Freesurfer September 2005

freesurfer@nmr.mgh.harvard.edu

44 participants
91 discussions

RE: [Freesurfer] new 'dev' release for Linux rh9, centos4 and centos4_x86_64
by Fornito, Alexander 05 Sep '05

05 Sep '05

HI Nick, I downloaded the new redhat distribution from this site and the GUIs seem to work ok, but got an error message when reunning recon-all (see below). We are running Debian 3.1. Thanks heaps for your help. recon-all -autorecon1 -subjid 27_new -hemi lh -echo breaksw end while ( 0 != 0 ) goto parse_args_return goto check_params if ( ! 0 ) then if ( 1 != 1 ) then if ( ! 1 ) then if ( ! -e /data/flanders/work/alex/freesurfer/subjects ) then pushd /data/flanders/work/alex/freesurfer/subjects setenv SUBJECTS_DIR `$PWD` pwd popd echo INFO: SUBJECTS_DIR is /data/flanders/work/alex/freesurfer/subjects INFO: SUBJECTS_DIR is /data/flanders/work/alex/freesurfer/subjects set subjdir = /data/flanders/work/alex/freesurfer/subjects/27_new if ( ! -e /data/flanders/work/alex/freesurfer/subjects/27_new ) then if ( ! -w /data/flanders/work/alex/freesurfer/subjects/27_new ) then else if ( ! 1 ) then pushd /usr/local/freesurfer-dev20050905 set freesurfer_home_true = `pwd` pwd popd echo Actual FREESURFER_HOME /usr/local/freesurfer-dev20050905 Actual FREESURFER_HOME /usr/local/freesurfer-dev20050905 if ( ! -e /usr/local/freesurfer-dev20050905 ) then if ( 0 ) then if ( 0 || 0 ) then if ( 0 && ! 0 ) then foreach hemi ( lh ) if ( 0 || 0 || 0 ) then if ( 0 ) then if ( 0 ) then end if ( 0 != 0 ) then if ( 0 != 0 ) then if ( ! 0 && ! 0 ) then if ( ! 1 && ! 1 && ! 1 && ! 0 && ! 0 && ! 0 && ! 1 && ! 0 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 ) then endif if ( 0 && ! 0 ) then if ( 0 && ! 0 ) then if ( 0 ) then if ( 0 ) then if ( 0 && 0 ) then if ( ( 0 || 0 ) && ) then if ( 1 ) then which nu_correct if ( 0 ) then endif goto check_params_return cd /data/flanders/work/alex/freesurfer/subjects/27_new mkdir -p scripts mkdir -p touch set touchdir = /data/flanders/work/alex/freesurfer/subjects/27_new/touch mkdir -p stats if ( ! 0 ) then set CF = /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.cmd rm -f /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.cmd set ENVF = /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.env if ( -e /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.env ) mv /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.env /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.env.bak mv /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.env /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.env.bak date echo FREESURFER_HOME /usr/local/freesurfer-dev20050905 echo Actual FREESURFER_HOME /usr/local/freesurfer-dev20050905 pwd echo setenv SUBJECTS_DIR /data/flanders/work/alex/freesurfer/subjects echo -autorecon1 -subjid 27_new -hemi lh -echo uname -a echo limit echo printenv endif if ( 0 ) then if ( 0 == 0 ) then set LF = ( /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ) if ( -e /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ) then if ( ! 1 ) then echo \n\n echo New invokation of recon-all echo \n\n endif endif else date pwd echo /usr/local/freesurfer-dev20050905/bin//recon-all echo -autorecon1 -subjid 27_new -hemi lh -echo echo subjid 27_new echo setenv SUBJECTS_DIR /data/flanders/work/alex/freesurfer/subjects echo FREESURFER_HOME /usr/local/freesurfer-dev20050905 echo Actual FREESURFER_HOME /usr/local/freesurfer-dev20050905 uname -a tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log Linux flanders 2.4.26 #2 SMP Tue Dec 14 03:07:23 EST 2004 i686 GNU/Linux limit echo ######################################## tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ######################################## echo program versions used tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log program versions used echo $Id: recon-all-nmr,v 1.102 2005/09/02 18:03:58 greve Exp $ tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log $Id: recon-all-nmr,v 1.102 2005/09/02 18:03:58 greve Exp $ tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log mri_motion_correct2 -version $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $ $Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $ talairach2 -version tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ nu_correct -version tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@martinos01 (i686-pc-linux-gnu) on 2005-08-29 at 19:41:40 mri_normalize -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mri_watershed -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mri_watershed.cpp,v 1.34 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mri_segment -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mri_fill -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mri_fill.c,v 1.94 2005/08/15 14:30:08 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mri_tessellate -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mris_smooth -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mris_inflate -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mris_sphere -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mris_fix_topology -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mris_fix_topology.c,v 1.31 2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mris_euler_number -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mris_make_surfaces -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mris_sphere -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mris_register -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mris_register.c,v 1.30 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mrisp_paint -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mri_label2label -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mris2rgb -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mris2rgb ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mris2rgb.c,v 1.33 2005/06/08 19:45:07 nicks Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mri_em_register -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mri_em_register.c,v 1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mri_ca_normalize -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mri_ca_register -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mri_ca_register.c,v 1.34 2005/08/18 13:29:27 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 mri_ca_label -all-info tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/09/06-02:25:45-GMT CVS: $Id: mri_ca_label.c,v 1.62 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: flanders Platform: Linux PlatformVersion: 2.4.26 CompilerName: GCC CompilerVersion: 30200 echo ####################################### tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ####################################### echo GCA RB40_talairach_2005-07-20.gca tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log GCA RB40_talairach_2005-07-20.gca echo AvgCurvTif average.curvature.filled.buckner40.tif tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log AvgCurvTif average.curvature.filled.buckner40.tif echo GCS curvature.buckner40.filled.desikan_killiany.gcs tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log GCS curvature.buckner40.filled.desikan_killiany.gcs echo ####################################### tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log ####################################### if ( 0 ) exit 0 set CSDF = /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/csurfdir if ( -e /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/csurfdir ) then set tmp = `cat $CSDF` cat /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/csurfdir if ( /usr/local/freesurfer-dev20050905 != /usr/local/freesurfer-dev20050905 ) then else if ( 0 == 0 ) then set SF = /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.status if ( -e /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.status ) then if ( ! 1 ) then echo \n\n echo New invokation of recon-all echo \n\n endif endif else echo status file for recon-all date if ( 0 != 0 ) then if ( ! 0 && ! 0 ) then pushd /data/flanders/work/alex/freesurfer/subjects/27_new/mri set tmp = `ls orig/[0-9][0-9][0-9].mgz >& /dev/null` if ( ! 1 || -e orig.mgz ) set MGZ = .mgz popd /data/flanders/work/alex/freesurfer/subjects/27_new endif tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log if ( 0 == 0 ) echo Using COR format echo Using COR format Using COR format tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log if ( 0 != 0 ) echo Using mgz format if ( 1 && 0 == 0 ) then tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log echo --------------------------------------------- --------------------------------------------- date tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.status echo MotionCor `date` MotionCor Tue Sep 6 12:25:45 EST 2005 if ( ! -e /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig ) then pushd /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig set RunList = ( ) set run = 1 set nohit = 0 while ( 0 < 100 ) set runid = `printf %03d $run` printf %03d 1 if ( -e 001/COR-.info ) then @ nohit = 0 + 1 endif @ run = 1 + 1 end while ( 1 < 100 ) set runid = `printf %03d $run` printf %03d 2 if ( -e 002/COR-.info ) then @ nohit = 1 + 1 endif @ run = 2 + 1 end while ( 2 < 100 ) set runid = `printf %03d $run` printf %03d 3 if ( -e 003/COR-.info ) then @ nohit = 2 + 1 endif @ run = 3 + 1 end while ( 3 < 100 ) set runid = `printf %03d $run` printf %03d 4 if ( -e 004/COR-.info ) then @ nohit = 3 + 1 endif @ run = 4 + 1 end while ( 4 < 100 ) set runid = `printf %03d $run` printf %03d 5 if ( -e 005/COR-.info ) then @ nohit = 4 + 1 endif @ run = 5 + 1 end while ( 5 < 100 ) set runid = `printf %03d $run` printf %03d 6 if ( -e 006/COR-.info ) then @ nohit = 5 + 1 endif @ run = 6 + 1 end while ( 6 < 100 ) set runid = `printf %03d $run` printf %03d 7 if ( -e 007/COR-.info ) then @ nohit = 6 + 1 endif @ run = 7 + 1 end while ( 7 < 100 ) set runid = `printf %03d $run` printf %03d 8 if ( -e 008/COR-.info ) then @ nohit = 7 + 1 endif @ run = 8 + 1 end while ( 8 < 100 ) set runid = `printf %03d $run` printf %03d 9 if ( -e 009/COR-.info ) then @ nohit = 8 + 1 endif @ run = 9 + 1 end while ( 9 < 100 ) set runid = `printf %03d $run` printf %03d 10 if ( -e 010/COR-.info ) then @ nohit = 9 + 1 endif @ run = 10 + 1 end while ( 10 < 100 ) set runid = `printf %03d $run` printf %03d 11 if ( -e 011/COR-.info ) then @ nohit = 10 + 1 endif @ run = 11 + 1 end while ( 11 < 100 ) set runid = `printf %03d $run` printf %03d 12 if ( -e 012/COR-.info ) then @ nohit = 11 + 1 endif @ run = 12 + 1 end while ( 12 < 100 ) set runid = `printf %03d $run` printf %03d 13 if ( -e 013/COR-.info ) then @ nohit = 12 + 1 endif @ run = 13 + 1 end while ( 13 < 100 ) set runid = `printf %03d $run` printf %03d 14 if ( -e 014/COR-.info ) then @ nohit = 13 + 1 endif @ run = 14 + 1 end while ( 14 < 100 ) set runid = `printf %03d $run` printf %03d 15 if ( -e 015/COR-.info ) then @ nohit = 14 + 1 endif @ run = 15 + 1 end while ( 15 < 100 ) set runid = `printf %03d $run` printf %03d 16 if ( -e 016/COR-.info ) then @ nohit = 15 + 1 endif @ run = 16 + 1 end while ( 16 < 100 ) set runid = `printf %03d $run` printf %03d 17 if ( -e 017/COR-.info ) then @ nohit = 16 + 1 endif @ run = 17 + 1 end while ( 17 < 100 ) set runid = `printf %03d $run` printf %03d 18 if ( -e 018/COR-.info ) then @ nohit = 17 + 1 endif @ run = 19 + 1 end while ( 19 < 100 ) set runid = `printf %03d $run` printf %03d 20 if ( -e 020/COR-.info ) then @ nohit = 19 + 1 endif @ run = 20 + 1 end while ( 20 < 100 ) set runid = `printf %03d $run` printf %03d 21 if ( -e 021/COR-.info ) then @ nohit = 20 + 1 endif @ run = 21 + 1 end while ( 21 < 100 ) set runid = `printf %03d $run` printf %03d 22 if ( -e 022/COR-.info ) then @ nohit = 21 + 1 endif @ run = 22 + 1 end while ( 22 < 100 ) set runid = `printf %03d $run` printf %03d 23 if ( -e 023/COR-.info ) then @ nohit = 22 + 1 endif @ run = 23 + 1 end while ( 23 < 100 ) set runid = `printf %03d $run` printf %03d 24 if ( -e 024/COR-.info ) then @ nohit = 23 + 1 endif @ run = 24 + 1 end while ( 24 < 100 ) set runid = `printf %03d $run` printf %03d 25 if ( -e 025/COR-.info ) then @ nohit = 24 + 1 endif @ run = 25 + 1 end while ( 25 < 100 ) set runid = `printf %03d $run` printf %03d 26 if ( -e 026/COR-.info ) then @ nohit = 25 + 1 endif @ run = 26 + 1 end while ( 26 < 100 ) set runid = `printf %03d $run` printf %03d 27 if ( -e 027/COR-.info ) then @ nohit = 26 + 1 endif @ run = 27 + 1 end while ( 27 < 100 ) set runid = `printf %03d $run` printf %03d 28 if ( -e 028/COR-.info ) then @ nohit = 27 + 1 endif @ run = 28 + 1 end while ( 28 < 100 ) set runid = `printf %03d $run` printf %03d 29 if ( -e 029/COR-.info ) then @ nohit = 28 + 1 endif @ run = 29 + 1 end while ( 29 < 100 ) set runid = `printf %03d $run` printf %03d 30 if ( -e 030/COR-.info ) then @ nohit = 29 + 1 endif @ run = 30 + 1 end while ( 30 < 100 ) set runid = `printf %03d $run` printf %03d 31 if ( -e 031/COR-.info ) then @ nohit = 30 + 1 endif @ run = 31 + 1 end while ( 31 < 100 ) set runid = `printf %03d $run` printf %03d 32 if ( -e 032/COR-.info ) then @ nohit = 31 + 1 endif @ run = 32 + 1 end while ( 32 < 100 ) set runid = `printf %03d $run` printf %03d 33 if ( -e 033/COR-.info ) then @ nohit = 32 + 1 endif @ run = 33 + 1 end while ( 33 < 100 ) set runid = `printf %03d $run` printf %03d 34 if ( -e 034/COR-.info ) then @ nohit = 33 + 1 endif @ run = 34 + 1 end while ( 34 < 100 ) set runid = `printf %03d $run` printf %03d 35 if ( -e 035/COR-.info ) then @ nohit = 34 + 1 endif @ run = 35 + 1 end while ( 35 < 100 ) set runid = `printf %03d $run` printf %03d 36 if ( -e 036/COR-.info ) then @ nohit = 35 + 1 endif @ run = 36 + 1 end while ( 36 < 100 ) set runid = `printf %03d $run` printf %03d 37 if ( -e 037/COR-.info ) then @ nohit = 36 + 1 endif @ run = 37 + 1 end while ( 37 < 100 ) set runid = `printf %03d $run` printf %03d 38 if ( -e 038/COR-.info ) then @ nohit = 37 + 1 endif @ run = 38 + 1 end while ( 38 < 100 ) set runid = `printf %03d $run` printf %03d 39 if ( -e 039/COR-.info ) then @ nohit = 38 + 1 endif @ run = 39 + 1 end while ( 39 < 100 ) set runid = `printf %03d $run` printf %03d 40 if ( -e 040/COR-.info ) then @ nohit = 39 + 1 endif @ run = 40 + 1 end while ( 40 < 100 ) set runid = `printf %03d $run` printf %03d 41 if ( -e 041/COR-.info ) then @ nohit = 40 + 1 endif @ run = 41 + 1 end while ( 41 < 100 ) set runid = `printf %03d $run` printf %03d 42 if ( -e 042/COR-.info ) then @ nohit = 41 + 1 endif @ run = 42 + 1 end while ( 42 < 100 ) set runid = `printf %03d $run` printf %03d 43 if ( -e 043/COR-.info ) then @ nohit = 42 + 1 endif @ run = 43 + 1 end while ( 43 < 100 ) set runid = `printf %03d $run` printf %03d 44 if ( -e 044/COR-.info ) then @ nohit = 43 + 1 endif @ run = 44 + 1 end while ( 44 < 100 ) set runid = `printf %03d $run` printf %03d 45 if ( -e 045/COR-.info ) then @ nohit = 44 + 1 endif @ run = 46 + 1 end while ( 46 < 100 ) set runid = `printf %03d $run` printf %03d 47 if ( -e 047/COR-.info ) then @ nohit = 46 + 1 endif @ run = 47 + 1 end while ( 47 < 100 ) set runid = `printf %03d $run` printf %03d 48 if ( -e 048/COR-.info ) then @ nohit = 47 + 1 endif @ run = 48 + 1 end while ( 48 < 100 ) set runid = `printf %03d $run` printf %03d 49 if ( -e 049/COR-.info ) then @ nohit = 48 + 1 endif @ run = 49 + 1 end while ( 49 < 100 ) set runid = `printf %03d $run` printf %03d 50 if ( -e 050/COR-.info ) then @ nohit = 49 + 1 endif @ run = 50 + 1 end while ( 50 < 100 ) set runid = `printf %03d $run` printf %03d 51 if ( -e 051/COR-.info ) then @ nohit = 50 + 1 endif @ run = 51 + 1 end while ( 51 < 100 ) set runid = `printf %03d $run` printf %03d 52 if ( -e 052/COR-.info ) then @ nohit = 51 + 1 endif @ run = 52 + 1 end while ( 52 < 100 ) set runid = `printf %03d $run` printf %03d 53 if ( -e 053/COR-.info ) then @ nohit = 52 + 1 endif @ run = 53 + 1 end while ( 53 < 100 ) set runid = `printf %03d $run` printf %03d 54 if ( -e 054/COR-.info ) then @ nohit = 53 + 1 endif @ run = 54 + 1 end while ( 54 < 100 ) set runid = `printf %03d $run` printf %03d 55 if ( -e 055/COR-.info ) then @ nohit = 54 + 1 endif @ run = 55 + 1 end while ( 55 < 100 ) set runid = `printf %03d $run` printf %03d 56 if ( -e 056/COR-.info ) then @ nohit = 55 + 1 endif @ run = 56 + 1 end while ( 56 < 100 ) set runid = `printf %03d $run` printf %03d 57 if ( -e 057/COR-.info ) then @ nohit = 56 + 1 endif @ run = 57 + 1 end while ( 57 < 100 ) set runid = `printf %03d $run` printf %03d 58 if ( -e 058/COR-.info ) then @ nohit = 57 + 1 endif @ run = 58 + 1 end while ( 58 < 100 ) set runid = `printf %03d $run` printf %03d 59 if ( -e 059/COR-.info ) then @ nohit = 58 + 1 endif @ run = 59 + 1 end while ( 59 < 100 ) set runid = `printf %03d $run` printf %03d 60 if ( -e 060/COR-.info ) then @ nohit = 59 + 1 endif @ run = 60 + 1 end while ( 60 < 100 ) set runid = `printf %03d $run` printf %03d 61 if ( -e 061/COR-.info ) then @ nohit = 60 + 1 endif @ run = 61 + 1 end while ( 61 < 100 ) set runid = `printf %03d $run` printf %03d 62 if ( -e 062/COR-.info ) then @ nohit = 61 + 1 endif @ run = 62 + 1 end while ( 62 < 100 ) set runid = `printf %03d $run` printf %03d 63 if ( -e 063/COR-.info ) then @ nohit = 62 + 1 endif @ run = 63 + 1 end while ( 63 < 100 ) set runid = `printf %03d $run` printf %03d 64 if ( -e 064/COR-.info ) then @ nohit = 63 + 1 endif @ run = 64 + 1 end while ( 64 < 100 ) set runid = `printf %03d $run` printf %03d 65 if ( -e 065/COR-.info ) then @ nohit = 64 + 1 endif @ run = 65 + 1 end while ( 65 < 100 ) set runid = `printf %03d $run` printf %03d 66 if ( -e 066/COR-.info ) then @ nohit = 65 + 1 endif @ run = 66 + 1 end while ( 66 < 100 ) set runid = `printf %03d $run` printf %03d 67 if ( -e 067/COR-.info ) then @ nohit = 66 + 1 endif @ run = 67 + 1 end while ( 67 < 100 ) set runid = `printf %03d $run` printf %03d 68 if ( -e 068/COR-.info ) then @ nohit = 67 + 1 endif @ run = 68 + 1 end while ( 68 < 100 ) set runid = `printf %03d $run` printf %03d 69 if ( -e 069/COR-.info ) then @ nohit = 68 + 1 endif @ run = 69 + 1 end while ( 69 < 100 ) set runid = `printf %03d $run` printf %03d 70 if ( -e 070/COR-.info ) then @ nohit = 69 + 1 endif @ run = 70 + 1 end while ( 70 < 100 ) set runid = `printf %03d $run` printf %03d 71 if ( -e 071/COR-.info ) then @ nohit = 70 + 1 endif @ run = 71 + 1 end while ( 71 < 100 ) set runid = `printf %03d $run` printf %03d 72 if ( -e 072/COR-.info ) then @ nohit = 71 + 1 endif @ run = 72 + 1 end while ( 72 < 100 ) set runid = `printf %03d $run` printf %03d 73 if ( -e 073/COR-.info ) then @ nohit = 72 + 1 endif @ run = 73 + 1 end while ( 73 < 100 ) set runid = `printf %03d $run` printf %03d 74 if ( -e 074/COR-.info ) then @ nohit = 73 + 1 endif @ run = 74 + 1 end while ( 74 < 100 ) set runid = `printf %03d $run` printf %03d 75 if ( -e 075/COR-.info ) then @ nohit = 74 + 1 endif @ run = 75 + 1 end while ( 75 < 100 ) set runid = `printf %03d $run` printf %03d 76 if ( -e 076/COR-.info ) then @ nohit = 75 + 1 endif @ run = 76 + 1 end while ( 76 < 100 ) set runid = `printf %03d $run` printf %03d 77 if ( -e 077/COR-.info ) then @ nohit = 76 + 1 endif @ run = 77 + 1 end while ( 77 < 100 ) set runid = `printf %03d $run` printf %03d 78 if ( -e 078/COR-.info ) then @ nohit = 77 + 1 endif @ run = 78 + 1 end while ( 78 < 100 ) set runid = `printf %03d $run` printf %03d 79 if ( -e 079/COR-.info ) then @ nohit = 78 + 1 endif @ run = 79 + 1 end while ( 79 < 100 ) set runid = `printf %03d $run` printf %03d 80 if ( -e 080/COR-.info ) then @ nohit = 79 + 1 endif @ run = 80 + 1 end while ( 80 < 100 ) set runid = `printf %03d $run` printf %03d 81 if ( -e 081/COR-.info ) then @ nohit = 80 + 1 endif @ run = 81 + 1 end while ( 81 < 100 ) set runid = `printf %03d $run` printf %03d 82 if ( -e 082/COR-.info ) then @ nohit = 81 + 1 endif @ run = 82 + 1 end while ( 82 < 100 ) set runid = `printf %03d $run` printf %03d 83 if ( -e 083/COR-.info ) then @ nohit = 82 + 1 endif @ run = 83 + 1 end while ( 83 < 100 ) set runid = `printf %03d $run` printf %03d 84 if ( -e 084/COR-.info ) then @ nohit = 83 + 1 endif @ run = 84 + 1 end while ( 84 < 100 ) set runid = `printf %03d $run` printf %03d 85 if ( -e 085/COR-.info ) then @ nohit = 84 + 1 endif @ run = 85 + 1 end while ( 85 < 100 ) set runid = `printf %03d $run` printf %03d 86 if ( -e 086/COR-.info ) then @ nohit = 85 + 1 endif @ run = 86 + 1 end while ( 86 < 100 ) set runid = `printf %03d $run` printf %03d 87 if ( -e 087/COR-.info ) then @ nohit = 86 + 1 endif @ run = 87 + 1 end while ( 87 < 100 ) set runid = `printf %03d $run` printf %03d 88 if ( -e 088/COR-.info ) then @ nohit = 87 + 1 endif @ run = 88 + 1 end while ( 88 < 100 ) set runid = `printf %03d $run` printf %03d 89 if ( -e 089/COR-.info ) then @ nohit = 88 + 1 endif @ run = 89 + 1 end while ( 89 < 100 ) set runid = `printf %03d $run` printf %03d 90 if ( -e 090/COR-.info ) then @ nohit = 89 + 1 endif @ run = 90 + 1 end while ( 90 < 100 ) set runid = `printf %03d $run` printf %03d 91 if ( -e 091/COR-.info ) then @ nohit = 90 + 1 endif @ run = 91 + 1 end while ( 91 < 100 ) set runid = `printf %03d $run` printf %03d 92 if ( -e 092/COR-.info ) then @ nohit = 91 + 1 endif @ run = 92 + 1 end while ( 92 < 100 ) set runid = `printf %03d $run` printf %03d 93 if ( -e 093/COR-.info ) then @ nohit = 92 + 1 endif @ run = 93 + 1 end while ( 93 < 100 ) set runid = `printf %03d $run` printf %03d 94 if ( -e 094/COR-.info ) then @ nohit = 93 + 1 endif @ run = 94 + 1 end while ( 94 < 100 ) set runid = `printf %03d $run` printf %03d 95 if ( -e 095/COR-.info ) then @ nohit = 94 + 1 endif @ run = 95 + 1 end while ( 95 < 100 ) set runid = `printf %03d $run` printf %03d 96 if ( -e 096/COR-.info ) then @ nohit = 95 + 1 endif @ run = 96 + 1 end while ( 96 < 100 ) set runid = `printf %03d $run` printf %03d 97 if ( -e 097/COR-.info ) then @ nohit = 96 + 1 endif @ run = 97 + 1 end while ( 97 < 100 ) set runid = `printf %03d $run` printf %03d 98 if ( -e 098/COR-.info ) then @ nohit = 97 + 1 endif @ run = 98 + 1 end while ( 98 < 100 ) set runid = `printf %03d $run` printf %03d 99 if ( -e 099/COR-.info ) then @ nohit = 98 + 1 endif @ run = 99 + 1 end while ( 99 < 100 ) set runid = `printf %03d $run` printf %03d 100 if ( -e 100/COR-.info ) then @ nohit = 99 + 1 endif @ run = 100 + 1 end while ( 100 < 100 ) if ( 0 == 0 ) then set cor = /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig/COR if ( -e /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig/COR-.info && -e /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig/COR-001 && -e /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig/COR-256 ) then echo tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log echo INFO: no runs were found in /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig/XXX, tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log INFO: no runs were found in /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig/XXX, echo however, there is a volume in /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig, tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log however, there is a volume in /data/flanders/work/alex/freesurfer/subjects/27_new/mri/orig, echo so I am just going to proceed with that as the input. tee -a /data/flanders/work/alex/freesurfer/subjects/27_new/scripts/recon-all.log so I am just going to proceed with that as the input. sleep 2 else endif if ( 0 == 1 ) then if ( 0 > 1 ) then cmd: Undefined variable. -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Tue 9/6/2005 6:32 AM To: Freesurfer Mailing List Cc: Subject: [Freesurfer] new 'dev' release for Linux rh9,centos4 and centos4_x86_64 Freesurfer community, For those who wish to install a 'development' release of Freesurfer on Linux RedHat 9, CentOS 4 or CentOS 4 x86_64 platforms, distribution files are now posted at: http://surfer.nmr.mgh.harvard.edu/pub/dist/?M=D On this distribution site, a README is available: freesurfer-Linux-platform-dev20050905-full.README.txt The new distributions include: freesurfer-Linux-rh9-dev20050905-full.tar.gz freesurfer-Linux-centos4-dev20050905-full.tar.gz freesurfer-Linux-centos4_x86_64-dev20050905-full.tar.gz The 'dev' release contains all the functionality of the upcoming 'stable' release, but has not been fully tested, particularly in regards to installation issues. This 'dev' release is intended for those who wish to attempt an installation on their Linux platform, and are willing to give feedback on possible installation problems. This 'dev' release contains most of the libraries that Freesurfer requires: the MINC toolkit, Tcl/Tk/Tix and BLT libraries, GSL and Qt, as well as sample MRI data. The release may be installed in any directory. A Mac OS X 'dev' build is not available just yet. Please direct comments or questions to this mailing list. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

