(base) vinicius@vinicius-virtual-machine:~/fsteste$ mri_glmfit-sim --debug --glmdir lh.thickness.example.10.glmd --cache 1.3 pos --cwp 0.05 --2spaces 

set echo = 1 ;

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 8 != 0 )



set flag = $argv[1] ; shift ;

set flag = --glmdir

shift



switch ( $flag )

switch ( --glmdir )

if ( $#argv < 0 ) goto arg1err ;

if ( 7 < 0 ) goto arg1err

set glmdir = $argv[1] ; shift ;

set glmdir = lh.thickness.example.10.glmd

shift

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 6 != 0 )



set flag = $argv[1] ; shift ;

set flag = --cache

shift



switch ( $flag )

switch ( --cache )

if ( $#argv < 2 ) goto arg2err ;

if ( 5 < 2 ) goto arg2err

set thresh = $argv[1] ; shift ;

set thresh = 1.3

shift

set simsign = $argv[1] ; shift ;

set simsign = pos

shift

set UseCache = 1 ;

set UseCache = 1

set DoSim = 0 ;

set DoSim = 0

set thresh = `printf %2.1f $thresh`

set thresh = `printf %2.1f $thresh`

printf %2.1f 1.3

if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 3.0 && $thresh != 3.3 && $thresh != 4.0 ) then

if ( 1.3 != 1.3 && 1.3 != 2.0 && 1.3 != 2.3 && 1.3 != 3.0 && 1.3 != 3.3 && 1.3 != 4.0 ) then

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 3 != 0 )



set flag = $argv[1] ; shift ;

set flag = --cwp

shift



switch ( $flag )

switch ( --cwp )

if ( $#argv < 1 ) goto arg1err ;

if ( 2 < 1 ) goto arg1err

set cwpvalthresh = $argv[1] ; shift ;

set cwpvalthresh = 0.05

shift

breaksw

breaksw



end

end

while ( $#argv != 0 )

while ( 1 != 0 )



set flag = $argv[1] ; shift ;

set flag = --2spaces

shift



switch ( $flag )

switch ( --2spaces )

set Bonferroni = 2 ;

set Bonferroni = 2

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 ( 0 ) then

set residual = ( )

set residual = ( )

if ( $nulltype == perm && $PermResid ) then

if ( == 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 && 0 == 0 ) then



if ( $PermNonStatCor ) then

if ( 0 ) then



goto check_params_return ;

goto check_params_return



if ( ! -e $glmdir ) then

if ( ! -e lh.thickness.example.10.glmd ) then



set glmfitlog = $glmdir/mri_glmfit.log

set glmfitlog = lh.thickness.example.10.glmd/mri_glmfit.log

if ( ! -e $glmfitlog ) then

if ( ! -e lh.thickness.example.10.glmd/mri_glmfit.log ) then



if ( $nulltype != perm ) then

if ( != perm ) then

set fwhmfile = $glmdir/fwhm.dat

set fwhmfile = lh.thickness.example.10.glmd/fwhm.dat

if ( ! -e $fwhmfile ) then

if ( ! -e lh.thickness.example.10.glmd/fwhm.dat ) then



set fwhm = `cat $fwhmfile` ;

set fwhm = `cat $fwhmfile`

cat lh.thickness.example.10.glmd/fwhm.dat

else

else



set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`

awk {if($1 == "cwd") print $2}

cat lh.thickness.example.10.glmd/mri_glmfit.log

if ( 0 && ! -e $glmfitcwd ) then

if ( 0 && ! -e /home/vinicius/fsteste ) 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}'`

awk {if($1 == "cwd") print $2}

cat lh.thickness.example.10.glmd/mri_glmfit.log





set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`

set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`

awk {if($1 == "cmdline") print $0}

cat lh.thickness.example.10.glmd/mri_glmfit.log

set glmfitcmd = ( $glmfitcmd0 ) ;

