1) Yes. mri_convert x249.img 001.mgz
2) It's missing libstd++.so.5. I suggest you run find / -name "libstd*"
-print
If you find a libstd++.so.6 for instance create a libstd++.so.5 as a
symbolic link.
3) It's ok.
-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
mgh.harvard.edu] On Behalf Of ???
Sent: quinta-feira, 4 de outubro de 2007 05:30
To: freesurfer
Subject: [Freesurfer] problems
Hi,
I had downloaded the freesurfer to my system (Linux Fedora Core 4)
and had completed all the installation procedures.
Question 1:
I would like to convert analyze format to .mgz. What command line do I
use?
Can I type "mri_convert x249.img 001.mgz "?
Question 2:
When I type "recon-all -s x249 -nuintensitycor", it doesn't run and
has a error" nu_correct." What would I do to resolve the problem?
Question 3:
It doesn't find talairach.xfm. What would I do to get the file?
thanks~~
FreeSurfer problem report
---------------------------------------------------------------------
FREESURFER_HOME: /usr/local/freesurfer
Build stamp: freesurfer-Linux-centos4-stable-pub-v4.0.1
RedHat release: Fedora Core release 4 (Stentz)
Kernel info: Linux 2.6.11-1.1369_FC4 i686
---------------------------------------------------------------------
1) subject name
x249
2) the entire command-line executed
[EMAIL PROTECTED] ~]# ksh
# tcsh
[EMAIL PROTECTED] ~]# setenv FREESURFER_HOME /usr/local/freesurfer
[EMAIL PROTECTED] ~]# source $FREESURFER_HOME/SetUpFreeSurfer.csh
[EMAIL PROTECTED] ~]# cd $SUBJECTS_DIR
[EMAIL PROTECTED] subjects]# cd x249/mri/orig
[EMAIL PROTECTED] orig]# mri_convert x249.img 001.mgz
[EMAIL PROTECTED] mri]# recon-all -s x249 -nuintensitycor
3) the error message generated
ERROR: nu_correct
4) optionally include the subject's /script/recon-all.log
Thu Oct 4 13:38:14 CST 2007
/usr/local/freesurfer/subjects/x249
/usr/local/freesurfer/bin/recon-all
-s x249 -nuintensitycor
subjid x249
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v4.0.1
Linux cgu.edu.tw 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 16383
########################################
program versions used
$Id: recon-all,v 1.133.2.5 2007/09/17 16:38:00 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.7 2007/01/06 00:01:14 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion:
$Name: stable4 $ TimeStamp: 2007/10/04-05:38:14-GMT BuildTimeStamp:
Sep 18 2007 04:54:49 CVS: $Id: mri_convert.c,v 1.146 2007/07/26
19:26:26 greve Exp $ User: root Machine: cgu.edu.tw Platform: Linux
PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
FLIRT version 5.4.2
$Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $
mri_convert --version
stable4
ProgramName: tkregister2_cmdl ProgramArguments: --all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:14-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: tkregister2.c,v
1.86.2.1 2007/08/15 15:39:42 nicks Exp $ User: root Machine:
cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4
CompilerName: GCC CompilerVersion: 30400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED]
(i686-pc-linux-gnu) on 2005-11-15 at 21:02:27
ProgramName: mri_normalize ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_normalize.c,v 1.52
2007/01/02 21:34:40 nicks Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_watershed.cpp,v
1.67 2007/06/29 13:40:47 fischl Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName:
GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion:
$Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp:
Sep 18 2007 04:54:49 CVS: $Id: mri_segment.c,v 1.33 2007/02/14
19:59:27 fischl Exp $ User: root Machine: cgu.edu.tw Platform:
Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_label2label.c,v
1.33 2007/08/10 18:23:46 greve Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_em_register.c,v
1.57 2006/12/29 02:09:06 nicks Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_ca_normalize.c,v
1.38 2007/01/02 13:37:33 fischl Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName:
GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_ca_register.c,v
1.63 2007/01/18 22:58:55 nicks Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_ca_label.c,v 1.80
2007/04/13 13:22:32 fischl Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion:
$Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp:
Sep 18 2007 04:54:49 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18
20:23:47 nicks Exp $ User: root Machine: cgu.edu.tw Platform: Linux
PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
unknown option -ALL-INFO
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion:
$Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp:
Sep 18 2007 04:54:49 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38
fischl Exp $ User: root Machine: cgu.edu.tw Platform: Linux
PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_tessellate.c,v
