Dear Freesurfers,
I have had a problem when running recon-all on your tutorial data (bert). Please find following the content of recon-all.log:
*$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $*
* $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $*
*MRISread(../surf/lh.inflated): could not open file*
*No such file or directory*
*mris_sphere: could not read surface file ../surf/lh.inflated*
*No such file or directory*
*Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux*
* *
*recon-all exited with ERRORS at Fri Nov 20 17:32:05 EST 2009*
I suspected that the problem occurred at “mri_ca_register” and reran it as following:
*mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.m3z*
* *
It said the following at the end of the process and “talairach.m3z” could not be found in dir “transforms/”
*…*
*0621: dt=0.056000, rms=0.414 (0.016%), neg=0, invalid=3625*
*0622: dt=0.056000, rms=0.414 (0.020%), neg=0, invalid=3625*
*0623: dt=0.056000, rms=0.414 (0.005%), neg=0, invalid=3625* **
*writing output transformation to transforms/talairach.m3z...*
*Segmentation fault*
* *
Here is what given by “bugr” command:
*FREESURFER_HOME: /usr/local/freesurfer*
*Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0*
*Debian version: 5.0 *
*Kernel info: Linux 2.6.28-11-generic i686*
I am running the VirtualBox Ubuntu version.
I have looked at previous posts but have not been able to figure out an appropriate answer to my problem. Any of your help would be highly appreciated.
Thank you.
Kind regards,
Long
Hi Long,
have you run out of disk space? Bruce On Tue, 24 Nov 2009, L wrote:
Dear Freesurfers,
I have had a problem when running recon-all on your tutorial data (bert). Please find following the content of recon-all.log:
*$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $*
- $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $*
*MRISread(../surf/lh.inflated): could not open file*
*No such file or directory*
*mris_sphere: could not read surface file ../surf/lh.inflated*
*No such file or directory*
*Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux*
*recon-all exited with ERRORS at Fri Nov 20 17:32:05 EST 2009*
I suspected that the problem occurred at ?mri_ca_register? and reran it as following:
*mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.m3z*
It said the following at the end of the process and ?talairach.m3z? could not be found in dir ?transforms/?
*?*
*0621: dt=0.056000, rms=0.414 (0.016%), neg=0, invalid=3625*
*0622: dt=0.056000, rms=0.414 (0.020%), neg=0, invalid=3625*
*0623: dt=0.056000, rms=0.414 (0.005%), neg=0, invalid=3625* **
*writing output transformation to transforms/talairach.m3z...*
*Segmentation fault*
Here is what given by ?bugr? command:
*FREESURFER_HOME: /usr/local/freesurfer*
*Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0*
*Debian version: 5.0 *
*Kernel info: Linux 2.6.28-11-generic i686*
I am running the VirtualBox Ubuntu version.
I have looked at previous posts but have not been able to figure out an appropriate answer to my problem. Any of your help would be highly appreciated.
Thank you.
Kind regards,
Long
Dear Bruce, I have tried running mri_ca_register again twice with the following cases: Case 1: on VirtualBox with 9.2GB available free disk space. I gave 1GB RAM to this Virtual Machine. Case 2: on Ubuntu installed on a machine with 2 core Dual 2.5Ghz , 4G RAM, and 6GB free disk space. In both cases, I have got the same result as described in the previous mail: segmentation fault. Would you have any suggestion for this problem? Thank you. Bests, Long
On Tue, Nov 24, 2009 at 9:05 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Long,
have you run out of disk space? Bruce
On Tue, 24 Nov 2009, L wrote:
Dear Freesurfers,
I have had a problem when running recon-all on your tutorial data (bert). Please find following the content of recon-all.log:
*$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $*
- $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $*
*MRISread(../surf/lh.inflated): could not open file*
*No such file or directory*
*mris_sphere: could not read surface file ../surf/lh.inflated*
*No such file or directory*
*Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux*
*recon-all exited with ERRORS at Fri Nov 20 17:32:05 EST 2009*
I suspected that the problem occurred at ?mri_ca_register? and reran it as following:
*mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.m3z*
It said the following at the end of the process and ?talairach.m3z? could not be found in dir ?transforms/?
*?*
*0621: dt=0.056000, rms=0.414 (0.016%), neg=0, invalid=3625*
*0622: dt=0.056000, rms=0.414 (0.020%), neg=0, invalid=3625*
*0623: dt=0.056000, rms=0.414 (0.005%), neg=0, invalid=3625* **
*writing output transformation to transforms/talairach.m3z...*
*Segmentation fault*
Here is what given by ?bugr? command:
*FREESURFER_HOME: /usr/local/freesurfer*
*Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0*
*Debian version: 5.0 *
*Kernel info: Linux 2.6.28-11-generic i686*
I am running the VirtualBox Ubuntu version.
I have looked at previous posts but have not been able to figure out an appropriate answer to my problem. Any of your help would be highly appreciated.
Thank you.
Kind regards,
Long
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
L -
Long