Hi,

I just installed the newest freesurfer and modified make_average_surface as suggestion by Nick and Brian. When I run make_average_surface, it stop with the following error. Did anyone meet the simialr probelm? Thanks

[antao@freesurfer subjects]$ make_average_surface --subjects AD1293 AD1297 --out average_cn

set VERSION = '$Id: make_average_surface,v 1.14 2005/09/27 19:42:14 greve Exp $' ; set VERSION = $Id: make_average_surface,v 1.14 2005/09/27 19:42:14 greve Exp $

set PrintHelp = 0 ; set PrintHelp = 0

if ( $?SUBJECTS ) then if ( 0 ) then if ( $?SUBJECTS_DIR ) then if ( 1 ) then set SUBJECTS_DIR= ( $SUBJECTS_DIR ) set SUBJECTS_DIR= ( /home/antao/freesurfer/subjects ) endif endif

set average_subject=average set average_subject=average set ddir = ${SUBJECTS_DIR}/${average_subject} set ddir = /home/antao/freesurfer/subjects/average set transform_fname="" set transform_fname= set XFORM_FLAG="" set XFORM_FLAG=

if ( $#argv == 0 ) then if ( 5 == 0 ) then

set PWD = `getpwdcmd` ; set PWD = `getpwdcmd` getpwdcmd if ( $status ) exit 1 ; if ( 0 ) exit 1

goto parse_args ; goto parse_args set cmdline = ( $argv ) ; set cmdline = ( --subjects AD1293 AD1297 --out average_cn ) set getting_subjects = 0 ; set getting_subjects = 0 while ( $#argv != 0 ) while ( 5 != 0 )

set flag = $argv[1] ; set flag = --subjects if ( ! $getting_subjects ) then if ( ! 0 ) then shift ; shift endif endif

switch ( $flag ) switch ( --subjects ) if ( $#argv == 0 ) goto arg1moreerr ; if ( 4 == 0 ) goto arg1moreerr set SUBJECTS = $argv[1] ; shift ; set SUBJECTS = AD1293 shift

set getting_subjects = 1 ; set getting_subjects = 1 breaksw breaksw

end end while ( $#argv != 0 ) while ( 3 != 0 )

set flag = $argv[1] ; set flag = AD1297 if ( ! $getting_subjects ) then if ( ! 1 ) then

switch ( $flag ) switch ( AD1297 ) if ( $getting_subjects ) then if ( 1 ) then

set SUBJECTS = "$SUBJECTS $argv[1]" ; shift ; set SUBJECTS = AD1293 AD1297 shift set getting_subjects = 1 ; set getting_subjects = 1 else else breaksw breaksw

end end while ( $#argv != 0 ) while ( 2 != 0 )

set flag = $argv[1] ; set flag = --out if ( ! $getting_subjects ) then if ( ! 1 ) then

switch ( $flag ) switch ( --out ) if ( $getting_subjects ) then if ( 1 ) then

set getting_subjects = 0 ; set getting_subjects = 0 shift ; shift endif endif if ( $#argv == 0 ) goto arg1err ; if ( 1 == 0 ) goto arg1err set average_subject = $argv[1] ; shift ; set average_subject = average_cn shift set ddir = ${SUBJECTS_DIR}/${average_subject} set ddir = /home/antao/freesurfer/subjects/average_cn breaksw breaksw

end end while ( $#argv != 0 ) while ( 0 != 0 )

goto parse_args_return ; goto parse_args_return

goto check_params ; goto check_params if ( ! $?SUBJECTS ) then if ( ! 1 ) then if ( ! $?SUBJECTS_DIR ) then if ( ! 1 ) then if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /home/antao/freesurfer/subjects ) then if ( ! $?FREESURFER_HOME ) then if ( ! 1 ) then if ( ! -e $FREESURFER_HOME ) then if ( ! -e /home/antao/freesurfer ) then if ( x$transform_fname != x ) then if ( x != x ) then goto check_params_return ; goto check_params_return

echo ==================== echo ==================== ==================== echo make_average_surface echo make_average_surface make_average_surface echo ==================== echo ==================== ==================== echo input subjects: ${SUBJECTS} echo input subjects: AD1293 AD1297 input subjects: AD1293 AD1297 echo output subject: ${average_subject} echo output subject: average_cn output subject: average_cn