regarding talairach & nuintensitycor
by Yuan-Fen Kuo 02 Sep '05

02 Sep '05

Hi: I have a skull stripped structural image. How may I begin the recon-all work flow from the segmentation stage? While many stages requires talairach coordinate, should I get the coordinates by running talairach with the original T1 image ( with skull )? however, that would require nuintensitycor to be run, will freesufer have trouble with the intensity during segmentation, because it's not intensity corrected images produced by freesurfer? I actually have made a few different attempts, but I always get a grey matter outline in the WM volume. Also may I use some other software to give freesurfer a segmentation starting point, meaning feeding some segmented images into the wm directory? if so, how should the files be stored? Thanks in advance, Yuan-Fen Kuo Associate Imaging Processing Specialist Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison

2 2

Re: [Freesurfer] Lib prob?
by xmeadow＠uchicago.edu 02 Sep '05

02 Sep '05

Hi, I tried what you said, and after setting up the path and checking that $FREESURFER_HOME/lib/tcltktixblt/bin is at the front of the path I tried running tkmedit <subject> orig. When I did that a window popped up that had 'Medit:' in the title bar. The window had nothing but a gray background. The window stays open for about 7 seconds, and then the title switches from 'Medit:' to the name of the subject, but then the window closes. There are no error messages produced, the window just closes. >Xander ---- Original message ---- >Date: Fri, 02 Sep 2005 15:09:33 -0400 >From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Lib prob? >To: Xander Meadow <xmeadow(a)uchicago.edu> >Cc: "Fornito, Alexander" <Alexander.Fornito(a)wh.org.au>, Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > >Xander, > >Can you try executing these two statements after issuing the source >SetUpFreeSurfer.csh command? > > set path = ( $FREESURFER_HOME/lib/tcltktixblt/bin $path ) > rehash > >This will add to the binary search path the location of the tcl-tk-tix- >blt tools. I noticed it is missing from the FreeSurferEnv.csh setup >script. It is possible that the problem you are seeing is because some >of the old tools are being used (from prior installed search paths). > >Can you then try running tkmedit, such as like this: > > tkmedit <subjectname> orig > >(replacing <subjectname> with your subject id). > >Thanks, > >Nick > > >On Fri, 2005-09-02 at 11:39 -0500, Xander Meadow wrote: >> Hi, >> >> Everything was just as you predicted, but I still get the tcl and tk >> errors. >> >> >source freesurfer/dev/SetUpFreeSurfer.csh >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /home/people/xmeadow/freesurfer/dev >> FSFAST_HOME /home/people/xmeadow/freesurfer/dev/fsfast >> SUBJECTS_DIR /home/people/xmeadow/freesurfer/dev/subjects >> FUNCTIONALS_DIR /home/people/xmeadow/freesurfer/dev/sessions >> MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin >> MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib >> PERL5LIB /usr/pubsw/packages/mni/current/lib/perl5/5.8.5 >> >> >> >echo $LD_LIBRARY_PATH >> /usr/pubsw/packages/mni/current/lib:/home/people/xmeadow/freesurfer/ >> dev/lib/tclt >> ktixblt/lib:/home/people/xmeadow/freesurfer/dev/lib/ >> >> > which tkmedit >> /home/people/xmeadow/freesurfer/dev/bin//tkmedit >> >> >ldd `which tkmedit` >> libtix8.1.8.3.so => >> /home/people/xmeadow/freesurfer/dev/lib/tcltktixblt/ >> lib/libtix8.1.8.3.so (0x005a2000) >> libtk8.4.so => >> /home/people/xmeadow/freesurfer/dev/lib/tcltktixblt/lib/l >> ibtk8.4.so (0x004c1000) >> libtcl8.4.so => >> /home/people/xmeadow/freesurfer/dev/lib/tcltktixblt/lib/ >> libtcl8.4.so (0x003b8000) >> libglut.so.3 => /usr/lib/libglut.so.3 (0x007ec000) >> libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x00af8000) >> libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x00b02000) >> libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x00123000) >> libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x00101000) >> libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x00139000) >> libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x001b0000) >> libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x009f9000) >> libgsl.so.0 => /usr/lib/libgsl.so.0 (0x0021e000) >> libgslcblas.so.0 => /usr/lib/libgslcblas.so.0 (0x00382000) >> libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x00dad000) >> libtiff.so.3 => /usr/lib/libtiff.so.3 (0x04a99000) >> libz.so.1 => /usr/lib/libz.so.1 (0x00ad2000) >> libm.so.6 => /lib/tls/libm.so.6 (0x00451000) >> libcrypt.so.1 => /lib/libcrypt.so.1 (0x03e64000) >> libc.so.6 => /lib/tls/libc.so.6 (0x008a3000) >> libdl.so.2 => /lib/libdl.so.2 (0x009f3000) >> libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x00ac2000) >> libXxf86vm.so.1 => /usr/X11R6/lib/libXxf86vm.so.1 (0x003b2000) >> libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x005dc000) >> libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00ce0000) >> libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00cd6000) >> libpthread.so.0 => /lib/tls/libpthread.so.0 (0x00ae4000) >> /lib/ld-linux.so.2 (0x0088a000) >> >> Also, I am using the rh9 installation, because it is the latest redhat >> installation available, but the machine is currently running Enterprise >> version 4. >> >> Thanks very much. >> >> >Xander >> >> On Sep 2, 2005, at 10:43 AM, Nick Schmansky wrote: >> >> > Xander, >> > >> > The new download includes the tcl/tk/tix and blt libraries in the >> > $FREESURFER_HOME/lib/tcltktixblt directory, so this freesurfer should >> > not be using any prior installation of tix (such at that in >> > /usr/share). >> > >> > You do not need to delete any prior installations of tix/tcl/tk/blt. >> > The SetUpFreeSurfer.csh script (which calls FreeSurferEnv.csh) will set >> > the LD_LIBRARY_PATH to contain $FREESURFER_HOME/lib/tcltktixblt/lib. >> > You can confirm this setting by typing: >> > >> > env |grep LD_ >> > >> > and checking that the path is found in LD_LIBRARY_PATH. >> > >> > Also, can you run the following commands for me? >> > >> > which tkmedit >> > ldd `which tkmedit` >> > >> > The first will tell you which tkmedit you are using, to confirm that it >> > is the one that you installed. The second command will tell you >> > exactly >> > which libraries tkmedit uses (note: the ` character is not the ' >> > character, rather ` is in the upper left-hand corner of the keyboard, >> > usually). >> > >> > You should see something like this for a rh9 system: >> > >> > [kani:lib] (nmr-dev-env) which tkmedit >> > /usr/local/freesurfer/dev/bin//tkmedit >> > [kani:lib] (nmr-dev-env) ldd `which tkmedit` >> > libtix8.1.8.3.so >> > => /usr/local/freesurfer/dev/lib/tcltktixblt/lib/libtix8.1.8.3.so >> > (0x40017000) >> > libtk8.4.so >> > => /usr/local/freesurfer/dev/lib/tcltktixblt/lib/libtk8.4.so >> > (0x40051000) >> > libtcl8.4.so >> > => /usr/local/freesurfer/dev/lib/tcltktixblt/lib/libtcl8.4.so >> > (0x40111000) >> > libglut.so.3 => /usr/lib/libglut.so.3 (0x401be000) >> > libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x401f3000) >> > libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x401fc000) >> > libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x40214000) >> > libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x4022a000) >> > libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x40232000) >> > libGL.so.1 => /usr/lib/tls/libGL.so.1 (0x402af000) >> > libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x40318000) >> > libgsl.so.0 => /usr/lib/libgsl.so.0 (0x403f7000) >> > libgslcblas.so.0 => /usr/lib/libgslcblas.so.0 (0x40570000) >> > libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x405a2000) >> > libtiff.so.3 => /usr/lib/libtiff.so.3 (0x405c0000) >> > libz.so.1 => /usr/lib/libz.so.1 (0x40602000) >> > libm.so.6 => /lib/tls/libm.so.6 (0x40610000) >> > libcrypt.so.1 => /lib/libcrypt.so.1 (0x40632000) >> > libc.so.6 => /lib/tls/libc.so.6 (0x42000000) >> > libdl.so.2 => /lib/libdl.so.2 (0x40660000) >> > libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x40664000) >> > libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x406b6000) >> > libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x406c4000) >> > libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x40777000) >> > libGLcore.so.1 => /usr/lib/tls/libGLcore.so.1 (0x40780000) >> > /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) >> > [kani:lib] (nmr-dev-env) >> > >> > Notice that the tix/tk/tcl libraries are found in the new >> > freesurfer/dev >> > installation path. It is necessary to have consistency among these >> > libraries (BLT is loaded dynamically). >> > >> > I'm curious to know the output of this for your machine. It seems to >> > be >> > difficult for us to predict exactly how a rh9 machine will respond to >> > our install. >> > >> > Thanks! And again, I appreciate your patience! We're trying to make >> > this install easier to use. >> > >> > Nick >> > >> > >> > >> > On Fri, 2005-09-02 at 22:24 +0700, xmeadow(a)uchicago.edu