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 <ahoo...@mgh.harvard.edu> wrote: > > Hi Haoran, are you able to load the subject’s mri/brain.mgz in freeview > without getting this error? > 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 2:33 PM > To: FS Help <freesurfer@nmr.mgh.harvard.edu> > 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: > -1.00000 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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