Folks:
In our first attempt at a complete run of recon-all, we hit this odd failure: recon-all stopped after the mri_remove_neck stage, claiming that:
1. mri_remove_neck couldn't mghWrite to nu_noneck.mgz
2. But then appeared to perform the neck removal anyway and write the output
3. But then the subsequent step: mri_em_register failed saying that it can't read nu_noneck.mgz
... and sure enough, there is no such file there.
The recon-all.log for these steps is copied below.
This doesn't appear to be a permissions problem, as the script happily wrote other files to the same mri directory.
I do wonder whether mri_remove_neck was actually using the correct directory (we are not using the default SUBJECTS_DIR), but the logic for that is in an executable that I don't think we have source for?
But the primary troubleshooting question is why the mghWrite failed, but processing continued anyway, with the subsequent "writing output" message suggesting success of this step (but no file to show for it).
Clues?
Thanks,
Graham
=============== #-------------------------------------- New invocation of recon-all
Sun May 28 12:44:36 PDT 2006 /data/Structural/FreeSurferData/Testing20060528/subjects/40588a /brain-bin/fs_20060528/centos4/freesurfer/bin//recon-all -s 40588a -autorecon2 subjid 40588a setenv SUBJECTS_DIR /data/Structural/FreeSurferData/Testing20060528/subjects FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer Actual FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 8180 ######################################## program versions used $Id: recon-all,v 1.17.2.4 2006/05/02 18:28:49 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:36-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version stable3 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_normalize.c,v 1.44.2.1 2006/04/12 02:02:57 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.1 2006/04/12 02:02:59 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_label2label.c,v 1.23 2006/02/19 17:55:08 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_register.c,v 1.48 2006/02/23 15:53:27 xhan Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 #######################################
[...]
#@# Remove Neck Mon May 29 03:13:29 PDT 2006
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... mghWrite(nu_noneck.mgz, -1): could not open file gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 9 minutes and 55 seconds. #-------------------------------------- #@# SkullLTA Mon May 29 03:23:27 PDT 2006
mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_withskull_2006-02-15.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_withskull_2006-02-15.gca'... setting gca type = Normal gca type average std = 23.5 using min determinant for regularization = 55.2 0 singular and 6473 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... zcat: /data/Structural/FreeSurferData/Testing20060528/subjects/40588a/mri/nu_noneck.mgz.gz: No such file or directory mghRead(/data/Structural/FreeSurferData/Testing20060528/subjects/40588a/mri/nu_noneck.mgz, -1): read error mri_em_register: could not open input volume nu_noneck.mgz.
Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Mon May 29 03:23:35 PDT 2006
Can you verify that the disk was not full?
doug
Graham Wideman wrote:
Folks:
In our first attempt at a complete run of recon-all, we hit this odd failure: recon-all stopped after the mri_remove_neck stage, claiming that:
mri_remove_neck couldn't mghWrite to nu_noneck.mgz
But then appeared to perform the neck removal anyway and write the output
But then the subsequent step: mri_em_register failed saying that it can't read nu_noneck.mgz
... and sure enough, there is no such file there.
The recon-all.log for these steps is copied below.
This doesn't appear to be a permissions problem, as the script happily wrote other files to the same mri directory.
I do wonder whether mri_remove_neck was actually using the correct directory (we are not using the default SUBJECTS_DIR), but the logic for that is in an executable that I don't think we have source for?
But the primary troubleshooting question is why the mghWrite failed, but processing continued anyway, with the subsequent "writing output" message suggesting success of this step (but no file to show for it).
Clues?
Thanks,
Graham
=============== #-------------------------------------- New invocation of recon-all
Sun May 28 12:44:36 PDT 2006 /data/Structural/FreeSurferData/Testing20060528/subjects/40588a /brain-bin/fs_20060528/centos4/freesurfer/bin//recon-all -s 40588a -autorecon2 subjid 40588a setenv SUBJECTS_DIR /data/Structural/FreeSurferData/Testing20060528/subjects FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer Actual FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 8180 ######################################## program versions used $Id: recon-all,v 1.17.2.4 2006/05/02 18:28:49 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:36-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version stable3 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_normalize.c,v 1.44.2.1 2006/04/12 02:02:57 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.1 2006/04/12 02:02:59 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_label2label.c,v 1.23 2006/02/19 17:55:08 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_register.c,v 1.48 2006/02/23 15:53:27 xhan Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 #######################################
[...]
