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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 AHOOPES@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-bounces@nmr.mgh.harvard.edu on behalf of Haoran Xu < haoran.x@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 fsbuild@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 haoran.x@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!
- FreeSurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.
- Platform: UBUNTU 16.04 LTS with 23.5GB memory and 1.4TB available
space. (With this, 1.7G should be fine.)
- 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
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