Re: [Freesurfer] recon-all error

Hi Rafa, there is something wrong with the ribbon.mgz file. Try deleting it and regenerating it with recon-all -s subject -cortribbon

doug

On 06/05/2013 10:17 AM, Rafa X wrote:

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 mailto: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
    <mailto: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/BugReporting



                Any help will be appreaciated,

                Many thanks in advance
                Rafa




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