Dear All,
The problem is fixed as Brian suggested (Thanks Brian), but there is a new problem while running the recon-all. Nu_correct somehow crashes during the proceesing. The follows are the details. Could anyone give me an idea?
Thanks a lot in advance!
p.s. nu_correct seems fine while typing nuc_correct, it returns vesion info (1.04).
[riobravo@localhost ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05 INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects Actual FREESURFER_HOME /home/riobravo/freesurfer Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux ######################################## program versions used $Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ Program nu_correct, built from: Package MNI N3, version 1.04, compiled by pubsw@lyon (i686-pc-linux-gnu) on 2001-08-09 at 10:52:16 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_watershed.cpp,v 1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_fill.c,v 1.95 2005/09/05 20:49:50 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_fix_topology.c,v 1.31 2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_register.c,v 1.30 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris2rgb ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08 19:45:07 nicks Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_em_register.c,v 1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_ca_register.c,v 1.34 2005/08/18 13:29:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_ca_label.c,v 1.62 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB40_talairach_2005-07-20.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### ~/freesurfer/subjects/Sub05 Using mgz format --------------------------------------------- MotionCor Wed Sep 21 10:13:44 EDT 2005 WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. /home/riobravo/freesurfer/subjects/Sub05 mri_convert /home/riobravo/freesurfer/subjects/Sub05/mri/rawavg.mgz /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz --conform mri_convert /home/riobravo/freesurfer/subjects/Sub05/mri/rawavg.mgz /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz --conform reading from /home/riobravo/freesurfer/subjects/Sub05/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (-1, 0, 0) Original Data has (1, 1, 1) mm size and (256, 256, 160) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 4 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz... --------------------------------------------- Nu Intensity Correction Wed Sep 21 10:14:06 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc nu_estimate_np_and_em: data directory for package "N3" not found in /home/riobravo/freesurfer/lib/mni/data [riobravo@localhost.localdomain:/home/riobravo/freesurfer/subjects/Sub05/mri/] [2005-09-21 10:14:18] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_7260/ nu0.mnc nu1.imp
nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) ERROR: nu_correct Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux recon-all exited with errors at Wed Sep 21 10:14:18 EDT 2005
-----Original Message----- From: Brian T. Quinn [mailto:btquinn@nmr.mgh.harvard.edu] Sent: Wed 9/21/2005 10:01 AM To: Hsu, Shen-Mou Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A problem occurred while running recon-all in the new dev version
try renaming the .mgz volume (Sub05.mgz) in orig with a 3 digit zero padded number such as 001.mgz
thanks, brian
On Wed, 21 Sep 2005, Hsu, Shen-Mou wrote:
Hi!
I am running the freesurfer on redhat 9 with the latest release (freesurfer-Linux-rh9-dev20050915-full.tar.gz.) Unfortunately, while running recon-all -autorecon1, it returns that no data is found, but the data exists indeed. Could anyone help me this out?
Many thanks!
Shen-Mou Hsu
Here are the details.
[riobravo@localhost freesurfer]$ tcsh Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/riobravo/freesurfer FSFAST_HOME /home/riobravo/freesurfer/fsfast SUBJECTS_DIR /home/riobravo/freesurfer/subjects FUNCTIONALS_DIR /home/riobravo/freesurfer/sessions MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib PERL5LIB GSL_DIR /home/riobravo/freesurfer/lib/gsl QTDIR /home/riobravo/freesurfer/lib/qt TCLLIBPATH /home/riobravo/freesurfer/lib/tcltktixblt/lib FSL_DIR /home/riobravo/fsl
riobravo@localhost orig]$ mri_convert /home/riobravo/Exp3/prefreesurfer/Sub05MP_ave+orig.BRIK Sub05.mgz [riobravo@localhost orig]$ ls Sub05.mgz
riobravo@localhost ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05 INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects Actual FREESURFER_HOME /home/riobravo/freesurfer Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux ######################################## program versions used $Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ Program nu_correct, built from: Package MNI N3, version 1.04, compiled by pubsw@lyon (i686-pc-linux-gnu) on 2001-08-09 at 10:52:16 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_watershed.cpp,v 1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_fill.c,v 1.95 2005/09/05 20:49:50 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_fix_topology.c,v 1.31 2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_register.c,v 1.30 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris2rgb ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08 19:45:07 nicks Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_em_register.c,v 1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_register.c,v 1.34 2005/08/18 13:29:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_label.c,v 1.62 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB40_talairach_2005-07-20.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### ~/freesurfer/subjects/Sub05 Using COR format
MotionCor Wed Sep 21 09:51:01 EDT 2005 ERROR: no data found in /home/riobravo/freesurfer/subjects/Sub05/mri/orig Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux recon-all exited with errors at Wed Sep 21 09:51:01 EDT 2005
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Hsu,
The MINC toolkit is now included in the Freesurfer distribution, and nu_correct should be version 1.10.
Since you say that nu_correct returns a version 1.04, its my guess that you have an older version of the MINC toolkit installed somewhere in your path. Remove any setup commands to older MINC toolkits in your .cshrc file.
The new $FREESURFER_HOME/FreeSurferEnv.csh script (called by SetUpFreeSurfer.csh) will setup the paths to the newly installed MINC toolkit for you.