#@# Remove Neck Mon May 29 03:13:29 PDT 2006
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... mghWrite(nu_noneck.mgz, -1): could not open file gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 9 minutes and 55 seconds. #-------------------------------------- #@# SkullLTA Mon May 29 03:23:27 PDT 2006
mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_withskull_2006-02-15.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_withskull_2006-02-15.gca'... setting gca type = Normal gca type average std = 23.5 using min determinant for regularization = 55.2 0 singular and 6473 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... zcat: /data/Structural/FreeSurferData/Testing20060528/subjects/40588a/mri/nu_noneck.mgz.gz: No such file or directory mghRead(/data/Structural/FreeSurferData/Testing20060528/subjects/40588a/mri/nu_noneck.mgz, -1): read error mri_em_register: could not open input volume nu_noneck.mgz.
Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Mon May 29 03:23:35 PDT 2006 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Doug:
There's over 200 gig space on that drive, and I have since test copied over 100 Meg to the mri directory (as the same user, so permissions seem OK).
Questions:
1. Is mghWrite failure salient, or is this just mri_remove_neck checking for an existing file in order to delete it (ie: it's not really an error).
2. In general, does recon-all happily restart at wherever stage you tell it, and overwrite existing files, or is some special action necessary to deal with existing files?
Thanks,
Graham
At 5/30/2006 10:10 AM, Doug Greve wrote:
Can you verify that the disk was not full?
doug
Graham Wideman wrote:
Folks:
In our first attempt at a complete run of recon-all, we hit this odd failure: recon-all stopped after the mri_remove_neck stage, claiming that:
mri_remove_neck couldn't mghWrite to nu_noneck.mgz
But then appeared to perform the neck removal anyway and write the output
But then the subsequent step: mri_em_register failed saying that it
can't read nu_noneck.mgz
... and sure enough, there is no such file there.
The recon-all.log for these steps is copied below.
This doesn't appear to be a permissions problem, as the script happily wrote other files to the same mri directory.
I do wonder whether mri_remove_neck was actually using the correct directory (we are not using the default SUBJECTS_DIR), but the logic for that is in an executable that I don't think we have source for?
But the primary troubleshooting question is why the mghWrite failed, but processing continued anyway, with the subsequent "writing output" message suggesting success of this step (but no file to show for it).
Clues?
Thanks,
Graham
Hi Graham,
In regards to #2, below, there shouldn't be anything extra you have to do when re-running things. It will write over the old files that are there with no problem.
Jenni
On Tue, 30 May 2006, Graham Wideman wrote:
Doug:
There's over 200 gig space on that drive, and I have since test copied over 100 Meg to the mri directory (as the same user, so permissions seem OK).
Questions:
- Is mghWrite failure salient, or is this just mri_remove_neck checking for
an existing file in order to delete it (ie: it's not really an error).
- In general, does recon-all happily restart at wherever stage you tell it,
and overwrite existing files, or is some special action necessary to deal with existing files?
Thanks,
Graham
At 5/30/2006 10:10 AM, Doug Greve wrote:
Can you verify that the disk was not full?
doug
Graham Wideman wrote:
Folks:
In our first attempt at a complete run of recon-all, we hit this odd failure: recon-all stopped after the mri_remove_neck stage, claiming that:
mri_remove_neck couldn't mghWrite to nu_noneck.mgz
But then appeared to perform the neck removal anyway and write the
output
- But then the subsequent step: mri_em_register failed saying that it
can't read nu_noneck.mgz
... and sure enough, there is no such file there.
The recon-all.log for these steps is copied below.
This doesn't appear to be a permissions problem, as the script happily wrote other files to the same mri directory.
I do wonder whether mri_remove_neck was actually using the correct directory (we are not using the default SUBJECTS_DIR), but the logic for that is in an executable that I don't think we have source for?
But the primary troubleshooting question is why the mghWrite failed, but processing continued anyway, with the subsequent "writing output" message suggesting success of this step (but no file to show for it).
Clues?
Thanks,
Graham
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I've put a new Linux version of mri_remove_neck at:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_remove_neck
Can you run this? It prints more info about why it's failing.
doug
Graham Wideman wrote:
Folks:
In our first attempt at a complete run of recon-all, we hit this odd failure: recon-all stopped after the mri_remove_neck stage, claiming that:
mri_remove_neck couldn't mghWrite to nu_noneck.mgz
But then appeared to perform the neck removal anyway and write the output
But then the subsequent step: mri_em_register failed saying that it can't read nu_noneck.mgz
... and sure enough, there is no such file there.
