Feng-Xian, If you have fedora core 4, then you should the centos4 build of freesurfer which is built against the libstdc++.so.6 libs, unlike the rh9 build of freesurfer, which it appears you are using, which is built against the libstdc++.so.5 libs.
Nick > Hi, Pedro Paulo Oliveira: > Thank you for your answers. But, I'm a rookie of Linux. > I don't know what do you mean and how to do that for the answer 2? > Can you tell me detail and get me some command lines? > Thank you again. > > > > 2007/10/4, Pedro Paulo Oliveira Jr <[EMAIL PROTECTED]>: >> 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 >> _______________________________________________ >> 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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
