Hi Bruce,
It’s a custom atlas with minor changes that was build with the rebuild_gca_atlas.csh script. What is puzzling to me is the fact that if I omit the align-after flag the mri_ca_register command works perfectly fine.
Many thanks & best wishes, Florian
Am 24.01.17, 21:48 schrieb "Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von fischl@nmr.mgh.harvard.edu>:
I think that should be enough, but your data doesn't segfault for me. I also noticed the following in your recon-all.log file:
usr/local/freesurfer/bin/recon-all -all -gca RB_all_2017-01-23.gca -gca-skull RB_all_withskull_2017-01-23.gca -subjid vco1573test_mpr
are you using your own version of our atlases? Or did you rename them? I don't think we rebuilt any in 2017.
cheers Bruce
On Tue, 24 Jan 2017, Florian Krismer wrote:
> 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-bounces@nmr.mgh.harvard.edu im Auftrag von fischl@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 > > > > > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. 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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.