mkdir -p ${ddir} ${ddir}/surf ${ddir}/mri ${ddir}/mri/transforms ${ddir}/mri/T1 ${ddir}/mri/orig ${ddir}/mri/label mkdir -p /home/antao/freesurfer/subjects/average_cn /home/antao/freesurfer/subjects/average_cn/surf /home/antao/freesurfer/subjects/average_cn/mri /home/antao/freesurfer/subjects/average_cn/mri/transforms /home/antao/freesurfer/subjects/average_cn/mri/T1 /home/antao/freesurfer/subjects/average_cn/mri/orig /home/antao/freesurfer/subjects/average_cn/mri/label

if ( -e ${SUBJECTS_DIR}/${average_subject} == 0 ) then if ( -e /home/antao/freesurfer/subjects/average_cn == 0 ) then

mkdir -p ${SUBJECTS_DIR}/${average_subject}/surf mkdir -p /home/antao/freesurfer/subjects/average_cn/surf endif endif

set tmp_subjects = ( $SUBJECTS ) set tmp_subjects = ( AD1293 AD1297 )

foreach hemi ( rh lh ) foreach hemi ( rh lh )

cd ${SUBJECTS_DIR}/${average_subject} cd /home/antao/freesurfer/subjects/average_cn foreach s ( orig white pial inflated ) foreach s ( orig white pial inflated ) echo mris_make_average_surface... echo mris_make_average_surface... mris_make_average_surface... mris_make_average_surface $XFORM_FLAG -i 7 -o $s ${hemi} ${s}_avg sphere.reg ${average_subject} $SUBJECTS mris_make_average_surface -i 7 -o orig rh orig_avg sphere.reg average_cn AD1293 AD1297 reading vertex positions from orig... processing subject AD1293... Applying transform. processing subject AD1297... Applying transform. reading icosahedron from /home/antao/freesurfer/lib/bem/ic7.tri... writing average orig_avg surface to /home/antao/freesurfer/subjects/average_cn/surf/rh.orig_avg mris_make_average_surface done end end echo mris_make_average_surface... echo mris_make_average_surface... mris_make_average_surface... mris_make_average_surface $XFORM_FLAG -i 7 -o $s ${hemi} ${s}_avg sphere.reg ${average_subject} $SUBJECTS mris_make_average_surface -i 7 -o white rh white_avg sphere.reg average_cn AD1293 AD1297 reading vertex positions from white... processing subject AD1293... Applying transform. processing subject AD1297... Applying transform. reading icosahedron from /home/antao/freesurfer/lib/bem/ic7.tri... writing average white_avg surface to /home/antao/freesurfer/subjects/average_cn/surf/rh.white_avg mris_make_average_surface done end end echo mris_make_average_surface... echo mris_make_average_surface... mris_make_average_surface... mris_make_average_surface $XFORM_FLAG -i 7 -o $s ${hemi} ${s}_avg sphere.reg ${average_subject} $SUBJECTS mris_make_average_surface -i 7 -o pial rh pial_avg sphere.reg average_cn AD1293 AD1297 reading vertex positions from pial... processing subject AD1293... Applying transform. processing subject AD1297... Applying transform. reading icosahedron from /home/antao/freesurfer/lib/bem/ic7.tri... writing average pial_avg surface to /home/antao/freesurfer/subjects/average_cn/surf/rh.pial_avg mris_make_average_surface done end end echo mris_make_average_surface... echo mris_make_average_surface... mris_make_average_surface... mris_make_average_surface $XFORM_FLAG -i 7 -o $s ${hemi} ${s}_avg sphere.reg ${average_subject} $SUBJECTS mris_make_average_surface -i 7 -o inflated rh inflated_avg sphere.reg average_cn AD1293 AD1297 reading vertex positions from inflated... processing subject AD1293... Applying transform. processing subject AD1297... Applying transform. reading icosahedron from /home/antao/freesurfer/lib/bem/ic7.tri... writing average inflated_avg surface to /home/antao/freesurfer/subjects/average_cn/surf/rh.inflated_avg mris_make_average_surface done end end