wrote: >> >> Hi, >> >> >> >> I installed the version you recommeneded and I had to make a >> >> few changes (for instance tix8.1 is installed in /usr/share >> >> instead of /usr/lib) on my machine. After creating some soft >> >> links to get around this I started up Freesurfer with the >> >> csurf command, and then inflated a brain. The brain came up >> >> like last time but I'm still getting errors in the logs, and >> >> the tools pallette still doesn't appear. However, Freesurfer >> >> no longer becomes unresponsive, it's just none of the tools >> >> are available. The errors I'm getting are: >> >> >> >> surfer: Error sending tcl command SelectVertex -1: invalid >> >> command name "SelectVertex" >> >> >> >> Whenever I move the mouse over the image of the brain. One >> >> thing to note, I don't have enough room on my /usr partition >> >> so I installed Freesurfer in my home space, but I did change >> >> the FREESURFER_HOME variable in SetUpFreeSurf.csh. Any >> >> thoughts on why I'm still getting tcl errors? Thanks very much. >> >> >> >>> Xander >> >> >> >> ---- Original message ---- >> >>> Date: Thu, 01 Sep 2005 21:30:34 -0400 >> >>> From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >> >>> Subject: Re: [Freesurfer] Lib prob? >> >>> To: xmeadow(a)uchicago.edu >> >>> Cc: "Fornito, Alexander" <Alexander.Fornito(a)wh.org.au>, >> >> Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> >> >>> >> >>> Xander and Alex, >> >>> >> >>> The special rh9 dev release is available now to download at: >> >>> >> >>> http://surfer.nmr.mgh.harvard.edu/pub/dist/ >> >>> >> >>> Look for the file: >> >>> >> >>> freesurfer-Linux-rh9-dev20050901.tar.gz >> >>> >> >>> The installation readme is: >> >>> >> >>> freesurfer-Linux-rh9-dev20050901.README.txt >> >>> >> >>> You will also need the MINC tools if you don't already have them: >> >>> >> >>> mni-Linux2-2.3-i386.tar.gz >> >>> >> >>> and its readme is: >> >>> >> >>> mni-Linux2-README.txt >> >>> >> >>> Nick >> >>> >> >>> >> >>> >> >>> On Fri, 2005-09-02 at 03:33 +0700, xmeadow(a)uchicago.edu wrote: >> >>>> Hi, >> >>>> >> >>>> I downloaded what hopefully is the correct version of blt, and >> >>>> after that ran your script and said everything was fine in >> >>>> terms of libraries. However, I did have to create two soft >> >>>> links. The first one was a softlink from libtix8.1.8.3 to >> >>>> libtix8.1.8.4 in /usr/lib. The second was a softlink from >> >>>> tixwish8.1.8.3 to tixwish8.1.8.4 in /usr/bin. After making >> >>>> both of these changes I was able to run csurf, but when I >> >>>> tried to view an inflated brain the brain image would come up, >> >>>> but then freesurfer freezes and I can't do anything. In the >> >>>> logs I get the following errors: >> >>>> >> >>>> can't read "glMenuGroups(mg_FieldSignLoaded)": no such >> >>>> varialble surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: >> >>>> >> >>>> can't read "glMenuGroups(mg_FieldMaskLoaded)": no such >> >>>> variable tksurfer: run tcl script: /tmp/TmpTclSurf.13311 >> >>>> >> >>>> Unfortunately these error messages mean nothing to me, so I >> >>>> was wondering if anyone else had seen them before. Thanks >> >>>> very much. >> >>>> >> >>>>> Xander >> >>>> >> >>>> >> >>>> >> >>>> ---- Original message ---- >> >>>>> Date: Thu, 01 Sep 2005 11:08:52 -0400 >> >>>>> From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >> >>>>> Subject: Re: [Freesurfer] Lib prob? >> >>>>> To: xmeadow(a)uchicago.edu, "Fornito, Alexander" >> >>>> <Alexander.Fornito(a)wh.org.au> >> >>>>> Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> >> >>>>> >> >>>>> Alex and Xander, >> >>>>> >> >>>>>> From reading the error messages in your emails, it >> >> appears that >> >>>>> freesurfer is not able to find the tcl/tk, and tix libraries >> >>>> on your >> >>>>> platform. >> >>>>> >> >>>>> We have been working on trying to provide a seamless solution >> >>>> to the >> >>>>> problem of freesurfer finding the external libraries upon >> >>>> which it >> >>>>> depends, on the varied platforms that it supports. >> >>>>> >> >>>>> To help, later today, a new 'dev' build for rh9 that includes >> >>>> many of >> >>>>> the necessary libraries will be posted for download. This is >> >>>> not a >> >>>>> 'stable' release (which is still undergoing testing), but a >> >>>>> 'development' (dev) build, so it is still possible to have >> >>>> installation >> >>>>> problems, but hopefully it will install and work for you. I >> >>>> will email >> >>>>> you again when it is ready, and your patience is appreciated. >> >>>>> >> >>>>> In the meantime, I've attached a script, called >> >>>> 'fs_lib_check', which >> >>>>> will check your system for the libraries that freesurfer >> >>>> requires. I'm >> >>>>> curious to know the results of its output for your systems. >> >>>> Just type >> >>>>> 'fs_lib_check' to run it, and 'fs_lib_check --help' for help >> >>>> text. >> >>>>> >> >>>>> Nick >> >>>>> >> >>>>> >> >>>>> On Thu, 2005-09-01 at 17:06 +1000, Fornito, Alexander wrote: >> >>>>>> Hi, >> >>>>>> We've recently installed the >> >>>> freesurfer-Linux-rh9-dev20050729.tar.gz distribution along >> >>>> with fs_supportlibs.tar.gz. >> >>>>>> csurf works ok, but if i try to run tksurfer, I get the >> >>>> error message below. We'd appreciate any help as we've been >> >>>> stuck for a while. >> >>>>>> Thanks! >> >>>>>> >> >>>>>> tksurfer 1000027 rh white >> >>>>>> surfer: current subjects dir: >> >>>> /data/flanders/work/alex/freesurfer/subjects >> >>>>>> surfer: not in "scripts" dir ==> using cwd for session root >> >>>>>> surfer: session root data dir ($session) set to: >> >>>>>> surfer: /data/flanders/work/alex/freesurfer/subjects >> >>>>>> surfer: Reading header info from >> >>>> >> >> /data/flanders/work/alex/freesurfer/subjects/1000027/mri/T1/COR-.info >> >>>>>> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be >> >>>> found. >> >>>>>> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be >> >>>> found. >> >>>>>> surfer: vertices=152190, faces=304376 >> >>>>>> surfer: single buffered window >> >>>>>> Xlib: extension "XFree86-DRI" missing on display ":0.0". >> >>>>>> Tix_Init failed: version conflict for package "Tcl": have >> >>>> 8.3, need 8.4 >> >>>>>> surfer: using interface >> >>>> /usr/local/freesurfer-linux9/lib/tcl/tksurfer.tcl >> >>>>>> Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_common.tcl >> >>>>>> Reading >> >> /usr/local/freesurfer-linux9/lib/tcl/tkm_wrappers.tcl >> >>>>>> Reading /usr/local/freesurfer-linux9/lib/tcl/fsgdfPlot.tcl >> >>>>>> couldn't load file "/usr/lib/libtix8.1.8.4.so": >> >>>> /usr/lib/libtix8.1.8.4.so: cannot open shared object file: No >> >>>> such file or directorysurfer: Error sending tcl command >> >>>> UpdateUndoItemLabel "Nothing to Undo": >> >>>>>> invalid command name "UpdateUndoItemLabel" >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_OriginalVSetLoaded 1: >> >>>>>> can't read "glMenuGroups(mg_OriginalVSetLoaded)": no such >> >>>> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_InflatedVSetLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_InflatedVSetLoaded)": no such >> >>>> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_WhiteVSetLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_WhiteVSetLoaded)": no such >> >>>> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_PialVSetLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_PialVSetLoaded)": no such >> >> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_TimeCourseLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_TimeCourseLoaded)": no such >> >>>> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_OverlayLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_OverlayLoaded)": no such >> >> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_CurvatureLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_CurvatureLoaded)": no such >> >>>> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_LabelLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_LabelLoaded)": no such variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_FieldSignLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_FieldSignLoaded)": no such >> >>>> variable >> >>>>>> surfer: Error sending tcl command >> >>>> tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: >> >>>>>> can't read "glMenuGroups(mg_FieldMaskLoaded)": no such >> >>>> variable >> >>>>>> % surfer: Error sending tcl command MoveToolWindow 663 670: >> >>>>>> invalid command name "MoveToolWindow" >> >>>>>> surfer: Error sending tcl command MoveToolWindow 663 670: >> >>>>>> invalid command name "MoveToolWindow" >> >>>>>> surfer: Error sending tcl command MoveToolWindow 663 670: >> >>>>>> invalid command name "MoveToolWindow" >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> >> >>>>>> _______________________________________________ >> >>>>>> Freesurfer mailing list >> >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>>>>> >> >>>>>> >> >>>>> ________________ >> >>>>> fs_lib_check (4k bytes) >> >>>> >> >>>> >> >>> >> >> >> >> >> > >> >> >

