RE: [Freesurfer] new 'dev' release for Linux rh9, centos4 and centos4_x86_64 - Freesurfer

5 Sep 2005


      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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