Hi,
I'm running recon-all in the stable4 FreeSurfer environment and am getting an error at the Fill stage I'm unfamiliar with. When I run this command:
recon-all -subjid 065036777_nrecon_stable4 -fill
I get this error message:
INFO: SUBJECTS_DIR is /autofs/space/jabba_003/users/LONI_nrecon Actual FREESURFER_HOME /autofs/space/windu_006/users/freesurfer_stable4_release/stable4 -rwxrwx--- 1 monaco cagn 270977 Jul 2 08:38 /autofs/space/jabba_003/users/LONI_nrecon/065036777_nrecon_stable4/scripts/recon-all.log Linux luke 2.6.18-53.1.14.el5 #1 SMP Wed Mar 5 11:37:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Fill Wed Jul 2 08:41:06 EDT 2008 /autofs/space/jabba_003/users/LONI_nrecon/065036777_nrecon_stable4/mri
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz
logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.983 -0.086 0.013 -0.725; 0.056 1.018 0.424 -82.711; -0.042 -0.425 0.943 81.256; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 0.983 -0.086 0.013 -0.725; 0.056 1.018 0.424 -82.712; -0.042 -0.425 0.943 81.256; 0.000 0.000 0.000 1.000; reading segmented volume aseg.mgz... mri_fill: could not find any points where lh and rh wm are nbrs Linux luke 2.6.18-53.1.14.el5 #1 SMP Wed Mar 5 11:37:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Wed Jul 2 08:41:15 EDT 2008
Thanks for your help!
-Bill