gd lh.gender-age.fsgd --C lh-Avg-thickness-FemaleMale.age.mtx --C lh-Avg-thickness-FemaleMale.intercept.mtx --C lh-Avg-thickness-Gender.diff.mtx --C lh-Avg-thickness-Gender*Age-Inter.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir )
echo $glmfitcmd
echo cmdline mri_glmfit.bin --y lh.gender_age.thickness.10.mgh --fsgd lh.gender-age.fsgd --C lh-Avg-thickness-FemaleMale.age.mtx --C lh-Avg-thickness-FemaleMale.intercept.mtx --C lh-Avg-thickness-Gender.diff.mtx --C lh-Avg-thickness-Gender*Age-Inter.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir
cmdline mri_glmfit.bin --y lh.gender_age.thickness.10.mgh --fsgd lh.gender-age.fsgd --C lh-Avg-thickness-FemaleMale.age.mtx --C lh-Avg-thickness-FemaleMale.intercept.mtx --C lh-Avg-thickness-Gender.diff.mtx --C lh-Avg-thickness-Gender*Age-Inter.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir
set gd2mtx = dods
set gd2mtx = dods
set UseTable = 0 ;
set UseTable = 0
set label = ( ) ;
set label = ( )
while ( $#glmfitcmd )
while ( 20 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = cmdline
shift glmfitcmd

switch ( $flag )
switch ( cmdline )
case "mri_glmfit"
case mri_glmfit
case "--osgm"
case --osgm
case "--prune"
case --prune
case "--no-prune"
case --no-prune
case "--pca"
case --pca
case "--synth"
case --synth
case "--allowsubjrep"
case --allowsubjrep
case "--illcond"
case --illcond
case "--debug"
case --debug
case "--synth"
case --synth
case "--cortex"
case --cortex
case "--kurtosis"
case --kurtosis
case "--nii"
case --nii
case "--nii.gz"
case --nii.gz
case "--rescale-x"
case --rescale-x
case "--no-rescale-x"
case --no-rescale-x
case "--fisher"
case --fisher
case "--no-pcc"
case --no-pcc
case "dods"
case dods
case "mri_glmfit.bin"
case mri_glmfit.bin
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 19 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = mri_glmfit.bin
shift glmfitcmd

switch ( $flag )
switch ( mri_glmfit.bin )
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 18 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --y
shift glmfitcmd

switch ( $flag )
switch ( --y )
if ( $#y == 0 ) set y = $glmfitcmd[1] ;
if ( 0 == 0 ) set y = lh.gender_age.thickness.10.mgh
set y = lh.gender_age.thickness.10.mgh
shift glmfitcmd ;
shift glmfitcmd
if ( $DoClusterMean ) then
if ( 1 ) then
if ( ! -e $y ) then
if ( ! -e lh.gender_age.thickness.10.mgh ) then
endif
endif
if ( "$flag" == "--table" ) set UseTable = 1 ;
if ( --y == --table ) set UseTable = 1
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 16 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --fsgd
shift glmfitcmd

switch ( $flag )
switch ( --fsgd )
shift glmfitcmd ;
shift glmfitcmd
if ( $#glmfitcmd > 0 ) then
if ( 14 > 0 ) then
if ( $glmfitcmd[1] == doss ) set gd2mtx = doss
if ( --C == doss ) set gd2mtx = doss
endif
endif
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 14 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --C
shift glmfitcmd

switch ( $flag )
switch ( --C )
case "--X"
case --X
case "--w"
case --w
case "--fwhm"
case --fwhm
case "--mask"
case --mask
case "--seed"
case --seed
case "--var-fwhm"
case --var-fwhm
case "--yffxvar"
case --yffxvar
case "--ffxdof"
case --ffxdof
case "--ffxdofdat"
case --ffxdofdat
case "--exclude-frame"
case --exclude-frame
shift glmfitcmd ;
shift glmfitcmd
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 12 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --C
shift glmfitcmd

switch ( $flag )
switch ( --C )
case "--X"
case --X
case "--w"
case --w
case "--fwhm"
case --fwhm
case "--mask"
case --mask
case "--seed"
case --seed
case "--var-fwhm"
case --var-fwhm
case "--yffxvar"
case --yffxvar
case "--ffxdof"
case --ffxdof
case "--ffxdofdat"
case --ffxdofdat
case "--exclude-frame"
case --exclude-frame
shift glmfitcmd ;
shift glmfitcmd
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 10 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --C
shift glmfitcmd

switch ( $flag )
switch ( --C )
case "--X"
case --X
case "--w"
case --w
case "--fwhm"
case --fwhm
case "--mask"
case --mask
case "--seed"
case --seed
case "--var-fwhm"
case --var-fwhm
case "--yffxvar"
case --yffxvar
case "--ffxdof"
case --ffxdof
case "--ffxdofdat"
case --ffxdofdat
case "--exclude-frame"
case --exclude-frame
shift glmfitcmd ;
shift glmfitcmd
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 8 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --C
shift glmfitcmd

