Hi, I am receiving this error for every subject I send through recon-all. I am checking for edits that need to be made but it seems very odd that 30 subjects or so would all error out at the same step. Any suggestions? Cameron
Subject 'Ponce_033d2': make all recon-all -s /autofs/space/grouch_004/users/ponce/Ponce_033d2 -hemi lh -cortribbon INFO: SUBJECTS_DIR is /autofs/space/grouch_004/users/ponce Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/stable4 -rw-rw-r-- 1 cameo zenuwgp 1257898 Jan 29 17:38 /autofs/space/grouch_004/users/ponce/Ponce_033d2/scripts/recon-all.log Linux node0325 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Cortical ribbon mask Wed Jan 30 11:41:19 EST 2008 /autofs/space/grouch_004/users/ponce/Ponce_033d2/mri
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance Ponce_033d2
Segmentation fault Linux node0325 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Wed Jan 30 11:41:42 EST 2008
Hi,
Two things:
1) Try running mris_volmask from the command line and see if it runs. You may be missing a library (I recall having a similar error). 2) Running out of memory might be a factor. How much do you have?
Padraig
Cameron Ellis wrote:
Hi, I am receiving this error for every subject I send through recon-all. I am checking for edits that need to be made but it seems very odd that 30 subjects or so would all error out at the same step. Any suggestions? Cameron
Subject 'Ponce_033d2': make all recon-all -s /autofs/space/grouch_004/users/ponce/Ponce_033d2 -hemi lh -cortribbon INFO: SUBJECTS_DIR is /autofs/space/grouch_004/users/ponce Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/stable4 -rw-rw-r-- 1 cameo zenuwgp 1257898 Jan 29 17:38 /autofs/space/grouch_004/users/ponce/Ponce_033d2/scripts/recon-all.log Linux node0325 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Cortical ribbon mask Wed Jan 30 11:41:19 EST 2008 /autofs/space/grouch_004/users/ponce/Ponce_033d2/mri
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance Ponce_033d2
Segmentation fault Linux node0325 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Wed Jan 30 11:41:42 EST 2008 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Cameron and Padraig,
This is a problem local to the NMR Center (MGH), where the VTK libraries (of which mris_volmask makes use) were recently updated, and the update contains a bug. I'm working on a local fix now, which should be ready within an hour (locally). The public freesurfer is not affected by this bug.
Thanks for the suggestions though.
Nick
On Wed, 2008-01-30 at 17:08 +0000, Pádraig Kitterick wrote:
Hi,
Two things:
- Try running mris_volmask from the command line and see if it runs.
You may be missing a library (I recall having a similar error). 2) Running out of memory might be a factor. How much do you have?
Padraig
Cameron Ellis wrote:
Hi, I am receiving this error for every subject I send through recon-all. I am checking for edits that need to be made but it seems very odd that 30 subjects or so would all error out at the same step. Any suggestions? Cameron
Subject 'Ponce_033d2': make all recon-all -s /autofs/space/grouch_004/users/ponce/Ponce_033d2 -hemi lh -cortribbon INFO: SUBJECTS_DIR is /autofs/space/grouch_004/users/ponce Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/stable4 -rw-rw-r-- 1 cameo zenuwgp 1257898 Jan 29 17:38 /autofs/space/grouch_004/users/ponce/Ponce_033d2/scripts/recon-all.log Linux node0325 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Cortical ribbon mask Wed Jan 30 11:41:19 EST 2008 /autofs/space/grouch_004/users/ponce/Ponce_033d2/mri
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance Ponce_033d2
Segmentation fault Linux node0325 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Wed Jan 30 11:41:42 EST 2008 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nick, I don't know if this is important but when I try to send these subjects to seychelles and continue the recon process where it left off the job errors immediately, but if I specify a node (-l nodes=1:P4) the job seems to run. Are the updated VTK libraries currently only available to certain nodes? Just curious. I'll wait to submit any more jobs until later this afternoon. Cameron
Cameron and Padraig,
This is a problem local to the NMR Center (MGH), where the VTK libraries (of which mris_volmask makes use) were recently updated, and the update contains a bug. I'm working on a local fix now, which should be ready within an hour (locally). The public freesurfer is not affected by this bug.
Thanks for the suggestions though.
Nick
On Wed, 2008-01-30 at 17:08 +0000, Pádraig Kitterick wrote:
Hi,
Two things:
- Try running mris_volmask from the command line and see if it runs.
You may be missing a library (I recall having a similar error). 2) Running out of memory might be a factor. How much do you have?
Padraig
Cameron Ellis wrote:
Hi, I am receiving this error for every subject I send through recon-all.
I am
checking for edits that need to be made but it seems very odd that 30 subjects or so would all error out at the same step. Any suggestions? Cameron
Subject 'Ponce_033d2': make all recon-all -s /autofs/space/grouch_004/users/ponce/Ponce_033d2 -hemi lh -cortribbon INFO: SUBJECTS_DIR is /autofs/space/grouch_004/users/ponce Actual FREESURFER_HOME
/autofs/space/freesurfer/centos4.0_x86_64/stable4
-rw-rw-r-- 1 cameo zenuwgp 1257898 Jan 29 17:38 /autofs/space/grouch_004/users/ponce/Ponce_033d2/scripts/recon-all.log Linux node0325 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Cortical ribbon mask Wed Jan 30 11:41:19 EST 2008 /autofs/space/grouch_004/users/ponce/Ponce_033d2/mri
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance Ponce_033d2
Segmentation fault Linux node0325 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:28:26 CDT 2006 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Wed Jan 30 11:41:42 EST 2008 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Cameron Ellis -
Nick Schmansky -
Pádraig Kitterick