed in a strange way (i.e. if you hit ctrl-c during processing)
cheers Bruce
On Tue, 8 Nov 2011, nooshin n.zade wrote:
Dear Freesurfer Group I have found a problem in running my subjects. With "recon-all -autorecon1 -autorecon2 -autorecon3 -subjid N?" I ran several subjects after making corrections, but suddenly I received error message as following, and I can not run rest of the subjects. It is saying the subject is already running but I am running the subject elsewhere. Can you please help me to face this issue. Thanks a lot in advance.
INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /Users/christine/CorrectedOnes Actual FREESURFER_HOME /Applications/freesurfer -rw-r--r-- 1 christine staff 469592 Nov 4 12:46 /Users/christine/CorrectedOnes/N3237c/scripts/recon-all.log Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386
ERROR: it appears that recon-all is already running for N3237c based on the presence of /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh. It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type:
rm /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh
and re-run. Or you can add -no-isrunning to the recon-all command-line. The contents of this file are:
SUBJECT N3237c HEMI lh rh DATE Wed Nov 2 12:03:39 EDT 2011 USER christine HOST administrators-mac-pro.local PROCESSID 40999 PROCESSOR i386 OS Darwin Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $
Best Regards
Nooshin N. Zadeh Graduate Assistant
Departments of Electrical Engineering and Neurology University of Miami
--
Best Regards
Nooshin N. Zadeh Graduate Assistant
Departments of Electrical Engineering and Neurology University of Miami
Or you can delete the IsRunning file in the scripts directory (make sure it's not actually running!). doug
Bruce Fischl wrote:
Hi Nooshin,
you can jsut add -no-isrunning to the command line if you are sure the process has finished. This happens when it was killed in a strange way (i.e. if you hit ctrl-c during processing)
cheers Bruce
On Tue, 8 Nov 2011, nooshin n.zade wrote:
Dear Freesurfer Group I have found a problem in running my subjects. With "recon-all -autorecon1 -autorecon2 -autorecon3 -subjid N?" I ran several subjects after making corrections, but suddenly I received error message as following, and I can not run rest of the subjects. It is saying the subject is already running but I am running the subject elsewhere. Can you please help me to face this issue. Thanks a lot in advance.
INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /Users/christine/CorrectedOnes Actual FREESURFER_HOME /Applications/freesurfer -rw-r--r-- 1 christine staff 469592 Nov 4 12:46 /Users/christine/CorrectedOnes/N3237c/scripts/recon-all.log Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386
ERROR: it appears that recon-all is already running for N3237c based on the presence of /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh. It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type:
rm /Users/christine/CorrectedOnes/N3237c/scripts/IsRunning.lh+rh
and re-run. Or you can add -no-isrunning to the recon-all command-line. The contents of this file are:
SUBJECT N3237c HEMI lh rh DATE Wed Nov 2 12:03:39 EDT 2011 USER christine HOST administrators-mac-pro.local PROCESSID 40999 PROCESSOR i386 OS Darwin Darwin administrators-mac-pro.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $
Best Regards
Nooshin N. Zadeh Graduate Assistant
Departments of Electrical Engineering and Neurology University of Miami
--
Best Regards
Nooshin N. Zadeh Graduate Assistant
Departments of Electrical Engineering and Neurology University of Miami
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Douglas N Greve -
nooshin n.zade