set glmfitcmd = ( cmdline mri_glmfit --debug --y lh.thickness.example.10.mgh --fsgd /home/vinicius/fsteste/example.fsgd --C /home/vinicius/fsteste/Contrasts/CONTROLE-PK.mtx --C /home/vinicius/fsteste/Contrasts/PK-CONTROLE.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.example.10.glmd )

echo $glmfitcmd

echo cmdline mri_glmfit --debug --y lh.thickness.example.10.mgh --fsgd /home/vinicius/fsteste/example.fsgd --C /home/vinicius/fsteste/Contrasts/CONTROLE-PK.mtx --C /home/vinicius/fsteste/Contrasts/PK-CONTROLE.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.example.10.glmd

cmdline mri_glmfit --debug --y lh.thickness.example.10.mgh --fsgd /home/vinicius/fsteste/example.fsgd --C /home/vinicius/fsteste/Contrasts/CONTROLE-PK.mtx --C /home/vinicius/fsteste/Contrasts/PK-CONTROLE.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.example.10.glmd

set gd2mtx = dods

set gd2mtx = dods

set UseTable = 0 ;

set UseTable = 0

set label = ( ) ;

set label = ( )

while ( $#glmfitcmd )

while ( 17 )

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 ( 16 )

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 ( 15 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = --debug

shift glmfitcmd



switch ( $flag )

switch ( --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 ( 14 )

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.thickness.example.10.mgh

set y = lh.thickness.example.10.mgh

shift glmfitcmd ;

shift glmfitcmd

if ( $DoClusterMean ) then

if ( 1 ) then

if ( ! -e $y ) then

if ( ! -e lh.thickness.example.10.mgh ) then

endif

endif

if ( "$flag" == "--table" ) set UseTable = 1 ;

if ( --y == --table ) set UseTable = 1

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 12 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = --fsgd

shift glmfitcmd



switch ( $flag )

switch ( --fsgd )

shift glmfitcmd ;

shift glmfitcmd

if ( $#glmfitcmd > 0 ) then

if ( 10 > 0 ) then

if ( $glmfitcmd[1] == doss ) set gd2mtx = doss

if ( --C == doss ) set gd2mtx = doss

endif

endif

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

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 ( 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.thickness.example.10.glmd/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 /home/vinicius/fsteste/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.thickness.example.10.glmd/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 lh.thickness.example.10.glmd/y.fsgd

wc -l

awk {if($1 == "Contrast") print 1}

endif

endif

if ( $#tmpdir == 0 ) set tmpdir = $glmdir/tmp.mri_glmfit-sim-$$

if ( 0 == 0 ) set tmpdir = lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727

set tmpdir = lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727

mkdir -p $tmpdir

mkdir -p lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727

set clist = ( $glmdir/*/C.dat )

set clist = ( lh.thickness.example.10.glmd/*/C.dat )

if ( $status ) then

if ( 0 ) then

set clist2 = ( ) ;

set clist2 = ( )

set conlist = ( ) ;

set conlist = ( )

foreach c ( $clist )

foreach c ( lh.thickness.example.10.glmd/CONTROLE-PK/C.dat lh.thickness.example.10.glmd/PK-CONTROLE/C.dat )

set tmp = `dirname $c`

set tmp = `dirname $c`

dirname lh.thickness.example.10.glmd/CONTROLE-PK/C.dat

set conname = `basename $tmp`

set conname = `basename $tmp`

basename lh.thickness.example.10.glmd/CONTROLE-PK

set conlist = ( $conlist $conname ) ;

set conlist = ( CONTROLE-PK )

set confile = $tmpdir/$conname.mtx

set confile = lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727/CONTROLE-PK.mtx

cp $c $confile

cp lh.thickness.example.10.glmd/CONTROLE-PK/C.dat lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727/CONTROLE-PK.mtx



if ( $FSGDhasCon == 0 ) set clist2 = ( $clist2 --C $confile ) ;

if ( 0 == 0 ) set clist2 = ( --C lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727/CONTROLE-PK.mtx )

