External Email - Use Caution Thank you Andrew! The log is copied here below. Haoran
$ surfreg --s subj001 --t fsaverage_sym --lh --xhemi Thu Dec 20 13:01:31 EST 2018 setenv SUBJECTS_DIR /home/haoran/FP/data/NBMLdata/anatomicals/ cd /home/haoran/FP/data/NBMLdata/anatomicals/subj001 /usr/local/freesurfer/bin/surfreg --s subj001 --t fsaverage_sym --lh --xhemi Linux haoranPC 4.15.0-43-generic #46~16.04.1-Ubuntu SMP Fri Dec 7 13:31:08 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux xhemi does not exist for subj001, running now xhemireg --s subj001 outdir is /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi Logfile is /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/xhemireg.lh.log /usr/local/freesurfer/bin/xhemireg --s subj001 $Id: xhemireg,v 1.26.2.1 2016/08/02 21:16:35 greve Exp $ Thu Dec 20 13:01:31 EST 2018 Linux haoranPC 4.15.0-43-generic #46~16.04.1-Ubuntu SMP Fri Dec 7 13:31:08 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux /home/haoran/FP/data/NBMLdata/anatomicals/subj001 setenv SUBJECTS_DIR /home/haoran/FP/data/NBMLdata/anatomicals/ Thu Dec 20 13:01:31 EST 2018 Thu Dec 20 13:01:31 EST 2018 vol orig -------------- mri_vol2vol --mov mri/orig.mgz --targ mri/orig.mgz --reg /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/lrrev.register.dat --o /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/mri/orig.mgz --keep-precision --no-save-reg Matrix from regfile: -1.00000 0.00000 0.00000 1.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; movvol mri/orig.mgz targvol mri/orig.mgz outvol /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/mri/orig.mgz regfile /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/lrrev.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1546000118 Final tkRAS-to-tkRAS Matrix is: -1.00000 0.00000 0.00000 1.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -1.00000 0.00000 0.00000 255.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done vol T1 -------------- mri_vol2vol --mov mri/T1.mgz --targ mri/T1.mgz --reg /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/lrrev.register.dat --o /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/mri/T1.mgz --keep-precision --no-save-reg Matrix from regfile: -1.00000 0.00000 0.00000 1.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; movvol mri/T1.mgz targvol mri/T1.mgz outvol /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/mri/T1.mgz regfile /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/lrrev.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1545834350 Final tkRAS-to-tkRAS Matrix is: -1.00000 0.00000 0.00000 1.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -1.00000 0.00000 0.00000 255.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done vol brain -------------- mri_vol2vol --mov mri/brain.mgz --targ mri/brain.mgz --reg /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/lrrev.register.dat --o /home/haoran/FP/data/NBMLdata/anatomicals//subj001/xhemi/mri/brain.mgz --keep-precision --no-save-reg Matrix from regfile: -1.00000 0.00000 0.00000 1.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; znzTAGskip: tag=1952870258, failed to calloc 1768846336 bytes! Cannot allocate memory On Thu, Dec 20, 2018 at 1:53 PM Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote: > Hi Haoran, that error is the hallmark of a corrupted volume file. Do you > mind sending the log, or at least the end of it? It’d be helpful to see > when this error is actually occurring. > > > > thanks > > Andrew > > > > > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Haoran Xu < > haora...@gmail.com> > *Reply-To: *FS Help <freesurfer@nmr.mgh.harvard.edu> > *Date: *Thursday, December 20, 2018 at 1:05 PM > *To: *FS Help <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] surfreg cannot allocate memory > > > > * External Email - Use Caution * > > Thanks for the suggestion! But it seems the max memory size was unlimited > already. Any more thoughts about this? > > Best, > > Haroan > > > > > > $ ulimit -a > > core file size (blocks, -c) 0 > > data seg size (kbytes, -d) unlimited > > scheduling priority (-e) 0 > > file size (blocks, -f) unlimited > > pending signals (-i) 96121 > > max locked memory (kbytes, -l) 64 > > > *max memory size (kbytes, -m) unlimited * > open files (-n) 1024 > > pipe size (512 bytes, -p) 8 > > POSIX message queues (bytes, -q) 819200 > > real-time priority (-r) 0 > > stack size (kbytes, -s) 8192 > > cpu time (seconds, -t) unlimited > > max user processes (-u) 96121 > > virtual memory (kbytes, -v) unlimited > > file locks (-x) unlimited > > > > > > On Wed, Dec 19, 2018 at 7:14 PM fsbuild <fsbu...@contbay.com> wrote: > > * External Email - Use Caution * > > Hello Haoran, > > > > You could try looking at your shell limits and see if the memory size is > listed as something other than “unlimited”. > > > > In bash shell, > > > > $ bash > $ ulimit -a > core file size (blocks, -c) 0 > data seg size (kbytes, -d) unlimited > scheduling priority (-e) 0 > file size (blocks, -f) unlimited > pending signals (-i) 256605 > max locked memory (kbytes, -l) 64 > > *max memory size (kbytes, -m) unlimited *open files > (-n) 65535 > pipe size (512 bytes, -p) 8 > POSIX message queues (bytes, -q) 819200 > real-time priority (-r) 0 > stack size (kbytes, -s) unlimited > cpu time (seconds, -t) unlimited > max user processes (-u) 256605 > virtual memory (kbytes, -v) unlimited > file locks (-x) unlimited > > If memory does not read as unlimited then, > > > > $ ulimit -m unlimited > > > > - R. > > > > > > On Dec 19, 2018, at 18:30, Haoran Xu <haora...@gmail.com> wrote: > > > > * External Email - Use Caution * > > > > Hello FreeSurfer Developers, > > I am using surfreg to map one of my subject "subj001" to "fsaverage_sym" > by these commands: > > > > surfreg --s subj001 --t fsaverage_sym --lh > surfreg --s subj001 --t fsaverage_sym --lh --xhemi > > > > The first command worked well, however the second did not. It showed error: > > > > "znzTAGskip: tag=1952870258, failed to calloc 1768846336 bytes! > Cannot allocate memory" > > > > Searched the archive but without good luck. Any suggestions? Appreciated! > > > > 1) FreeSurfer version: > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. > > 2) Platform: UBUNTU 16.04 LTS with 23.5GB memory and 1.4TB available > space. (With this, 1.7G should be fine.) > > 3) uname -a: Linux haoranPC 4.15.0-43-generic #46~16.04.1-Ubuntu SMP Fri > Dec 7 13:31:08 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux > > > > Regards, > > Haoran Xu > > > > _______________________________________________ > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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