That’s odd – seems like somehow the file got corrupted. I suggest just regenerating the brain.mgz by running:
mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
from your subject’s mri directory. That should fix things.
best
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 5:47 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: 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 <AHOOPES@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-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 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 <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) unlimitedIf 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!
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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