switch ( $flag )
switch ( --C )
case "--X"
case --X
case "--w"
case --w
case "--fwhm"
case --fwhm
case "--mask"
case --mask
case "--seed"
case --seed
case "--var-fwhm"
case --var-fwhm
case "--yffxvar"
case --yffxvar
case "--ffxdof"
case --ffxdof
case "--ffxdofdat"
case --ffxdofdat
case "--exclude-frame"
case --exclude-frame
shift glmfitcmd ;
shift glmfitcmd
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 6 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --surf
shift glmfitcmd

switch ( $flag )
switch ( --surf )
case "--surface"
case --surface
set subject = $glmfitcmd[1] ; shift glmfitcmd ;
set subject = fsaverage
shift glmfitcmd
set hemi = $glmfitcmd[1] ; shift glmfitcmd ;
set hemi = lh
shift glmfitcmd
set anattype = surface ;
set anattype = surface
if ( $#glmfitcmd != 0 ) then
if ( 3 != 0 ) then
set c = `echo $glmfitcmd[1] | cut -c 1-2` ;
set c = `echo $glmfitcmd[1] | cut -c 1-2`
cut -c 1-2
echo --cortex
if ( "$c" != "--" ) then
if ( -- != -- ) then
endif
endif
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 3 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --cortex
shift glmfitcmd

switch ( $flag )
switch ( --cortex )
case "--kurtosis"
case --kurtosis
case "--nii"
case --nii
case "--nii.gz"
case --nii.gz
case "--rescale-x"
case --rescale-x
case "--no-rescale-x"
case --no-rescale-x
case "--fisher"
case --fisher
case "--no-pcc"
case --no-pcc
case "dods"
case dods
case "mri_glmfit.bin"
case mri_glmfit.bin
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 2 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --glmdir
shift glmfitcmd

switch ( $flag )
switch ( --glmdir )
case "--o"
case --o
case "--C"
case --C
case "--X"
case --X
case "--w"
case --w
case "--fwhm"
case --fwhm
case "--mask"
case --mask
case "--seed"
case --seed
case "--var-fwhm"
case --var-fwhm
case "--yffxvar"
case --yffxvar
case "--ffxdof"
case --ffxdof
case "--ffxdofdat"
case --ffxdofdat
case "--exclude-frame"
case --exclude-frame
shift glmfitcmd ;
shift glmfitcmd
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 0 )

set mask = ( ) ;
set mask = ( )
if ( ! $UseTable ) then
if ( ! 0 ) then
set mask = `stem2fname $glmdir/mask`
set mask = `stem2fname $glmdir/mask`
stem2fname lh.gender_age.glmdir/mask
if ( $status ) then
if ( 0 ) then
endif
endif


if ( 0 && $UseGRF && $anattype != volume ) then
if ( 0 && 0 && surface != volume ) then
if ( $UseGRF ) then
if ( 0 ) then

if ( $#subjectOverride ) set subject = $subjectOverride
if ( 0 ) set subject =


if ( $#subject != 0 ) then
if ( 1 != 0 ) then
if ( ! -e $SUBJECTS_DIR/$subject ) then
if ( ! -e /media/3B110EAE3B9DE8E0/OASIS_Data/fsaverage ) then
echo "SURFACE: $subject $hemi"
echo SURFACE: fsaverage lh
SURFACE: fsaverage lh
endif
endif


set FSGDhasCon = 0 ;
set FSGDhasCon = 0
if ( -e $glmdir/y.fsgd ) then
if ( -e lh.gender_age.glmdir/y.fsgd ) then

