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: >> >> 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 >> > #-------------------------------------------- >> > [EMAIL PROTECTED] 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
