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.
[EMAIL PROTECTED] 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
[EMAIL PROTECTED] orig]$ mri_convert
/home/riobravo/Exp3/prefreesurfer/Sub05MP_ave+orig.BRIK Sub05.mgz
[EMAIL PROTECTED] orig]$ ls
Sub05.mgz
[EMAIL PROTECTED] ~/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 [EMAIL PROTECTED] (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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--
brian t. quinn
_______________________________________________
Freesurfer mailing list
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