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
sounds pretty catastrophic. Check the aseg and see how it looks. Something failed previously (e.g. skull stripping, talairach, etc...) On Wed, 2 Jul 2008, Bill Monaco wrote:
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
Hi Bruce,
Nothing had failed in the recon stream prior to this. I checked the talairachs, skull stripping, ageg.mgz, and wm.mgz and didn't see any problems. If you'd like, I can copy what's been outputted already somewhere. Out of curiosity, what does nbrs stand for?
Thanks,
Bill
On Wed, 2 Jul 2008, Bruce Fischl wrote:
sounds pretty catastrophic. Check the aseg and see how it looks. Something failed previously (e.g. skull stripping, talairach, etc...) On Wed, 2 Jul 2008, Bill Monaco wrote:
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
neighbors. It means that it couldn't find any place where the left and right wm touch, which is what is used to detect the callosum. Sure, copy it somewhere and I'll take a look. Does the aseg look accurate? On Wed, 2 Jul 2008, Bill Monaco wrote:
Hi Bruce,
Nothing had failed in the recon stream prior to this. I checked the talairachs, skull stripping, ageg.mgz, and wm.mgz and didn't see any problems. If you'd like, I can copy what's been outputted already somewhere. Out of curiosity, what does nbrs stand for?
Thanks,
Bill
On Wed, 2 Jul 2008, Bruce Fischl wrote:
sounds pretty catastrophic. Check the aseg and see how it looks. Something failed previously (e.g. skull stripping, talairach, etc...) On Wed, 2 Jul 2008, Bill Monaco wrote:
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
freesurfer@nmr.mgh.harvard.edu
-
Bill Monaco -
Bruce Fischl