[upddkp224:average_IPS_FS7_Linux/stats/glm_group_n135] jurgenhanggi% mri_glmfit-sim --debug --glmdir IPS_2groups_n135_Thickness_LH_test.glmdir --sim mc-z 5000 1.302 lh_mc-z.abs_5000p1.3 --sim-sign abs --overwrite --cwpvalthresh 0.25
set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 12 != 0 )

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

switch ( $flag )
switch ( --glmdir )
if ( $#argv < 0 ) goto arg1err ;
if ( 11 < 0 ) goto arg1err
set glmdir = $argv[1] ; shift ;
set glmdir = IPS_2groups_n135_Thickness_LH_test.glmdir
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 10 != 0 )

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

switch ( $flag )
switch ( --sim )
if ( $#argv < 4 ) goto arg4err ;
if ( 9 < 4 ) goto arg4err
set nulltype = $argv[1] ; shift ;
set nulltype = mc-z
shift
set nsim = $argv[1] ; shift ;
set nsim = 5000
shift
set thresh = $argv[1] ; shift ;
set thresh = 1.302
shift
set csdbase = $argv[1] ; shift ;
set csdbase = lh_mc-z.abs_5000p1.3
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 5 != 0 )

set flag = $argv[1] ; shift ;
set flag = --sim-sign
shift

switch ( $flag )
switch ( --sim-sign )
if ( $#argv < 1 ) goto arg1err ;
if ( 4 < 1 ) goto arg1err
set simsign = $argv[1] ; shift ;
set simsign = abs
shift
breaksw
breaksw

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

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

switch ( $flag )
switch ( --overwrite )
set Overwrite = 1 ;
set Overwrite = 1
breaksw
breaksw

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

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

switch ( $flag )
switch ( --cwpvalthresh )
case "--cwp":
case --cwp:
if ( $#argv < 1 ) goto arg1err ;
if ( 1 < 1 ) goto arg1err
set cwpvalthresh = $argv[1] ; shift ;
set cwpvalthresh = 0.25
shift
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 ( $#glmdir == 0 ) then
if ( 1 == 0 ) then
if ( $DoSim ) then
if ( 1 ) then
if ( $#nulltype == 0 ) then
if ( 1 == 0 ) then
if ( $#simsign == 0 ) then
if ( 1 == 0 ) then
endif
endif
set residual = ( )
set residual = ( )
if ( $nulltype == perm && $PermResid ) then
if ( mc-z == perm && 1 ) then
if ( $DiagCluster && $DoBackground ) then
if ( 0 && 0 ) then
if ( $DiagCluster && $DoPBSubmit ) then
if ( 0 && 0 ) then
if ( $DiagCluster && $DoSim == 0 ) then
if ( 0 && 1 == 0 ) then

if ( $PermNonStatCor ) then
if ( 0 ) then

goto check_params_return ;
goto check_params_return

if ( ! -e $glmdir ) then
if ( ! -e IPS_2groups_n135_Thickness_LH_test.glmdir ) then

set glmfitlog = $glmdir/mri_glmfit.log
set glmfitlog = IPS_2groups_n135_Thickness_LH_test.glmdir/mri_glmfit.log
if ( ! -e $glmfitlog ) then
if ( ! -e IPS_2groups_n135_Thickness_LH_test.glmdir/mri_glmfit.log ) then

if ( $nulltype != perm ) then
if ( mc-z != perm ) then
set fwhmfile = $glmdir/fwhm.dat
set fwhmfile = IPS_2groups_n135_Thickness_LH_test.glmdir/fwhm.dat
if ( ! -e $fwhmfile ) then
if ( ! -e IPS_2groups_n135_Thickness_LH_test.glmdir/fwhm.dat ) then

set fwhm = `cat $fwhmfile` ;
set fwhm = `cat $fwhmfile`
cat IPS_2groups_n135_Thickness_LH_test.glmdir/fwhm.dat
else
else

