Hi Abi,

Take a look at the status log for this subject:

<subject>/scripts/recon-all-status.log

I bet it will indicate that this failed during the topology fixer on the right hemisphere.  When you run recon-all –all it first does everything on the left hemisphere, and then on the right, so this is why the lh files were created.  You can definitely start running from where it left off, without rerunning everything.  Please see:

https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable

for a list of the flags you should pass to recon-all for each individual step.  You can also use the flag ‘-hemi rh’ to just run the right hemisphere (since the left is likely finished).

Before restarting from the point that failed (likely the topology fixer) you should check visually the rh surfaces that have been created to see if there is a large defect that is causing the failure – this should then be fixed before you try rerunning in order to prevent another failure.

Jenni

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From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Abi Gopal
Sent: Monday, November 20, 2006 9:44 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all did not complete

Hello all

Below is my information:

rhinal

cat $FREESURFER_HOME/build-stamp.txt

source /usr/local/freesurfer/nmr-dev-env




setenv SUBJECTS_DIR /space/rhinal/2/users/gopal/lynch_data



which recon-all




cd /space/rhinal/2/users/gopal/lynch_data

I am not having an error per se, but recon-all keeps crashing before it is complete.  If i look at the files that were created in order of date modified, the last file created in the surf folder (before it crashed) is rh_defect labels.  files such as rh.sphere and rh.thickness were not created (although the corresponding lh files were).  Do I have to run the entire recon-all program again?  Or can I just run recon-all -s lynch -autorecon3?  I am just trying to figure out if there is a quicker way to create the remaining files other than running the entire recon-all process, which will take another 30 hrs.

I appreciate any suggestions.

Thanks very much
Abi