3 3

Re: [Freesurfer] Lib prob?
by xmeadow＠uchicago.edu 02 Sep '05

02 Sep '05

Hi, I installed the version you recommeneded and I had to make a few changes (for instance tix8.1 is installed in /usr/share instead of /usr/lib) on my machine. After creating some soft links to get around this I started up Freesurfer with the csurf command, and then inflated a brain. The brain came up like last time but I'm still getting errors in the logs, and the tools pallette still doesn't appear. However, Freesurfer no longer becomes unresponsive, it's just none of the tools are available. The errors I'm getting are: surfer: Error sending tcl command SelectVertex -1: invalid command name "SelectVertex" Whenever I move the mouse over the image of the brain. One thing to note, I don't have enough room on my /usr partition so I installed Freesurfer in my home space, but I did change the FREESURFER_HOME variable in SetUpFreeSurf.csh. Any thoughts on why I'm still getting tcl errors? Thanks very much. >Xander ---- Original message ---- >Date: Thu, 01 Sep 2005 21:30:34 -0400 >From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Lib prob? >To: xmeadow(a)uchicago.edu >Cc: "Fornito, Alexander" <Alexander.Fornito(a)wh.org.au>, Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > >Xander and Alex, > >The special rh9 dev release is available now to download at: > >http://surfer.nmr.mgh.harvard.edu/pub/dist/ > >Look for the file: > >freesurfer-Linux-rh9-dev20050901.tar.gz > >The installation readme is: > >freesurfer-Linux-rh9-dev20050901.README.txt > >You will also need the MINC tools if you don't already have them: > >mni-Linux2-2.3-i386.tar.gz > >and its readme is: > >mni-Linux2-README.txt > >Nick > > > >On Fri, 2005-09-02 at 03:33 +0700, xmeadow(a)uchicago.edu wrote: >> Hi, >> >> I downloaded what hopefully is the correct version of blt, and >> after that ran your script and said everything was fine in >> terms of libraries. However, I did have to create two soft >> links. The first one was a softlink from libtix8.1.8.3 to >> libtix8.1.8.4 in /usr/lib. The second was a softlink from >> tixwish8.1.8.3 to tixwish8.1.8.4 in /usr/bin. After making >> both of these changes I was able to run csurf, but when I >> tried to view an inflated brain the brain image would come up, >> but then freesurfer freezes and I can't do anything. In the >> logs I get the following errors: >> >> can't read "glMenuGroups(mg_FieldSignLoaded)": no such >> varialble surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: >> >> can't read "glMenuGroups(mg_FieldMaskLoaded)": no such >> variable tksurfer: run tcl script: /tmp/TmpTclSurf.13311 >> >> Unfortunately these error messages mean nothing to me, so I >> was wondering if anyone else had seen them before. Thanks >> very much. >> >> >Xander >> >> >> >> ---- Original message ---- >> >Date: Thu, 01 Sep 2005 11:08:52 -0400 >> >From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >> >Subject: Re: [Freesurfer] Lib prob? >> >To: xmeadow(a)uchicago.edu, "Fornito, Alexander" >> <Alexander.Fornito(a)wh.org.au> >> >Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> >> > >> >Alex and Xander, >> > >> >>From reading the error messages in your emails, it appears that >> >freesurfer is not able to find the tcl/tk, and tix libraries >> on your >> >platform. >> > >> >We have been working on trying to provide a seamless solution >> to the >> >problem of freesurfer finding the external libraries upon >> which it >> >depends, on the varied platforms that it supports. >> > >> >To help, later today, a new 'dev' build for rh9 that includes >> many of >> >the necessary libraries will be posted for download. This is >> not a >> >'stable' release (which is still undergoing testing), but a >> >'development' (dev) build, so it is still possible to have >> installation >> >problems, but hopefully it will install and work for you. I >> will email >> >you again when it is ready, and your patience is appreciated. >> > >> >In the meantime, I've attached a script, called >> 'fs_lib_check', which >> >will check your system for the libraries that freesurfer >> requires. I'm >> >curious to know the results of its output for your systems. >> Just type >> >'fs_lib_check' to run it, and 'fs_lib_check --help' for help >> text. >> > >> >Nick >> > >> > >> >On Thu, 2005-09-01 at 17:06 +1000, Fornito, Alexander wrote: >> >> Hi, >> >> We've recently installed the >> freesurfer-Linux-rh9-dev20050729.tar.gz distribution along >> with fs_supportlibs.tar.gz. >> >> csurf works ok, but if i try to run tksurfer, I get the >> error message below. We'd appreciate any help as we've been >> stuck for a while. >> >> Thanks! >> >> >> >> tksurfer 1000027 rh white >> >> surfer: current subjects dir: >> /data/flanders/work/alex/freesurfer/subjects >> >> surfer: not in "scripts" dir ==> using cwd for session root >> >> surfer: session root data dir ($session) set to: >> >> surfer: /data/flanders/work/alex/freesurfer/subjects >> >> surfer: Reading header info from >> /data/flanders/work/alex/freesurfer/subjects/1000027/mri/T1/COR-.info >> >> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be >> found. >> >> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be >> found. >> >> surfer: vertices=152190, faces=304376 >> >> surfer: single buffered window >> >> Xlib: extension "XFree86-DRI" missing on display ":0.0". >> >> Tix_Init failed: version conflict for package "Tcl": have >> 8.3, need 8.4 >> >> surfer: using interface >> /usr/local/freesurfer-linux9/lib/tcl/tksurfer.tcl >> >> Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_common.tcl >> >> Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_wrappers.tcl >> >> Reading /usr/local/freesurfer-linux9/lib/tcl/fsgdfPlot.tcl >> >> couldn't load file "/usr/lib/libtix8.1.8.4.so": >> /usr/lib/libtix8.1.8.4.so: cannot open shared object file: No >> such file or directorysurfer: Error sending tcl command >> UpdateUndoItemLabel "Nothing to Undo": >> >> invalid command name "UpdateUndoItemLabel" >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_OriginalVSetLoaded 1: >> >> can't read "glMenuGroups(mg_OriginalVSetLoaded)": no such >> variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_InflatedVSetLoaded 0: >> >> can't read "glMenuGroups(mg_InflatedVSetLoaded)": no such >> variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_WhiteVSetLoaded 0: >> >> can't read "glMenuGroups(mg_WhiteVSetLoaded)": no such >> variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_PialVSetLoaded 0: >> >> can't read "glMenuGroups(mg_PialVSetLoaded)": no such variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_TimeCourseLoaded 0: >> >> can't read "glMenuGroups(mg_TimeCourseLoaded)": no such >> variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_OverlayLoaded 0: >> >> can't read "glMenuGroups(mg_OverlayLoaded)": no such variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_CurvatureLoaded 0: >> >> can't read "glMenuGroups(mg_CurvatureLoaded)": no such >> variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_LabelLoaded 0: >> >> can't read "glMenuGroups(mg_LabelLoaded)": no such variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_FieldSignLoaded 0: >> >> can't read "glMenuGroups(mg_FieldSignLoaded)": no such >> variable >> >> surfer: Error sending tcl command >> tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: >> >> can't read "glMenuGroups(mg_FieldMaskLoaded)": no such >> variable >> >> % surfer: Error sending tcl command MoveToolWindow 663 670: >> >> invalid command name "MoveToolWindow" >> >> surfer: Error sending tcl command MoveToolWindow 663 670: >> >> invalid command name "MoveToolWindow" >> >> surfer: Error sending tcl command MoveToolWindow 663 670: >> >> invalid command name "MoveToolWindow" >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer(a)nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >________________ >> >fs_lib_check (4k bytes) >> >> >

3 3

Fix_topology error
by Clifford A. Smith, PhD 02 Sep '05

02 Sep '05

Ran recon-all autorecon1 without a problem. Ran recon-all autorecon2 with the following error being produced with mris_fix_topology. Any suggestions on proceeding? Cliff Fix Topology rh Wed Aug 31 19:49:23 CDT 2005 /Users/Shared/freesurfer/subjects/00139/scripts mris_fix_topology -ga -mgz 00139 rh ************************************************************* Setting options using genetic algorithm with optimized parameters ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* reading input surface /Users/Shared/freesurfer/subjects/00139/surf/rh.qsphere... INFO: Volume /tmp/mritotal_10838/nu_8_dxyz.mnc cannot be found. before topology correction, eno=-116 (nv=134843, nf=269928, ne=404887, g=59) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 8916 ambiguous faces found in tessellation segmenting defects... 57 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 6 into 4 -merging segment 24 into 21 55 defects to be corrected 0 vertices coincident Computing Initial Surface Statistics -face loglikelihood: -8.5791 (-4.2896) -vertex loglikelihood: -5.5509 (-2.7754) -normal dot loglikelihood: -3.5429 (-3.5429) -quad curv loglikelihood: -6.4438 (-3.2219) Total Loglikelihood : -24.1167 CORRECTING DEFECT 0 Computing statistics for defect 0 [ (128,159,42) - 91.055 ] -white ( 95.29 , 2.78 ) -gray ( 85.38 , 4.30 ) -gray ( 89.45 , 18.92 ) - white ( 99.58 , 17.72 ) -intensity (85.375229 [log = -2.390182 ]- 95.286507 [log = -1.957521 ]) -curvature(kmax=-0.093632 : rmin = 10.680127 | kmin=-0.036819 : rmax = 27.159932 ) - k1 ( -0.06 , 0.70 ) - k2 ( -0.02 , 0.26 ) retessellating defect 0 with 55 vertices (convex hull=80). 125 of 1360 overlapping edges discarded Defect size : 16 by 15 by 13 (scale = 2) Edge Clustering: 3 segments were found (1 were discarded ) cluster 0 has 29 edges cluster 1 has 13 edges cluster 2 has 13 edges l_mri = 1.00 l_unmri = 10.00 l_curv = 1.00 l_qcurv = 1.00 new optimal fitness found at 4: -68.6645 Initial population for defect 0: best fitness at 4: -68.6645 (-70.9431 +- 2.5561) Segmentation fault recon-all exited with errors at Wed Aug 31 19:50:44 CDT 2005 ------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893