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
cat IPS_2groups_n135_Thickness_LH_test.glmdir/mri_glmfit.log
awk {if($1 == "cwd") print $2}
if ( 0 && ! -e $glmfitcwd ) then
if ( 0 && ! -e /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135 ) then
set glmfitcwd = `pwd` ;
set glmfitcwd = `pwd`
pwd

set anattype = volume ;
set anattype = volume
set subject = ( ) ;
set subject = ( )
set hemi = ( ) ;
set hemi = ( )
set surf = "white" ;
set surf = white
set wls = ( ) ;
set wls = ( )

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
cat IPS_2groups_n135_Thickness_LH_test.glmdir/mri_glmfit.log
awk {if($1 == "cwd") print $2}


set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`
set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`
cat IPS_2groups_n135_Thickness_LH_test.glmdir/mri_glmfit.log
awk {if($1 == "cmdline") print $0}
set glmfitcmd = ( $glmfitcmd0 ) ;
set glmfitcmd = ( cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH_test.glmdir --surf fsaverage lh --C IPS_2groups.mat --cortex )
echo $glmfitcmd
echo cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH_test.glmdir --surf fsaverage lh --C IPS_2groups.mat --cortex
cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH_test.glmdir --surf fsaverage lh --C IPS_2groups.mat --cortex
set gd2mtx = dods
set gd2mtx = dods
set UseTable = 0 ;
set UseTable = 0
set label = ( ) ;
set label = ( )
while ( $#glmfitcmd )
while ( 14 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = cmdline
shift glmfitcmd

switch ( $flag )
switch ( cmdline )
case "mri_glmfit"
case mri_glmfit
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
case "--save-eres"
case --save-eres
case "--eres-save"
case --eres-save
case "--save-fwhm-map"
case --save-fwhm-map
case "--mgz"
case --mgz
case "--mgh"
case --mgh
case "--nii"
case --nii
case "--nii.gz"
case --nii.gz
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 13 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = mri_glmfit
shift glmfitcmd

switch ( $flag )
switch ( mri_glmfit )
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
case "--save-eres"
case --save-eres
case "--eres-save"
case --eres-save
case "--save-fwhm-map"
case --save-fwhm-map
case "--mgz"
case --mgz
case "--mgh"
case --mgh
case "--nii"
case --nii
case "--nii.gz"
case --nii.gz
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 12 )
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 = IPS_2groups_n135_lh_thickness.10.mgh
set y = IPS_2groups_n135_lh_thickness.10.mgh
shift glmfitcmd ;
shift glmfitcmd
if ( $DoClusterMean ) then
if ( 1 ) then
if ( ! -e $y ) then
if ( ! -e IPS_2groups_n135_lh_thickness.10.mgh ) then
endif
endif
if ( "$flag" == "--table" ) set UseTable = 1 ;
if ( --y == --table ) set UseTable = 1
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 10 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --fsgd
shift glmfitcmd