You can confirm which tools are used by typing:
which nu_correct
and
which nu_estimate_np_and_em
These binaries should be in a subdirectory of your new FreeSurfer installation. Also type:
echo $PERL5LIB
and confirm that the path points to your new installation.
Nick
On Wed, 2005-09-21 at 13:00 -0400, Hsu, Shen-Mou wrote:
Dear All,
The problem is fixed as Brian suggested (Thanks Brian), but there is a new problem while running the recon-all. Nu_correct somehow crashes during the proceesing. The follows are the details. Could anyone give me an idea?
Thanks a lot in advance!
p.s. nu_correct seems fine while typing nuc_correct, it returns vesion info (1.04).
[riobravo@localhost ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05 INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects Actual FREESURFER_HOME /home/riobravo/freesurfer Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux ######################################## program versions used $Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ Program nu_correct, built from: Package MNI N3, version 1.04, compiled by pubsw@lyon (i686-pc-linux-gnu) on 2001-08-09 at 10:52:16 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_watershed.cpp,v 1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_fill.c,v 1.95 2005/09/05 20:49:50 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_fix_topology.c,v 1.31 2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris_register.c,v 1.30 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris2rgb ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08 19:45:07 nicks Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_em_register.c,v 1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_ca_register.c,v 1.34 2005/08/18 13:29:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_ca_label.c,v 1.62 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB40_talairach_2005-07-20.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### ~/freesurfer/subjects/Sub05 Using mgz format
MotionCor Wed Sep 21 10:13:44 EDT 2005 WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. /home/riobravo/freesurfer/subjects/Sub05 mri_convert /home/riobravo/freesurfer/subjects/Sub05/mri/rawavg.mgz /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz --conform mri_convert /home/riobravo/freesurfer/subjects/Sub05/mri/rawavg.mgz /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz --conform reading from /home/riobravo/freesurfer/subjects/Sub05/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (-1, 0, 0) Original Data has (1, 1, 1) mm size and (256, 256, 160) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 4 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz...
Nu Intensity Correction Wed Sep 21 10:14:06 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc nu_estimate_np_and_em: data directory for package "N3" not found in /home/riobravo/freesurfer/lib/mni/data [riobravo@localhost.localdomain:/home/riobravo/freesurfer/subjects/Sub05/mri/] [2005-09-21 10:14:18] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_7260/ nu0.mnc nu1.imp
nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) ERROR: nu_correct Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux recon-all exited with errors at Wed Sep 21 10:14:18 EDT 2005
-----Original Message----- From: Brian T. Quinn [mailto:btquinn@nmr.mgh.harvard.edu] Sent: Wed 9/21/2005 10:01 AM To: Hsu, Shen-Mou Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A problem occurred while running recon-all in the new dev version
try renaming the .mgz volume (Sub05.mgz) in orig with a 3 digit zero padded number such as 001.mgz
thanks, brian
On Wed, 21 Sep 2005, Hsu, Shen-Mou wrote:
Hi!
I am running the freesurfer on redhat 9 with the latest release (freesurfer-Linux-rh9-dev20050915-full.tar.gz.) Unfortunately, while running recon-all -autorecon1, it returns that no data is found, but the data exists indeed. Could anyone help me this out?
Many thanks!
Shen-Mou Hsu
Here are the details.
[riobravo@localhost freesurfer]$ tcsh Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/riobravo/freesurfer FSFAST_HOME /home/riobravo/freesurfer/fsfast SUBJECTS_DIR /home/riobravo/freesurfer/subjects FUNCTIONALS_DIR /home/riobravo/freesurfer/sessions MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib PERL5LIB GSL_DIR /home/riobravo/freesurfer/lib/gsl QTDIR /home/riobravo/freesurfer/lib/qt TCLLIBPATH /home/riobravo/freesurfer/lib/tcltktixblt/lib FSL_DIR /home/riobravo/fsl
riobravo@localhost orig]$ mri_convert /home/riobravo/Exp3/prefreesurfer/Sub05MP_ave+orig.BRIK Sub05.mgz [riobravo@localhost orig]$ ls Sub05.mgz
riobravo@localhost ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05 INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects Actual FREESURFER_HOME /home/riobravo/freesurfer Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux ######################################## program versions used $Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ Program nu_correct, built from: Package MNI N3, version 1.04, compiled by pubsw@lyon (i686-pc-linux-gnu) on 2001-08-09 at 10:52:16 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_watershed.cpp,v 1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_fill.c,v 1.95 2005/09/05 20:49:50 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_fix_topology.c,v 1.31 2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_register.c,v 1.30 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris2rgb ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08 19:45:07 nicks Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_em_register.c,v 1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_register.c,v 1.34 2005/08/18 13:29:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_ca_label.c,v 1.62 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB40_talairach_2005-07-20.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### ~/freesurfer/subjects/Sub05 Using COR format
MotionCor Wed Sep 21 09:51:01 EDT 2005 ERROR: no data found in /home/riobravo/freesurfer/subjects/Sub05/mri/orig Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 i686 i686 i386 GNU/Linux recon-all exited with errors at Wed Sep 21 09:51:01 EDT 2005
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Hsu, Shen-Mou -
Nick Schmansky