2 2

Re: [Freesurfer] Lib prob?
by xmeadow＠uchicago.edu 01 Sep '05

01 Sep '05

Hi, I downloaded what hopefully is the correct version of blt, and after that ran your script and said everything was fine in terms of libraries. However, I did have to create two soft links. The first one was a softlink from libtix8.1.8.3 to libtix8.1.8.4 in /usr/lib. The second was a softlink from tixwish8.1.8.3 to tixwish8.1.8.4 in /usr/bin. After making both of these changes I was able to run csurf, but when I tried to view an inflated brain the brain image would come up, but then freesurfer freezes and I can't do anything. In the logs I get the following errors: can't read "glMenuGroups(mg_FieldSignLoaded)": no such varialble surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: can't read "glMenuGroups(mg_FieldMaskLoaded)": no such variable tksurfer: run tcl script: /tmp/TmpTclSurf.13311 Unfortunately these error messages mean nothing to me, so I was wondering if anyone else had seen them before. Thanks very much. >Xander ---- Original message ---- >Date: Thu, 01 Sep 2005 11:08:52 -0400 >From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] Lib prob? >To: xmeadow(a)uchicago.edu, "Fornito, Alexander" <Alexander.Fornito(a)wh.org.au> >Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > >Alex and Xander, > >>From reading the error messages in your emails, it appears that >freesurfer is not able to find the tcl/tk, and tix libraries on your >platform. > >We have been working on trying to provide a seamless solution to the >problem of freesurfer finding the external libraries upon which it >depends, on the varied platforms that it supports. > >To help, later today, a new 'dev' build for rh9 that includes many of >the necessary libraries will be posted for download. This is not a >'stable' release (which is still undergoing testing), but a >'development' (dev) build, so it is still possible to have installation >problems, but hopefully it will install and work for you. I will email >you again when it is ready, and your patience is appreciated. > >In the meantime, I've attached a script, called 'fs_lib_check', which >will check your system for the libraries that freesurfer requires. I'm >curious to know the results of its output for your systems. Just type >'fs_lib_check' to run it, and 'fs_lib_check --help' for help text. > >Nick > > >On Thu, 2005-09-01 at 17:06 +1000, Fornito, Alexander wrote: >> Hi, >> We've recently installed the freesurfer-Linux-rh9-dev20050729.tar.gz distribution along with fs_supportlibs.tar.gz. >> csurf works ok, but if i try to run tksurfer, I get the error message below. We'd appreciate any help as we've been stuck for a while. >> Thanks! >> >> tksurfer 1000027 rh white >> surfer: current subjects dir: /data/flanders/work/alex/freesurfer/subjects >> surfer: not in "scripts" dir ==> using cwd for session root >> surfer: session root data dir ($session) set to: >> surfer: /data/flanders/work/alex/freesurfer/subjects >> surfer: Reading header info from /data/flanders/work/alex/freesurfer/subjects/1000027/mri/T1/COR-.info >> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be found. >> INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be found. >> surfer: vertices=152190, faces=304376 >> surfer: single buffered window >> Xlib: extension "XFree86-DRI" missing on display ":0.0". >> Tix_Init failed: version conflict for package "Tcl": have 8.3, need 8.4 >> surfer: using interface /usr/local/freesurfer-linux9/lib/tcl/tksurfer.tcl >> Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_common.tcl >> Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_wrappers.tcl >> Reading /usr/local/freesurfer-linux9/lib/tcl/fsgdfPlot.tcl >> couldn't load file "/usr/lib/libtix8.1.8.4.so": /usr/lib/libtix8.1.8.4.so: cannot open shared object file: No such file or directorysurfer: Error sending tcl command UpdateUndoItemLabel "Nothing to Undo": >> invalid command name "UpdateUndoItemLabel" >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_OriginalVSetLoaded 1: >> can't read "glMenuGroups(mg_OriginalVSetLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_InflatedVSetLoaded 0: >> can't read "glMenuGroups(mg_InflatedVSetLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_WhiteVSetLoaded 0: >> can't read "glMenuGroups(mg_WhiteVSetLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_PialVSetLoaded 0: >> can't read "glMenuGroups(mg_PialVSetLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_TimeCourseLoaded 0: >> can't read "glMenuGroups(mg_TimeCourseLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_OverlayLoaded 0: >> can't read "glMenuGroups(mg_OverlayLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_CurvatureLoaded 0: >> can't read "glMenuGroups(mg_CurvatureLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_LabelLoaded 0: >> can't read "glMenuGroups(mg_LabelLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_FieldSignLoaded 0: >> can't read "glMenuGroups(mg_FieldSignLoaded)": no such variable >> surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: >> can't read "glMenuGroups(mg_FieldMaskLoaded)": no such variable >> % surfer: Error sending tcl command MoveToolWindow 663 670: >> invalid command name "MoveToolWindow" >> surfer: Error sending tcl command MoveToolWindow 663 670: >> invalid command name "MoveToolWindow" >> surfer: Error sending tcl command MoveToolWindow 663 670: >> invalid command name "MoveToolWindow" >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >________________ >fs_lib_check (4k bytes)

2 2

mri_convert with *.IMG
by Michele Perry 01 Sep '05

01 Sep '05

Hi, I was given some MRI structural data originally scanned on a GE Signa 5. It was converted from Genesis to 8-bit *.tif's and 16-bit *.IMG's (with corresponding *.HDR files). The raw data is 256 pixels x 256 pixels x 2 bytes, little endian Intel. There are 124 .TIF, .IMG and .HDR files I have tried to convert from .IMG to COR using mri_convert -it <see below> -ot cor /path/001.IMG $SUBJECTS_DIR/subjid/mri/orig Here's what I get... -it anaylze -ot cor (I get errors if I don't give an output type) (result: reading from /path/001.IMG... analyzeRead(): cannot find any files for /path/001.IMG) -it ge -ot cor (result: reading from /path/001.IMG... genesisRead(): can't determine file name format for /path/001.IMG) -it gelx -ot cor reading from /path/001.IMG... genesisRead(): can't determine file name format for /path/001.IMG I have tried running this with the .IMG files in their own separate directory and in a directory with the .HDRs and .TIFs. I've also tried running it without specifing the .IMG file, just the directory. Any ideas what I'm doing wrong? Michele

1 0

Mac OS Server and X11 forwarding
by Yuan-Fen Kuo 01 Sep '05

01 Sep '05

Hi: We have installed the Tiger distribution on our Xserve. When we SSH with X forwarding on, and run tkmedit with our Mac laptops and linux stations, we get GLUT: Fatal Error in tkmedit: OpenGL GLX extension not supported by display: localhost:13.0 We could only successfully launch tkmedit if we log in from a Sun station. Any suggestions is appreciated. Thanks, Yuan-Fen Kuo Associate Imaging Processing Specialist Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison

2 2

flattening full patch
by Don Hagler 01 Sep '05

01 Sep '05

When I try to do a full flattening of a surface I often get areas with extreme squishing, looking like wrinkles. Usually if I redo the cuts in slightly different ways (e.g. adjust the spacing between cuts, extend the cuts farther onto the lateral surface, etc) I can get the flattened surface to come out looking smooth. Sometimes it takes several attempts (with several hours of computation for each attempt) to get it right. Has anyone else noticed this, and has anyone attempted to improve the flattening algorithm?

1 0

Lib prob?
by Fornito, Alexander 01 Sep '05

01 Sep '05

Hi, We've recently installed the freesurfer-Linux-rh9-dev20050729.tar.gz distribution along with fs_supportlibs.tar.gz. csurf works ok, but if i try to run tksurfer, I get the error message below. We'd appreciate any help as we've been stuck for a while. Thanks! tksurfer 1000027 rh white surfer: current subjects dir: /data/flanders/work/alex/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/flanders/work/alex/freesurfer/subjects surfer: Reading header info from /data/flanders/work/alex/freesurfer/subjects/1000027/mri/T1/COR-.info INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be found. INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be found. surfer: vertices=152190, faces=304376 surfer: single buffered window Xlib: extension "XFree86-DRI" missing on display ":0.0". Tix_Init failed: version conflict for package "Tcl": have 8.3, need 8.4 surfer: using interface /usr/local/freesurfer-linux9/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer-linux9/lib/tcl/fsgdfPlot.tcl couldn't load file "/usr/lib/libtix8.1.8.4.so": /usr/lib/libtix8.1.8.4.so: cannot open shared object file: No such file or directorysurfer: Error sending tcl command UpdateUndoItemLabel "Nothing to Undo": invalid command name "UpdateUndoItemLabel" surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_OriginalVSetLoaded 1: can't read "glMenuGroups(mg_OriginalVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_InflatedVSetLoaded 0: can't read "glMenuGroups(mg_InflatedVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_WhiteVSetLoaded 0: can't read "glMenuGroups(mg_WhiteVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_PialVSetLoaded 0: can't read "glMenuGroups(mg_PialVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_TimeCourseLoaded 0: can't read "glMenuGroups(mg_TimeCourseLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_OverlayLoaded 0: can't read "glMenuGroups(mg_OverlayLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_CurvatureLoaded 0: can't read "glMenuGroups(mg_CurvatureLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_LabelLoaded 0: can't read "glMenuGroups(mg_LabelLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_FieldSignLoaded 0: can't read "glMenuGroups(mg_FieldSignLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: can't read "glMenuGroups(mg_FieldMaskLoaded)": no such variable % surfer: Error sending tcl command MoveToolWindow 663 670: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 663 670: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 663 670: invalid command name "MoveToolWindow"

3 2

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Freesurfer September 2005