1.32 2007/04/26 21:44:21 fischl Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName:
GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id:
mri_concatenate_lta.c,v 1.3 2007/05/17 19:56:59 nicks Exp $ User:
root Machine: cgu.edu.tw Platform: Linux PlatformVersion:
2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_normalize_tp2.c,v
1.6 2007/01/08 18:10:12 nicks Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion:
$Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp:
Sep 18 2007 04:54:49 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01
18:16:19 fischl Exp $ User: root Machine: cgu.edu.tw Platform:
Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_inflate.c,v
1.33.2.2 2007/08/16 01:40:10 nicks Exp $ User: root Machine:
cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4
CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_curvature.c,v
1.25 2007/07/20 16:42:32 fischl Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName:
GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion:
$Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp:
Sep 18 2007 04:54:49 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08
18:36:08 greve Exp $ User: root Machine: cgu.edu.tw Platform: Linux
PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_fix_topology.c,v
1.43 2007/01/05 16:57:16 nicks Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_topo_fixer.cpp,v
1.26 2007/02/13 19:30:47 segonne Exp $ User: root Machine:
cgu.edu.tw Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4
CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_ca_label.c,v 1.23
2007/03/23 20:00:07 fischl Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_euler_number.c,v
1.5 2006/12/29 02:09:10 nicks Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_make_surfaces.c,v
1.99 2007/08/14 01:56:01 fischl Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName:
GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_register.c,v 1.48
2007/07/19 15:58:50 fischl Exp $ User: root Machine: cgu.edu.tw
Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id:
mris_anatomical_stats.c,v 1.54 2007/08/02 17:37:13 nicks Exp $ User:
root Machine: cgu.edu.tw Platform: Linux PlatformVersion:
2.6.11-1.1369_FC4 CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion:
$Name: stable4 $ TimeStamp: 2007/10/04-05:38:15-GMT BuildTimeStamp:
Sep 18 2007 04:54:49 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13
16:57:23 fischl Exp $ User: root Machine: cgu.edu.tw Platform:
Linux PlatformVersion: 2.6.11-1.1369_FC4 CompilerName: GCC
CompilerVersion: 30400
#######################################
GCA RB_all_2007-08-08.gca
GCASkull RB_all_withskull_2007-08-08.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCS curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs
#######################################
#--------------------------------------------
[EMAIL PROTECTED] Nu Intensity Correction Thu Oct 4 13:38:15 CST 2007
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2
/usr/local/freesurfer/subjects/x249/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.7 2007/01/06 00:01:14 nicks Exp $
Linux cgu.edu.tw 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686
i686 i386 GNU/Linux
Thu Oct 4 13:38:15 CST 2007
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED]
(i686-pc-linux-gnu) on 2005-11-15 at 21:02:27
tmpdir is ./tmp.mri_nu_correct.mni.20457
/usr/local/freesurfer/subjects/x249/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20457/nu0.mnc
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20457/nu0.mnc
Can't find the talairach xform
'/usr/local/freesurfer/subjects/x249/mri/transforms/talairach.xfm'
Transform is not loaded into mri
$Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $
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 ./tmp.mri_nu_correct.mni.20457/nu0.mnc...
--------------------------------------------------------
Iteration 1 Thu Oct 4 13:38:31 CST 2007
nu_correct -clobber ./tmp.mri_nu_correct.mni.20457/nu0.mnc
./tmp.mri_nu_correct.mni.20457/nu1.mnc
[EMAIL PROTECTED]:/usr/local/freesurfer/subjects/x249/mri/] [2007-10-04
13:38:31] running:
/usr/local/freesurfer/mni/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_20509/
./tmp.mri_nu_correct.mni.20457/nu0.mnc
./tmp.mri_nu_correct.mni.20457/nu1.imp
/usr/local/freesurfer/mni/bin/volume_stats: error while loading shared
libraries: libstdc++.so.5: cannot open shared object file: No such
file or directory
nu_estimate_np_and_em: crashed while running volume_stats (termination
status=32512)
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=32512)
ERROR: nu_correct
Linux cgu.edu.tw 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 Thu Oct 4 13:38:32 CST 2007
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