The recon-all.log for these steps is copied below.
This doesn't appear to be a permissions problem, as the script happily wrote other files to the same mri directory.
I do wonder whether mri_remove_neck was actually using the correct directory (we are not using the default SUBJECTS_DIR), but the logic for that is in an executable that I don't think we have source for?
But the primary troubleshooting question is why the mghWrite failed, but processing continued anyway, with the subsequent "writing output" message suggesting success of this step (but no file to show for it).
Clues?
Thanks,
Graham
=============== #-------------------------------------- New invocation of recon-all
Sun May 28 12:44:36 PDT 2006 /data/Structural/FreeSurferData/Testing20060528/subjects/40588a /brain-bin/fs_20060528/centos4/freesurfer/bin//recon-all -s 40588a -autorecon2 subjid 40588a setenv SUBJECTS_DIR /data/Structural/FreeSurferData/Testing20060528/subjects FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer Actual FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 8180 ######################################## program versions used $Id: recon-all,v 1.17.2.4 2006/05/02 18:28:49 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:36-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version stable3 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_normalize.c,v 1.44.2.1 2006/04/12 02:02:57 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.1 2006/04/12 02:02:59 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_label2label.c,v 1.23 2006/02/19 17:55:08 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_register.c,v 1.48 2006/02/23 15:53:27 xhan Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 #######################################
[...]
#@# Remove Neck Mon May 29 03:13:29 PDT 2006
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... mghWrite(nu_noneck.mgz, -1): could not open file gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 9 minutes and 55 seconds. #-------------------------------------- #@# SkullLTA Mon May 29 03:23:27 PDT 2006
mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_withskull_2006-02-15.gca transforms/talairach_with_skull.lta
aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_withskull_2006-02-15.gca'... setting gca type = Normal gca type average std = 23.5 using min determinant for regularization = 55.2 0 singular and 6473 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... zcat: /data/Structural/FreeSurferData/Testing20060528/subjects/40588a/mri/nu_noneck.mgz.gz: No such file or directory mghRead(/data/Structural/FreeSurferData/Testing20060528/subjects/40588a/mri/nu_noneck.mgz, -1): read error mri_em_register: could not open input volume nu_noneck.mgz.
Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Mon May 29 03:23:35 PDT 2006 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
do you have gzip on your system? On Tue, 30 May 2006, Doug Greve wrote:
I've put a new Linux version of mri_remove_neck at:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_remove_neck
Can you run this? It prints more info about why it's failing.
doug
Graham Wideman wrote:
Folks:
In our first attempt at a complete run of recon-all, we hit this odd failure: recon-all stopped after the mri_remove_neck stage, claiming that:
mri_remove_neck couldn't mghWrite to nu_noneck.mgz
But then appeared to perform the neck removal anyway and write the
output
- But then the subsequent step: mri_em_register failed saying that it
can't read nu_noneck.mgz
... and sure enough, there is no such file there.
The recon-all.log for these steps is copied below.
This doesn't appear to be a permissions problem, as the script happily wrote other files to the same mri directory.
I do wonder whether mri_remove_neck was actually using the correct directory (we are not using the default SUBJECTS_DIR), but the logic for that is in an executable that I don't think we have source for?
But the primary troubleshooting question is why the mghWrite failed, but processing continued anyway, with the subsequent "writing output" message suggesting success of this step (but no file to show for it).
Clues?
Thanks,
Graham
=============== #-------------------------------------- New invocation of recon-all
Sun May 28 12:44:36 PDT 2006 /data/Structural/FreeSurferData/Testing20060528/subjects/40588a /brain-bin/fs_20060528/centos4/freesurfer/bin//recon-all -s 40588a -autorecon2 subjid 40588a setenv SUBJECTS_DIR /data/Structural/FreeSurferData/Testing20060528/subjects FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer Actual FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 8180 ######################################## program versions used $Id: recon-all,v 1.17.2.4 2006/05/02 18:28:49 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:36-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version stable3 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_normalize.c,v 1.44.2.1 2006/04/12 02:02:57 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.1 2006/04/12 02:02:59 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_label2label.c,v 1.23 2006/02/19 17:55:08 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_register.c,v 1.48 2006/02/23 15:53:27 xhan Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 06/05/28-19:44:37-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: graham Machine: gwlinux.ucsd.edu Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400 #######################################
[...]