set FSGDhasCon = `cat $glmdir/y.fsgd | awk '{if($1 == "Contrast") print 1}' | wc -l`
set FSGDhasCon = `cat $glmdir/y.fsgd | awk '{if($1 == "Contrast") print 1}' | wc -l`
wc -l
awk {if($1 == "Contrast") print 1}
cat lh.gender_age.glmdir/y.fsgd
endif
endif
if ( $#tmpdir == 0 ) set tmpdir = $glmdir/tmp.mri_glmfit-sim-$$
if ( 0 == 0 ) set tmpdir = lh.gender_age.glmdir/tmp.mri_glmfit-sim-56755
set tmpdir = lh.gender_age.glmdir/tmp.mri_glmfit-sim-56755
mkdir -p $tmpdir
mkdir -p lh.gender_age.glmdir/tmp.mri_glmfit-sim-56755
set clist = ( $glmdir/*/C.dat )
set clist = ( lh.gender_age.glmdir/*/C.dat )
if ( $status ) then
if ( 0 ) then
set clist2 = ( ) ;
set clist2 = ( )
set conlist = ( ) ;
set conlist = ( )
foreach c ( $clist )
foreach c ( lh.gender_age.glmdir/lh-Avg-thickness-FemaleMale.age/C.dat lh.gender_age.glmdir/lh-Avg-thickness-FemaleMale.intercept/C.dat lh.gender_age.glmdir/lh-Avg-thickness-Gender*Age-Inter/C.dat lh.gender_age.glmdir/lh-Avg-thickness-Gender.diff/C.dat )
set tmp = `dirname $c`
set tmp = `dirname $c`
dirname lh.gender_age.glmdir/lh-Avg-thickness-FemaleMale.age/C.dat
set conname = `basename $tmp`
set conname = `basename $tmp`
basename lh.gender_age.glmdir/lh-Avg-thickness-FemaleMale.age
set conlist = ( $conlist $conname ) ;
set conlist = ( lh-Avg-thickness-FemaleMale.age )
set confile = $tmpdir/$conname.mtx
set confile = lh.gender_age.glmdir/tmp.mri_glmfit-sim-56755/lh-Avg-thickness-FemaleMale.age.mtx
cp $c $confile
cp lh.gender_age.glmdir/lh-Avg-thickness-FemaleMale.age/C.dat lh.gender_age.glmdir/tmp.mri_glmfit-sim-56755/lh-Avg-thickness-FemaleMale.age.mtx

if ( $FSGDhasCon == 0 ) set clist2 = ( $clist2 --C $confile ) ;
if ( 0 == 0 ) set clist2 = ( --C lh.gender_age.glmdir/tmp.mri_glmfit-sim-56755/lh-Avg-thickness-FemaleMale.age.mtx )
set clist2 = ( --C lh.gender_age.glmdir/tmp.mri_glmfit-sim-56755/lh-Avg-thickness-FemaleMale.age.mtx )


set sig = `stem2fname $glmdir/$conname/sig`
set sig = `stem2fname $glmdir/$conname/sig`
stem2fname lh.gender_age.glmdir/lh-Avg-thickness-FemaleMale.age/sig
if ( $status ) then
if ( 0 ) then


if ( $DoSim ) then
if ( 0 ) then
end
end
set tmp = `dirname $c`
set tmp = `dirname $c`
dirname lh.gender_age.glmdir/lh-Avg-thickness-FemaleMale.intercept/C.dat
set conname = `basename $tmp`
set conname = `basename $tmp`
basename lh.gender_age.glmdir/lh-Avg-thickness-FemaleMale.intercept
set conlist = ( $conlist $conname ) ;
set conlist = ( lh-Avg-thickness-FemaleMale.age lh-Avg-thickness-FemaleMale.intercept )
set confile = $tmpdir/$conname.mtx
set confile = lh.gender_age.glmdir/tmp.mri_glmfit-sim-56755/lh-Avg-thickness-FemaleMale.intercept.mtx
cp $c $confile
cp lh.gender_age.glmdir/lh-Avg-thickness-FemaleMale.intercept/C.dat lh.gender_age.glmdir/tmp.mri_glmfit-sim-56755/lh-Avg-thickness-FemaleMale.intercept.mtx

if ( $FSGDhasCon == 0 ) set clist2 = ( $clist2 --C $confile ) ;
if ( 0 == 0 ) set clist2 = ( --C lh.gender_age.glmdir/tmp.mri_glmfit-sim-56755/lh-Avg-thickness-FemaleMale.age.mtx --C lh.gender_age.glmdir/tmp.mri_glmfit-sim-56755/lh-Avg-thickness-FemaleMale.intercept.mtx )
set clist2 = ( --C lh.gender_age.glmdir/tmp.mri_glmfit-sim-56755/lh-Avg-thickness-FemaleMale.age.mtx --C lh.gender_age.glmdir/tmp.mri_glmfit-sim-56755/lh-Avg-thickness-FemaleMale.intercept.mtx )


set sig = `stem2fname $glmdir/$conname/sig`
set sig = `stem2fname $glmdir/$conname/sig`
stem2fname lh.gender_age.glmdir/lh-Avg-thickness-FemaleMale.intercept/sig
if ( $status ) then
if ( 0 ) then


if ( $DoSim ) then
if ( 0 ) then
end
end
set tmp = `dirname $c`
set tmp = `dirname $c`
dirname lh.gender_age.glmdir/lh-Avg-thickness-Gender*Age-Inter/C.dat
set conname = `basename $tmp`
set conname = `basename $tmp`
basename lh.gender_age.glmdir/lh-Avg-thickness-Gender*Age-Inter
set conlist = ( $conlist $conname ) ;
set conlist = ( lh-Avg-thickness-FemaleMale.age lh-Avg-thickness-FemaleMale.intercept lh-Avg-thickness-Gender*Age-Inter )
set: No match.