Re: [Freesurfer] recon-all error

Dear Doug,

I have re-sent the whole subject via the file drop, I think everything was fine this time. Please let me know when you have an ide of what's going on with it.

Cheers, Rafa

2013/6/4 Bruce Fischl fischl@nmr.mgh.harvard.edu

Hi Rafa

this doesn't look like the whole subject dir, just some files from it (e.g. no mri/transforms/talairach.xfm). Don't email it to me - use our ftp site

cheers Bruce On Tue, 4 Jun 2013, Rafa X wrote:

Hi Bruce,Thanks for your reply. I have attached the zipped subject dir

...

(please, note that I had to compress it twice for sending

problems). Rafa.

2013/6/4 Bruce Fischl fischl@nmr.mgh.harvard.edu 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

        Any help will be appreaciated,

        Many thanks in advance
        Rafa

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