#@# Remove Neck Mon May 29 03:13:29 PDT 2006
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... mghWrite(nu_noneck.mgz, -1): could not open file gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 9 minutes and 55 seconds. #-------------------------------------- #@# SkullLTA Mon May 29 03:23:27 PDT 2006
mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_withskull_2006-02-15.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_withskull_2006-02-15.gca'... setting gca type = Normal gca type average std = 23.5 using min determinant for regularization = 55.2 0 singular and 6473 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... zcat: /data/Structural/FreeSurferData/Testing20060528/subjects/40588a/mri/nu_noneck.mgz.gz: No such file or directory mghRead(/data/Structural/FreeSurferData/Testing20060528/subjects/40588a/mri/nu_noneck.mgz, -1): read error mri_em_register: could not open input volume nu_noneck.mgz.
Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Mon May 29 03:23:35 PDT 2006 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
At 5/30/2006 01:38 PM, Doug Greve wrote:
I've put a new Linux version of mri_remove_neck at: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_remove_neck Can you run this? It prints more info about why it's failing. doug
Thanks Doug... here are the results, and it looks like Bruce's guess was in the right area :-)
I ran:
recon-all -autorecon2 -nogcareg -nocanorm -nocareg -nocareginv
... so as to run only the Remove Neck step, and here's what I get:
#-------------------------------------- #@# Remove Neck Tue May 30 13:56:46 PDT 2006
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... mghWrite(nu_noneck.mgz, -1): could not open file ERROR: opening pipe gzip -f -c > nu_noneck.mgz, errno = 12 Cannot allocate memory Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue May 30 14:08:38 PDT 2006 --------------------------------------------
Any ideas on this? I've not sure which program is issuing which error.
Graham
try running the mri_remove_neck command line manually. If that doesn't work try changing the nu_neck.mgz name to nu_noneck.mgh and running gzip on it
On Tue, 30 May 2006, Graham Wideman wrote:
At 5/30/2006 01:38 PM, Doug Greve wrote:
I've put a new Linux version of mri_remove_neck at: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_remove_neck Can you run this? It prints more info about why it's failing. doug
Thanks Doug... here are the results, and it looks like Bruce's guess was in the right area :-)
I ran:
recon-all -autorecon2 -nogcareg -nocanorm -nocareg -nocareginv
... so as to run only the Remove Neck step, and here's what I get:
#-------------------------------------- #@# Remove Neck Tue May 30 13:56:46 PDT 2006
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... mghWrite(nu_noneck.mgz, -1): could not open file ERROR: opening pipe gzip -f -c > nu_noneck.mgz, errno = 12 Cannot allocate memory Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue May 30 14:08:38 PDT 2006
Any ideas on this? I've not sure which program is issuing which error.
Graham
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It was running out of memory. I've copied a new version into that ftp site. It might do a little better with the memory managment.
doug
Graham Wideman wrote:
At 5/30/2006 01:38 PM, Doug Greve wrote:
I've put a new Linux version of mri_remove_neck at: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_remove_neck
Can you run this? It prints more info about why it's failing. doug
Thanks Doug... here are the results, and it looks like Bruce's guess was in the right area :-)
I ran:
recon-all -autorecon2 -nogcareg -nocanorm -nocareg -nocareginv
... so as to run only the Remove Neck step, and here's what I get:
#-------------------------------------- #@# Remove Neck Tue May 30 13:56:46 PDT 2006
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'...
setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... mghWrite(nu_noneck.mgz, -1): could not open file ERROR: opening pipe gzip -f -c > nu_noneck.mgz, errno = 12 Cannot allocate memory Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue May 30 14:08:38 PDT 2006
Any ideas on this? I've not sure which program is issuing which error.
Graham
At 5/30/2006 03:25 PM, Doug Greve wrote:
It was running out of memory. I've copied a new version into that ftp site. It might do a little better with the memory managment.
First off -- thanks for the quick response with new versions of the program to try, and obviously the addition of the diagnostic output has really helped.
Response with this version was basically the same as before... "Cannot allocate memory" (log excerpt below).
FWIW here's more info:
Linux box running FC4. "Only" half gig of memory, plus one gig swap space.
While running these last couple of times I watched memory allocation in KInfoCenter's Memory monitor pane.
With no FS script running:
Physical memory: 432 Meg free Swap: 933 Meg free.
With mri_remove_neck running: Physical memory: fluctuates between 5 Meg and 40 Meg free. Swap memory: Generally about 500 Meg free.