switch ( $flag )
switch ( --fsgd )
shift glmfitcmd ;
shift glmfitcmd
if ( $#glmfitcmd > 0 ) then
if ( 8 > 0 ) then
if ( $glmfitcmd[1] == doss ) set gd2mtx = doss
if ( --glmdir == doss ) set gd2mtx = doss
endif
endif
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 8 )
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 ( 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 $glmfitcmd[1] | cut -c 1-2`
cut -c 1-2
echo --C
if ( "$c" != "--" ) then
if ( -- != -- ) then
endif
endif
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 3 )
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 ( 1 )
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
case "--save-eres"
case --save-eres
case "--eres-save"
case --eres-save
case "--save-fwhm-map"
case --save-fwhm-map
case "--mgz"
case --mgz
case "--mgh"
case --mgh
case "--nii"
case --nii
case "--nii.gz"
case --nii.gz
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 IPS_2groups_n135_Thickness_LH_test.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 /Applications/freesurfer/subjects/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 IPS_2groups_n135_Thickness_LH_test.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`
cat IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd
awk {if($1 == "Contrast") print 1}
wc -l
endif
endif
if ( $#tmpdir == 0 ) set tmpdir = $glmdir/tmp.mri_glmfit-sim-$$
if ( 0 == 0 ) set tmpdir = IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951
set tmpdir = IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951
mkdir -p $tmpdir
mkdir -p IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951
set clist = ( $glmdir/*/C.dat )
set clist = ( IPS_2groups_n135_Thickness_LH_test.glmdir/*/C.dat )
if ( $status ) then
if ( 0 ) then
set clist2 = ( ) ;
set clist2 = ( )
set conlist = ( ) ;
set conlist = ( )
foreach c ( $clist )
foreach c ( IPS_2groups_n135_Thickness_LH_test.glmdir/IPS_2groups/C.dat )
set tmp = `dirname $c`
set tmp = `dirname $c`
dirname IPS_2groups_n135_Thickness_LH_test.glmdir/IPS_2groups/C.dat
set conname = `basename $tmp`
set conname = `basename $tmp`
basename IPS_2groups_n135_Thickness_LH_test.glmdir/IPS_2groups
set conlist = ( $conlist $conname ) ;
set conlist = ( IPS_2groups )
set confile = $tmpdir/$conname.mtx
set confile = IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx
cp $c $confile
cp IPS_2groups_n135_Thickness_LH_test.glmdir/IPS_2groups/C.dat IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx

if ( $FSGDhasCon == 0 ) set clist2 = ( $clist2 --C $confile ) ;
if ( 0 == 0 ) set clist2 = ( --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx )
set clist2 = ( --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx )


set sig = `stem2fname $glmdir/$conname/sig`
set sig = `stem2fname $glmdir/$conname/sig`
stem2fname IPS_2groups_n135_Thickness_LH_test.glmdir/IPS_2groups/sig
if ( $status ) then
if ( 0 ) then


if ( $DoSim ) then
if ( 1 ) then
ls $glmdir/csd/$csdbase.j???-$conname.csd > & /dev/null
set csdexists = ( ! $status )
set csdexists = ( ! 1 )
if ( $csdexists ) then
if ( ! 1 ) then
endif
endif
end
end

set StartDate = `date`
set StartDate = `date`
date


if ( $#LF == 0 ) then
if ( 0 == 0 ) then
if ( $UseCache == 0 ) then
if ( 0 == 0 ) then
set LF = $glmdir/$csdbase.mri_glmfit-sim.log
set LF = IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
else
else
rm -f $LF
rm -f IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
endif
endif
echo "log file is $LF"
echo log file is IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
log file is IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log

echo "" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo 

echo "cd `pwd`" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo cd `pwd`
pwd
cd /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135
echo $0 | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo /Applications/freesurfer/bin/mri_glmfit-sim
/Applications/freesurfer/bin/mri_glmfit-sim
echo $inputargs | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo --debug --glmdir IPS_2groups_n135_Thickness_LH_test.glmdir --sim mc-z 5000 1.302 lh_mc-z.abs_5000p1.3 --sim-sign abs --overwrite --cwpvalthresh 0.25
--debug --glmdir IPS_2groups_n135_Thickness_LH_test.glmdir --sim mc-z 5000 1.302 lh_mc-z.abs_5000p1.3 --sim-sign abs --overwrite --cwpvalthresh 0.25
echo "" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo 

echo $VERSION | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo FreeSurferEnv.csh 7.1.1
FreeSurferEnv.csh 7.1.1
date | tee -a $LF
date
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
Mon Jun 28 07:34:24 CEST 2021
uname -a | tee -a $LF
uname -a
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
Darwin upddkp224.unibe.ch 19.6.0 Darwin Kernel Version 19.6.0: Thu May  6 00:48:39 PDT 2021; root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64
echo $user | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo jurgenhanggi
jurgenhanggi
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo setenv SUBJECTS_DIR /Applications/freesurfer/subjects
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
echo "FREESURFER_HOME $FREESURFER_HOME" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo FREESURFER_HOME /Applications/freesurfer
FREESURFER_HOME /Applications/freesurfer
echo "" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo 

