Hi Bruce,
it is a virtual machine with 8GB RAM dedicated to it. Any idea how much RAM
would be enough?
Thanks,
Florian
Am 24.01.17, 21:39 schrieb "Bruce Fischl"
<freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von
fis...@nmr.mgh.harvard.edu>:
Hi Florian
how much RAM do you have in that machine? I think it is not enough....
cheers
Bruce
On
Tue, 24 Jan 2017, Florian Krismer wrote:
> Dear FreeSurfer Developers,
>
> I'm attempting to run recon-all on a test subject (through recon-all –all
–subjid test001 in Freesurfer 6). Recon-all hangs at the mri_ca_register
command throwing a Segfault error.
>
> This is the corresponding part of the recon-all.log:
>
-------------------------------------------------------------------------------
> mri_ca_register -rusage
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca
transforms/talairach.m3z
>
> not handling expanded ventricles...
> using previously computed transform transforms/talairach.lta
> renormalizing sequences with structure alignment, equivalent to:
> -renormalize
> -regularize_mean 0.500
> -regularize 0.500
> using MR volume brainmask.mgz to mask input volume...
>
> == Number of threads available to mri_ca_register for OpenMP = 1 ==
> reading 1 input volumes...
> logging results to talairach.log
> reading input volume 'norm.mgz'...
> reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
> label assignment complete, 0 changed (0.00%)
> det(m_affine) = 1.26 (predicted orig area = 6.3)
> Segmentation fault
>
-------------------------------------------------------------------------------
>
>
> When debugging the error through gdb I get the following, additional
information:
>
>
-------------------------------------------------------------------------------
>
> [florian@freesurfer]$ gdb --args mri_ca_register -rusage
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca
transforms/talairach.m3z
> GNU gdb (GDB) Red Hat Enterprise Linux (7.2-90.el6)
> Copyright (C) 2010 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later
<http://gnu.org/licenses/gpl.html>
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law. Type "show copying"
> and "show warranty" for details.
> This GDB was configured as "x86_64-redhat-linux-gnu".
> For bug reporting instructions, please see:
> <http://www.gnu.org/software/gdb/bugs/>...
> Reading symbols from /usr/local/freesurfer/bin/mri_ca_register...(no
debugging symbols found)...done.
> (gdb) run
> Starting program: /usr/local/freesurfer/bin/mri_ca_register -rusage
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca
transforms/talairach.m3z
> warning: no loadable sections found in added symbol-file system-supplied
DSO at 0x7ffff7ffa000
> [Thread debugging using libthread_db enabled]
> not handling expanded ventricles...
> using previously computed transform transforms/talairach.lta
> renormalizing sequences with structure alignment, equivalent to:
> -renormalize
> -regularize_mean 0.500
> -regularize 0.500
> using MR volume brainmask.mgz to mask input volume...
>
> == Number of threads available to
/usr/local/freesurfer/bin/mri_ca_register for OpenMP = 1 ==
> reading 1 input volumes...
> logging results to talairach.log
> reading input volume 'norm.mgz'...
> reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
> freeing gibbs priors...done.
> average std[0] = 5.0
> label assignment complete, 0 changed (0.00%)
> det(m_affine) = 1.26 (predicted orig area = 6.3)
>
> Program received signal SIGSEGV, Segmentation fault.
> _int_free (av=0x7ffff6bb4120, p=0x619a5f30, have_lock=0) at malloc.c:5000
> 5000 if (__builtin_expect (!prev_inuse(nextchunk), 0))
> (gdb)
>
-------------------------------------------------------------------------------
>
>
> I run the command on a virtual machine (using XEN as hypervisor software)
with 2 cores and 8gb RAM assigned to the virtual machine.
> Some basic information about the platform:
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
(download date 24-Jan-17)
> 2) Platform: CentOS release 6.8 (Final)
> 3) uname –a: Linux 4.4.27-x86_64-jb1 #1 SMP Thu Oct 27 13:51:17 CEST
2016 x86_64 x86_64 x86_64 GNU/Linux
> 4) mri_ca_register –all-info: ProgramName: mri_ca_register
ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp:
2017/01/24-17:30:37-GMT BuildTimeStamp: Dec 29 2016 17:01:05 CVS: $Id:
mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman
> 5) libgcc.i686 4.4.7-17.el6
>
> Does anyone have any thoughts on how to trouble-shoot this one?
> The funny thing is that if I remove the –align-after flag, the command
works like a charm (I couldn’t find any documentation describing the purpose of
–align-after?).
>
> Many thanks for your support & best wishes,
> Florian
>
>
>
>
>
>
>
>
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