[Freesurfer] surfreg cannot allocate memory
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
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 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 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
Re: [Freesurfer] surfreg cannot allocate memory
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: -1.0 0.0 0.0 1.0; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0; 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 tal0 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: -1.0 0.0 0.0 1.0; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0; Vox2Vox Matrix is: -1.0 0.0 0.0 255.0; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0; 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: -1.0 0.0 0.0 1.0; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0; 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 tal0 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: -1.0 0.0 0.0 1.0; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0; Vox2Vox Matrix is: -1.0 0.0 0.0 255.0; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0; 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: -1.0 0.0 0.0 1.0; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0; znzTAGskip: tag=1952870258, failed to calloc 1768846336 bytes! Cannot allocate memory On Thu, Dec 20, 2018 at 1:53 PM Hoopes, Andrew 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: * on behalf of Haoran Xu < > haora...@gmail.com> > *Reply-To: *FS Help > *Date: *Thursday, December 20, 2018 at 1:05 PM > *To: *FS Help > *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
Re: [Freesurfer] surfreg cannot allocate memory
External Email - Use Caution WOW I cannot. Freeview showed “failed to load MRI .../mri/brain.mgz”. I had permission to read and write though... Haoran > On Dec 20, 2018, at 3:50 PM, Hoopes, Andrew wrote: > > Hi Haoran, are you able to load the subject’s mri/brain.mgz in freeview > without getting this error? > Andrew > > > From: on behalf of Haoran Xu > > Reply-To: FS Help > Date: Thursday, December 20, 2018 at 2:33 PM > To: FS Help > Subject: Re: [Freesurfer] surfreg cannot allocate memory > > 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: > -1.0 0.0 0.0 1.0; > 0.0 1.0 0.0 0.0; > 0.0 0.0 1.0 0.0; > 0.0 0.0 0.0 1.0; > > 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 > tal0 > 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: > -1.0 0.0 0.0 1.0; > 0.0 1.0 0.0 0.0; > 0.0 0.0 1.0 0.0; > 0.0 0.0 0.0 1.0; > > > Vox2Vox Matrix is: > -1.0 0.0 0.0 255.0; > 0.0 1.0 0.0 0.0; > 0.0 0.0 1.0 0.0; > 0.0 0.0 0.0 1.0; > > 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: > -1.0 0.0 0.0 1.0; > 0.0 1.0 0.0 0.0; > 0.0 0.0 1.0 0.0; > 0.0 0.0 0.0 1.0; > > 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 > tal0 > 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: > -1.0 0.0 0.0 1.0; > 0.0 1.0 0.0 0.0; > 0.0 0.0 1.0 0.0; > 0.0 0.0 0.0 1.0; > > > Vox2Vox Matrix is: > -1.0 0.0 0.0 255.0; > 0.0 1.0 0.0 0.0; > 0.0 0.0 1.0 0.0; > 0.0 0.0 0.0 1.0; > > 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/N
