Hi Florian
can you tar and gzip that subject dir and we will take a look?
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:
- FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 (download date 24-Jan-17)
- Platform: CentOS release 6.8 (Final)
- 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
- 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
- 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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