So, clearly mri_remove_neck sucks up a lot of memory, and one path-of-least-resistance is a trip to Fry's for some more memory :-).
Any other suggestions are welcome, of course.
Graham
####################################### #-------------------------------------- #@# Remove Neck Tue May 30 14:39:56 PDT 2006
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... mghWrite(nu_noneck.mgz, -1): could not open file ERROR: opening pipe gzip -f -c > nu_noneck.mgz, errno = 12 Cannot allocate memory Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue May 30 14:54:52 PDT 2006
oh, that's because it reads in the nonlinear morph which is big. I guess we need to recommend 1G/cpu from now on :)
Bruce On Tue, 30 May 2006, Graham Wideman wrote:
At 5/30/2006 03:25 PM, Doug Greve wrote:
It was running out of memory. I've copied a new version into that ftp site. It might do a little better with the memory managment.
First off -- thanks for the quick response with new versions of the program to try, and obviously the addition of the diagnostic output has really helped.
Response with this version was basically the same as before... "Cannot allocate memory" (log excerpt below).
FWIW here's more info:
Linux box running FC4. "Only" half gig of memory, plus one gig swap space.
While running these last couple of times I watched memory allocation in KInfoCenter's Memory monitor pane.
With no FS script running:
Physical memory: 432 Meg free Swap: 933 Meg free.
With mri_remove_neck running: Physical memory: fluctuates between 5 Meg and 40 Meg free. Swap memory: Generally about 500 Meg free.
So, clearly mri_remove_neck sucks up a lot of memory, and one path-of-least-resistance is a trip to Fry's for some more memory :-).
Any other suggestions are welcome, of course.
Graham
####################################### #-------------------------------------- #@# Remove Neck Tue May 30 14:39:56 PDT 2006
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... mghWrite(nu_noneck.mgz, -1): could not open file ERROR: opening pipe gzip -f -c > nu_noneck.mgz, errno = 12 Cannot allocate memory Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue May 30 14:54:52 PDT 2006
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I don't know why the new version did not work. I free the morph before it tries to write. Maybe there was not enough contiguous space.
Bruce Fischl wrote:
oh, that's because it reads in the nonlinear morph which is big. I guess we need to recommend 1G/cpu from now on :)
Bruce On Tue, 30 May 2006, Graham Wideman wrote:
At 5/30/2006 03:25 PM, Doug Greve wrote:
It was running out of memory. I've copied a new version into that ftp site. It might do a little better with the memory managment.
First off -- thanks for the quick response with new versions of the program to try, and obviously the addition of the diagnostic output has really helped.
Response with this version was basically the same as before... "Cannot allocate memory" (log excerpt below).
FWIW here's more info:
Linux box running FC4. "Only" half gig of memory, plus one gig swap space.
While running these last couple of times I watched memory allocation in KInfoCenter's Memory monitor pane.
With no FS script running:
Physical memory: 432 Meg free Swap: 933 Meg free.
With mri_remove_neck running: Physical memory: fluctuates between 5 Meg and 40 Meg free. Swap memory: Generally about 500 Meg free.
So, clearly mri_remove_neck sucks up a lot of memory, and one path-of-least-resistance is a trip to Fry's for some more memory :-).
Any other suggestions are welcome, of course.
Graham
####################################### #-------------------------------------- #@# Remove Neck Tue May 30 14:39:56 PDT 2006
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz
erasing everything more than 25 mm from possible brain reading atlas '/brain-bin/fs_20060528/centos4/freesurfer/average/RB_all_2006-02-15.gca'...
setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11495184 nonbrain voxels erased writing output to nu_noneck.mgz... mghWrite(nu_noneck.mgz, -1): could not open file ERROR: opening pipe gzip -f -c > nu_noneck.mgz, errno = 12 Cannot allocate memory Linux gwlinux.ucsd.edu 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue May 30 14:54:52 PDT 2006
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Doug and Bruce:
Turns out that 2 gig of memory causes mri_remove_neck to work. (Not known whether 1 gig would do the trick.)
Thanks for the crucial clues.
Graham
At 5/30/2006 04:44 PM, Doug Greve wrote:
I don't know why the new version did not work. I free the morph before it tries to write. Maybe there was not enough contiguous space.
Bruce Fischl wrote:
oh, that's because it reads in the nonlinear morph which is big. I guess we need to recommend 1G/cpu from now on :)
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Graham Wideman -
Jenni Pacheco