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.
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