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
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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
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1) subject name x249 2) the entire command-line executed
[root@cgu ~]# ksh # tcsh [root@cgu ~]# setenv FREESURFER_HOME /usr/local/freesurfer [root@cgu ~]# source $FREESURFER_HOME/SetUpFreeSurfer.csh
[root@cgu ~]# cd $SUBJECTS_DIR [root@cgu subjects]# cd x249/mri/orig [root@cgu orig]# mri_convert x249.img 001.mgz
[root@cgu 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 nicks@kani (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 ####################################### #-------------------------------------------- #@# 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 nicks@kani (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 [root@cgu.edu.tw:/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