Hi,
using FS 5.1 now, I encountered two problems:
1. when I try to start freeview on my personal laptop, this errors appears:
[georg@localhost ~]$ freeview freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory
However, libXss.so.1 is installed on my system running linux (Fedora 15). Do you habe any idea?
2. Running recon-all with -all flag on a cluster (Linux CentOs 5.6) the stream finishes with errors repeatedly showing this message:
#@# WM Segmentation Tue May 31 12:36:00 CEST 2011
mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt
znzTAGskip: tag=544043625, failed to calloc 1952413696 bytes!
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rwthfs/rz/cluster/work/gg855262/subjects_AN/4550/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux
input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Cannot allocate memory
recon-all -s 4550 exited with ERRORS at Tue May 31 12:36:01 CEST 2011
------------------------------------------------------------------------------ | Execution of Batch-Request stopped at Tue May 31 12:36:01 CEST 2011 | peak memory value: 2.386G | real time used: 04:58:38
I did allocate 4 GB of memory and did not face this error when using FS 5.0 or FS 5.1-beta-release with same settings.
Any recommendations? Thanks, Georg
Can you email me one of the wm.mgz volume that fails? On Wed, 1 Jun 2011, von Polier, Georg Ferdinand Anto wrote:
Hi,
using FS 5.1 now, I encountered two problems:
- when I try to start freeview on my personal laptop, this errors appears:
[georg@localhost ~]$ freeview freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory
However, libXss.so.1 is installed on my system running linux (Fedora 15). Do you habe any idea?
- Running recon-all with -all flag on a cluster (Linux CentOs 5.6) the stream finishes with errors repeatedly showing this message:
#@# WM Segmentation Tue May 31 12:36:00 CEST 2011
mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt
znzTAGskip: tag=544043625, failed to calloc 1952413696 bytes!
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rwthfs/rz/cluster/work/gg855262/subjects_AN/4550/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux
input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Cannot allocate memory
recon-all -s 4550 exited with ERRORS at Tue May 31 12:36:01 CEST 2011
| Execution of Batch-Request stopped at Tue May 31 12:36:01 CEST 2011 | peak memory value: 2.386G | real time used: 04:58:38
I did allocate 4 GB of memory and did not face this error when using FS 5.0 or FS 5.1-beta-release with same settings.
Any recommendations? Thanks, Georg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
1. is your installation 64b? is there a libXss.so in your /usr/lib64 dir?
2. was this run from scratch or rerun? if rerun, when was wm.mgz created and by what release? if created by a 5.1beta release late march to early april, it could have a bug responsible for this. if so, try rerunning with the -clean flag.
n.
On Wed, 2011-06-01 at 01:06 +0200, von Polier, Georg Ferdinand Anto wrote:
Hi,
using FS 5.1 now, I encountered two problems:
- when I try to start freeview on my personal laptop, this errors appears:
[georg@localhost ~]$ freeview freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory
However, libXss.so.1 is installed on my system running linux (Fedora 15). Do you habe any idea?
- Running recon-all with -all flag on a cluster (Linux CentOs 5.6) the stream finishes with errors repeatedly showing this message:
#@# WM Segmentation Tue May 31 12:36:00 CEST 2011
mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt
znzTAGskip: tag=544043625, failed to calloc 1952413696 bytes!
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rwthfs/rz/cluster/work/gg855262/subjects_AN/4550/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux
input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Cannot allocate memory
recon-all -s 4550 exited with ERRORS at Tue May 31 12:36:01 CEST 2011
| Execution of Batch-Request stopped at Tue May 31 12:36:01 CEST 2011 | peak memory value: 2.386G | real time used: 04:58:38
I did allocate 4 GB of memory and did not face this error when using FS 5.0 or FS 5.1-beta-release with same settings.
Any recommendations? Thanks, Georg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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von Polier, Georg Ferdinand Anto