Andres,

No that was all the output there was, "Abnormal termination: 255"

I tried again with the -fsl flag. The output is below. I think the file locking warnings might be caused by my home directory being nfs mounted. In the end, the result is still "Abnormal termination: 255".

Thanks,

Output:
hammer labelbrain -S subject_segmented_no_cere.img -M jakob_rad_convention_segmented_no_cere.img -L jakob_rad_convention_labels_no_cere.img -fsl
Running on: /raid/home/clwyatt/.hammer/hammertemp1006638702
Operating System: Linux
> Performing flirt from /home/scratch/clw-hammer-test/combined/subject_segmented_no_cere.hdr to /home/scratch/clw-hammer-test/combined/jakob_rad_convention_segmented_no_cere.hdr
Jan 17, 2008 1:18:41 PM java.util.prefs.FileSystemPreferences checkLockFile0ErrorCode
WARNING: Could not lock User prefs. Unix error code 37.
Jan 17, 2008 1:18:41 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jan 17, 2008 1:19:11 PM java.util.prefs.FileSystemPreferences checkLockFile0ErrorCode
WARNING: Could not lock User prefs. Unix error code 37.
Jan 17, 2008 1:19:11 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jan 17, 2008 1:19:41 PM java.util.prefs.FileSystemPreferences checkLockFile0ErrorCode
WARNING: Could not lock User prefs. Unix error code 37.
Jan 17, 2008 1:19:41 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jan 17, 2008 1:20:11 PM java.util.prefs.FileSystemPreferences checkLockFile0ErrorCode
WARNING: Could not lock User prefs. Unix error code 37.
Jan 17, 2008 1:20:11 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jan 17, 2008 1:20:41 PM java.util.prefs.FileSystemPreferences checkLockFile0ErrorCode
WARNING: Could not lock User prefs. Unix error code 37.
Jan 17, 2008 1:20:41 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jan 17, 2008 1:21:11 PM java.util.prefs.FileSystemPreferences checkLockFile0ErrorCode
WARNING: Could not lock User prefs. Unix error code 37.
Jan 17, 2008 1:21:11 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
Jan 17, 2008 1:21:41 PM java.util.prefs.FileSystemPreferences checkLockFile0ErrorCode
WARNING: Could not lock User prefs. Unix error code 37.
Jan 17, 2008 1:21:41 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock.
> Transforming FSL matrix to SBIA matrix
Abnormal termination: 255