set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 5 != 0 )

set flag = $argv[1] ; shift ;
set flag = -i
shift

switch ( $flag )
switch ( -i )
if ( $#argv < 1 ) goto arg1err ;
if ( 4 < 1 ) goto arg1err
set InputVol = "$argv[1]" ; shift ;
set InputVol = /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm
shift
if ( ! -e "$InputVol" ) then
if ( ! -e /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm ) then
if ( -d "$InputVol" ) then
if ( -d /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm ) then
if ( ! -r "$InputVol" ) then
if ( ! -r /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm ) then
set InVolDir = `dirname  "$InputVol"` ;
set InVolDir = `dirname  "$InputVol"`
dirname /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm
set InVolBase = `basename "$InputVol"` ;
set InVolBase = `basename "$InputVol"`
basename /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm
pushd $InVolDir > /dev/null
pushd /home/hurry01/r/resdep_mri_data/resdep014
set InVolDir = `pwd` ;
set InVolDir = `pwd`
pwd
popd > /dev/null
popd
set InputVol = "$InVolDir/$InVolBase" ;
set InputVol = /home/hurry01/.gvfs/as-rsch-urry$ on rstore1.uit.tufts.edu/resdep_mri_data/resdep014/265000-10-1.dcm
set InputList = ( $InputList "$InputVol" ) ;
set InputList = ( /home/hurry01/.gvfs/as-rsch-urry$ on rstore1.uit.tufts.edu/resdep_mri_data/resdep014/265000-10-1.dcm )
set DoConvertInput = 1 ;
set DoConvertInput = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 3 != 0 )

set flag = $argv[1] ; shift ;
set flag = -s
shift

switch ( $flag )
switch ( -s )
if ( $#argv < 1 ) goto arg1err ;
if ( 2 < 1 ) goto arg1err
set subjid = $argv[1] ; shift ;
set subjid = resdep214
shift
set subjid = `basename $subjid` ;
set subjid = `basename $subjid`
basename resdep214
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 1 != 0 )

set flag = $argv[1] ; shift ;
set flag = -all
shift

switch ( $flag )
switch ( -all )
case "-autorecon-all":
case -autorecon-all:
set DoCreateBaseInput = 1 ;
set DoCreateBaseInput = 1
set DoMotionCor = 1 ;
set DoMotionCor = 1
set DoTalairach = 1 ;
set DoTalairach = 1
set DoTalCheck = 1 ;
set DoTalCheck = 1
set DoNuIntensityCor = 1 ;
set DoNuIntensityCor = 1
set DoNormalization = 1 ;
set DoNormalization = 1
set DoSkullStrip = 1 ;
set DoSkullStrip = 1
set DoGCAReg = 1 ;
set DoGCAReg = 1
set DoCARegInv = 1 ;
set DoCARegInv = 1
set DoRemoveNeck = 1 ;
set DoRemoveNeck = 1
set DoSkullLTA = 1 ;
set DoSkullLTA = 1
set DoCANormalize = 1 ;
set DoCANormalize = 1
set DoCAReg = 1 ;
set DoCAReg = 1
set DoCALabel = 1 ;
set DoCALabel = 1
set DoNormalization2 = 1 ;
set DoNormalization2 = 1
set DoMaskBFS = 1 ;
set DoMaskBFS = 1
set DoSegmentation = 1 ;
set DoSegmentation = 1
set DoFill = 1 ;
set DoFill = 1
set DoTessellate = 1 ;
set DoTessellate = 1
set DoSmooth1 = 1 ;
set DoSmooth1 = 1
set DoInflate1 = 1 ;
set DoInflate1 = 1
set DoQSphere = 1 ;
set DoQSphere = 1
set DoFix = 1 ;
set DoFix = 1
set DoSmooth2 = 1 ;
set DoSmooth2 = 1
set DoInflate2 = 1 ;
set DoInflate2 = 1
set DoWhiteSurfs = 1 ;
set DoWhiteSurfs = 1
set DoSphere = 1 ;
set DoSphere = 1
set DoSurfReg = 1 ;
set DoSurfReg = 1
set DoContraSurfReg = 0 ;
set DoContraSurfReg = 0
set DoAvgCurv = 1 ;
set DoAvgCurv = 1
set DoJacobianWhite = 1 ;
set DoJacobianWhite = 1
set DoCortParc = 1 ;
set DoCortParc = 1
set DoPialSurfs = 1 ;
set DoPialSurfs = 1
set DoPctSurfCon = 1 ;
set DoPctSurfCon = 1
set DoParcStats = 1 ;
set DoParcStats = 1
set DoCortParc2 = 1 ;
set DoCortParc2 = 1
set DoParcStats2 = 1 ;
set DoParcStats2 = 1
set DoCortParc3 = 1 ;
set DoCortParc3 = 1
set DoParcStats3 = 1 ;
set DoParcStats3 = 1
set DoCortRibbonVolMask = 1 ;
set DoCortRibbonVolMask = 1
set DoSegStats = 1 ;
set DoSegStats = 1
set DoAParc2ASeg = 1 ;
set DoAParc2ASeg = 1
set DoWMParc = 1 ;
set DoWMParc = 1
set DoCurvStats = 1 ;
set DoCurvStats = 1
set DoBaLabels = 1 ;
set DoBaLabels = 1
set DoLabelExvivoEC = 1 ;
set DoLabelExvivoEC = 1
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 ( $DoT2pial && $DoFLAIRpial ) then
if ( 0 && 0 ) then

if ( $UseCuda || $GetCuda ) then
if ( 0 || 0 ) then

if ( ! $DoVersionsOnly ) then
if ( ! 0 ) then
if ( $#subjid != 1 ) then
if ( 1 != 1 ) then

if ( ! $?SUBJECTS_DIR ) then
if ( ! 1 ) then

if ( ! -e $SUBJECTS_DIR ) then
if ( ! -e /home/hurry01/w/projects/resdep/data/mri ) then


pushd $SUBJECTS_DIR > /dev/null
pushd /home/hurry01/w/projects/resdep/data/mri
setenv SUBJECTS_DIR `$PWD` ;
setenv SUBJECTS_DIR `$PWD`
/bin/pwd
popd > /dev/null
popd

set subjdir = $SUBJECTS_DIR/$subjid
set subjdir = /home/hurry01/.gvfs/ebblvm$ on callunavm.psy.tufts.edu/projects/resdep/data/mri/resdep214
set: Variable name must contain alphanumeric characters.