echo "Original mri_glmfit command line:" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo Original mri_glmfit command line:
Original mri_glmfit command line:
echo $glmfitcmd0 | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH_test.glmdir --surf fsaverage lh --C IPS_2groups.mat --cortex
cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH_test.glmdir --surf fsaverage lh --C IPS_2groups.mat --cortex
echo "" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo 

echo "DoSim = $DoSim" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo DoSim = 1
DoSim = 1
echo "UseCache = $UseCache" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo UseCache = 0
UseCache = 0
echo "DoPoll = $DoPoll" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo DoPoll = 0
DoPoll = 0
echo "DoPBSubmit = $DoPBSubmit" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo DoPBSubmit = 0
DoPBSubmit = 0
echo "DoBackground = $DoBackground" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo DoBackground = 0
DoBackground = 0
echo "DiagCluster = $DiagCluster" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo DiagCluster = 0
DiagCluster = 0
echo "gd2mtx = $gd2mtx" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo gd2mtx = dods
gd2mtx = dods
if ( $#Seed ) echo "Seed = $Seed" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
if ( 0 ) echo Seed = 
echo "fwhm = $fwhm" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo fwhm = 14.595954
fwhm = 14.595954
if ( $#fwhmOverride ) then
if ( 0 ) then

if ( $UseCache ) then
if ( 0 ) then

if ( $DoSim ) then
if ( 1 ) then

set fsgd = ( ) ;
set fsgd = ( )
set X = ( ) ;
set X = ( )
if ( -e $glmdir/y.fsgd ) then
if ( -e IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd ) then
set fsgd = $glmdir/y.fsgd
set fsgd = IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd
else
else


set nSimPerJob = `echo "$nsim/$nJobs" | bc` ;
set nSimPerJob = `echo "$nsim/$nJobs" | bc`
bc
echo 5000/1
echo "nSimPerJob = $nSimPerJob" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo nSimPerJob = 5000
nSimPerJob = 5000

if ( $DoPoll ) then
if ( 0 ) then



mkdir -p $glmdir/csd
mkdir -p IPS_2groups_n135_Thickness_LH_test.glmdir/csd
@ nthJob = 1
@ nthJob = 1
while ( $nthJob < = $nJobs )
while ( 1 < = 1 )
set jpad = `printf j%03d $nthJob`
set jpad = `printf j%03d $nthJob`
printf j%03d 1
echo "$nthJob/$nJobs `date`" | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo 1/1 `date`
date
1/1 Mon Jun 28 07:34:24 CEST 2021

set cmd = ( mri_glmfit $clist2 )
set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx )
set cmd = ( $cmd --sim $nulltype $nSimPerJob $thresh $glmdir/csd/$csdbase.$jpad )
set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 )
set cmd = ( $cmd --sim-sign $simsign --fwhm $fwhm )
set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 )
if ( $#fsgd ) set cmd = ( $cmd --fsgd $fsgd $gd2mtx )
if ( 1 ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods )
set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods )
if ( $#X ) set cmd = ( $cmd --X $X )
if ( 0 ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --X )
if ( $#wls ) set cmd = ( $cmd --wls $wls )
if ( 0 ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --wls )
if ( $#framemask ) set cmd = ( $cmd --frame-mask $framemask )
if ( 0 ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --frame-mask )

