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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Haoran Xu <haora...@gmail.com<mailto:haora...@gmail.com>>
Reply-To: FS Help 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, December 20, 2018 at 1:05 PM
To: FS Help 
<freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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<mailto: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

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