Use the centos4 build of freesurfer with fedora core 4. it uses libstdc ++.so.6.
On Thu, 2007-10-04 at 16:30 +0800, 顏鳳賢 wrote: > 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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