foreach c ( sulc curv thickness ) foreach c ( sulc curv thickness ) echo mris_average_curvature... echo mris_average_curvature... mris_average_curvature... mris_average_curvature $c ${hemi} sphere.reg $SUBJECTS $SUBJECTS_DIR/${average_subject}/surf/${hemi}.avg_${c} mris_average_curvature sulc rh sphere.reg AD1293 AD1297 /home/antao/freesurfer/subjects/average_cn/surf/rh.avg_sulc processing subject AD1293... processing subject AD1297... end end echo mris_average_curvature... echo mris_average_curvature... mris_average_curvature... mris_average_curvature $c ${hemi} sphere.reg $SUBJECTS $SUBJECTS_DIR/${average_subject}/surf/${hemi}.avg_${c} mris_average_curvature curv rh sphere.reg AD1293 AD1297 /home/antao/freesurfer/subjects/average_cn/surf/rh.avg_curv processing subject AD1293... processing subject AD1297... end end echo mris_average_curvature... echo mris_average_curvature... mris_average_curvature... mris_average_curvature $c ${hemi} sphere.reg $SUBJECTS $SUBJECTS_DIR/${average_subject}/surf/${hemi}.avg_${c} mris_average_curvature thickness rh sphere.reg AD1293 AD1297 /home/antao/freesurfer/subjects/average_cn/surf/rh.avg_thickness processing subject AD1293... processing subject AD1297... end end

cd ${SUBJECTS_DIR}/${average_subject}/surf cd /home/antao/freesurfer/subjects/average_cn/surf pwd pwd /home/antao/freesurfer/subjects/average_cn/surf mris_smooth -n 5 ./${hemi}.white_avg ./${hemi}.smoothwm mris_smooth -n 5 ./rh.white_avg ./rh.smoothwm smoothing for 5 iterations smoothing surface tessellation for 5 iterations... smoothing complete - recomputing first and second fundamental forms... writing smoothed curvature to ./rh.curv writing smoothed area to ./rh.area mris_inflate ./${hemi}.smoothwm ./${hemi}.inflated mris_inflate ./rh.smoothwm ./rh.inflated avg radius = 48.1 mm, total surface area = 76079 mm^2 tol=1.0e-04, host=frees, nav=16, nbrs=2, l_spring_norm=1.000, l_dist=0.100 mom=0.90, dt=0.90 desired rms height=0.015 inflating to desired rms height = 0.015 000: dt: 0.0000, rms height=0.116, avgs=16 005: dt: 0.9000, rms height=0.081, avgs=16, l_dist=0.40 010: dt: 0.9000, rms height=0.068, avgs=16, l_dist=0.40 015: dt: 0.9000, rms height=0.057, avgs=8, l_dist=0.28 020: dt: 0.9000, rms height=0.047, avgs=8, l_dist=0.28 025: dt: 0.9000, rms height=0.040, avgs=4, l_dist=0.20 030: dt: 0.9000, rms height=0.033, avgs=4, l_dist=0.20 035: dt: 0.9000, rms height=0.028, avgs=2, l_dist=0.14 040: dt: 0.9000, rms height=0.024, avgs=2, l_dist=0.14 045: dt: 0.9000, rms height=0.021, avgs=1, l_dist=0.10 050: dt: 0.9000, rms height=0.018, avgs=1, l_dist=0.10 055: dt: 0.9000, rms height=0.017, avgs=0, l_dist=0.00 060: dt: 0.9000, rms height=0.015, avgs=0, l_dist=0.00

inflation complete. writing inflated surface to ./rh.inflated writing sulcal depths to ./rh.sulc writing curvature file ./rh.sulc inflation took 2.8 minutes mris_curvature -a 10 -w ./${hemi}.white_avg mris_curvature -a 10 -w ./rh.white_avg averaging curvature patterns 10 times. total integrated curvature = 165.547*4pi (2080.322) --> -165 handles ICI = 410.5, FI = 7165.7, variation=101079.032 writing Gaussian curvature to ./rh.white_avg.K...done. writing mean curvature to ./rh.white_avg.H...done. cp ${hemi}.white_avg.H ${hemi}.curv cp rh.white_avg.H rh.curv cp ${FREESURFER_HOME}/average/surf/${hemi}.sphere.reg . cp /home/antao/freesurfer/average/surf/rh.sphere.reg . cp: cannot stat `/home/antao/freesurfer/average/surf/rh.sphere.reg': No such file or directory [antao@freesurfer subjects]