if ( ! $UseTable ) then
if ( ! 0 ) then
set cmd = ( $cmd --mask $mask )
set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh )
if ( $PermResid == 0 ) set cmd = ( $cmd --y $y )
if ( 1 == 0 ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y IPS_2groups_n135_lh_thickness.10.mgh )
if ( $PermResid == 1 ) set cmd = ( $cmd --y $residual )
if ( 1 == 1 ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y )
set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y )
if ( $PermSignFlip == 1 ) set cmd = ( $cmd --perm-1 )
if ( 0 == 1 ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-1 )
if ( $PermNonStatCor ) set cmd = ( $cmd --perm-nonstatcor )
if ( 0 ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-nonstatcor )
endif
endif
if ( $UseTable ) set cmd = ( $cmd --table $y )
if ( 0 ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --table IPS_2groups_n135_lh_thickness.10.mgh )

if ( $PermForce ) set cmd = ( $cmd --perm-force )
if ( 1 ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force )
set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force )
if ( $anattype == surface ) set cmd = ( $cmd --surf $subject $hemi $surf ) ;
if ( surface == surface ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white )
set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white )
if ( $#Seed ) set cmd = ( $cmd --seed $Seed ) ;
if ( 0 ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white --seed )
if ( $UseUniformPDF ) set cmd = ( $cmd --uniform $UniformPDFMin $UniformPDFMax ) ;
if ( 0 ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white --uniform )
if ( $DiagCluster ) set cmd = ( $cmd --diag-cluster --debug )
if ( 0 ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white --diag-cluster --debug )
if ( $?verbose ) set cmd = ( $cmd --debug )
if ( 1 ) set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white --debug )
set cmd = ( mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white --debug )
if ( $DoPoll ) then
if ( 0 ) then

echo $cmd | tee -a $LF
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
echo mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white --debug
mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white --debug
if ( ! $DoPoll ) then
if ( ! 0 ) then

$cmd | tee -a $LF
mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white --debug
tee -a IPS_2groups_n135_Thickness_LH_test.glmdir/lh_mc-z.abs_5000p1.3.mri_glmfit-sim.log
INFO: ignoring tag Creator 
INFO: ignoring tag SUBJECTS_DIR 
INFO: ignoring tag SynthSeed 
simbase IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001
FWHM = 14.595954
gdfRead(): reading IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd

WARNING: carriage returns have been detected in file IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd
Was it created on a Windows computer?
This may cause an error in reading the FSGD file.
If so, try running:
    cat IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd | sed 's/\r/\n/g' > new.IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd 
Then use new.IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd 

INFO: gd2mtx_method is dods
Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces    327680
Total area         65417.000000
AvgVtxArea       0.399269
AvgVtxDist       0.721953
StdVtxDist       0.195472
Surface smoothing by fwhm=14.595954, niters=157.000000

7.1.1
cwd /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135
cmdline mri_glmfit --C IPS_2groups_n135_Thickness_LH_test.glmdir/tmp.mri_glmfit-sim-7951/IPS_2groups.mtx --sim mc-z 5000 1.302 IPS_2groups_n135_Thickness_LH_test.glmdir/csd/lh_mc-z.abs_5000p1.3.j001 --sim-sign abs --fwhm 14.595954 --fsgd IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white --debug 
sysname  Darwin
hostname upddkp224.unibe.ch
machine  x86_64
user     jurgenhanggi
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
fwhm     14.595954
niters    157.000000
OneSampleGroupMean 0
y    /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
logyflag 0
usedti  0
FSGD IPS_2groups_n135_Thickness_LH_test.glmdir/y.fsgd
mask IPS_2groups_n135_Thickness_LH_test.glmdir/mask.mgh
maskinv 0
glmdir (null)
IllCondOK 0
ReScaleX 1
DoFFx 0
Loading y from /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
error: mri_read(): couldn't determine type of file /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
   ... done reading.
ERROR: loading y /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
if ( $status && ! $DiagCluster ) exit 1 ;
if ( 1 && ! 0 ) exit 1
exit 1
[upddkp224:average_IPS_FS7_Linux/stats/glm_group_n135] jurgenhanggi%