Dear freesurfer experts,
I was running an autorecon2 in the recon-all but always gives me this memory allocation error, only on this subject. Im using FS v5.1
#@# ASeg Stats Mon Jun 3 20:13:11 CEST 2013 /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject qsm1_17_stats2_g
$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject qsm1_17_stats2_g sysname Linux hostname localhost.localdomain machine x86_64 user root atlas_icv (eTIV) = 1196346 mm^3 (det: 1.628380 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 206011 rh white matter volume 198149 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 235659.045132, pTot = 416409.266434 c = 180750.221302 rh surface-based volumes (mm3): wTot = 223785.748405, pTot = 402494.420361 c = 178708.671956 MRIalloc: could not allocate 540094766 frames
Computing SupraTentVolCor Cannot allocate memory Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s qsm1_17_stats2_g exited with ERRORS at Mon Jun 3 20:18:36 CEST 2013
For more details, see the log file /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Any help will be appreaciated,
Many thanks in advance Rafa
Hi Rafa
that sounds like a bug. Can you gzip and upload the whole subject dir?
cheers Bruce On Tue, 4 Jun 2013, Rafa X wrote:
Dear freesurfer experts,
I was running an autorecon2 in the recon-all but always gives me this memory allocation error, only on this subject. Im using FS v5.1
#@# ASeg Stats Mon Jun 3 20:13:11 CEST 2013 /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject qsm1_17_stats2_g
$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /root/trabajo/freesurfer/ASegStatsLUT.txt --subject qsm1_17_stats2_g sysname Linux hostname localhost.localdomain machine x86_64 user root atlas_icv (eTIV) = 1196346 mm^3 (det: 1.628380 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 206011 rh white matter volume 198149 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 235659.045132, pTot = 416409.266434 c = 180750.221302 rh surface-based volumes (mm3): wTot = 223785.748405, pTot = 402494.420361 c = 178708.671956 MRIalloc: could not allocate 540094766 frames
Computing SupraTentVolCor Cannot allocate memory Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s qsm1_17_stats2_g exited with ERRORS at Mon Jun 3 20:18:36 CEST 2013
For more details, see the log file /root/trabajo/freesurfer/subjects/qsm1_17_stats2_g/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Any help will be appreaciated,
Many thanks in advance Rafa
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Rafa X