set clist2 = ( --C lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727/CONTROLE-PK.mtx )





set sig = `stem2fname $glmdir/$conname/sig`

set sig = `stem2fname $glmdir/$conname/sig`

stem2fname lh.thickness.example.10.glmd/CONTROLE-PK/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.thickness.example.10.glmd/PK-CONTROLE/C.dat

set conname = `basename $tmp`

set conname = `basename $tmp`

basename lh.thickness.example.10.glmd/PK-CONTROLE

set conlist = ( $conlist $conname ) ;

set conlist = ( CONTROLE-PK PK-CONTROLE )

set confile = $tmpdir/$conname.mtx

set confile = lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727/PK-CONTROLE.mtx

cp $c $confile

cp lh.thickness.example.10.glmd/PK-CONTROLE/C.dat lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727/PK-CONTROLE.mtx



if ( $FSGDhasCon == 0 ) set clist2 = ( $clist2 --C $confile ) ;

if ( 0 == 0 ) set clist2 = ( --C lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727/CONTROLE-PK.mtx --C lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727/PK-CONTROLE.mtx )

set clist2 = ( --C lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727/CONTROLE-PK.mtx --C lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727/PK-CONTROLE.mtx )





set sig = `stem2fname $glmdir/$conname/sig`

set sig = `stem2fname $glmdir/$conname/sig`

stem2fname lh.thickness.example.10.glmd/PK-CONTROLE/sig

if ( $status ) then

if ( 0 ) then





if ( $DoSim ) then

if ( 0 ) then

end

end



set StartDate = `date`

set StartDate = `date`

date





if ( $#LF == 0 ) then

if ( 0 == 0 ) then

if ( $UseCache == 0 ) then

if ( 1 == 0 ) then



set LF = $glmdir/cache.mri_glmfit-sim.log

set LF = lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

endif

endif

rm -f $LF

rm -f lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

endif

endif

echo "log file is $LF"

echo log file is lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

log file is lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log



echo "" | tee -a $LF

echo 

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log



echo "cd `pwd`" | tee -a $LF

echo cd `pwd`

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

pwd

cd /home/vinicius/fsteste

echo $0 | tee -a $LF

echo /usr/local/freesurfer/bin/mri_glmfit-sim

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

/usr/local/freesurfer/bin/mri_glmfit-sim

echo $inputargs | tee -a $LF

echo --debug --glmdir lh.thickness.example.10.glmd --cache 1.3 pos --cwp 0.05 --2spaces

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

--debug --glmdir lh.thickness.example.10.glmd --cache 1.3 pos --cwp 0.05 --2spaces

echo "" | tee -a $LF

echo 

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log



echo $VERSION | tee -a $LF

echo mri_glmfit-sim 7.1.0

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

mri_glmfit-sim 7.1.0

date | tee -a $LF

date

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

seg ago 24 21:29:28 -03 2020

uname -a | tee -a $LF

uname -a

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

Linux vinicius-virtual-machine 5.4.0-42-generic #46~18.04.1-Ubuntu SMP Fri Jul 10 07:21:24 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

echo $user | tee -a $LF

echo vinicius

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

vinicius

echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF

echo setenv SUBJECTS_DIR /home/vinicius/fsteste

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

setenv SUBJECTS_DIR /home/vinicius/fsteste

echo "FREESURFER_HOME $FREESURFER_HOME" | tee -a $LF

echo FREESURFER_HOME /usr/local/freesurfer

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

FREESURFER_HOME /usr/local/freesurfer

echo "" | tee -a $LF

echo 

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log



echo "Original mri_glmfit command line:" | tee -a $LF

echo Original mri_glmfit command line:

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

Original mri_glmfit command line:

echo $glmfitcmd0 | tee -a $LF

echo cmdline mri_glmfit --debug --y lh.thickness.example.10.mgh --fsgd /home/vinicius/fsteste/example.fsgd --C /home/vinicius/fsteste/Contrasts/CONTROLE-PK.mtx --C /home/vinicius/fsteste/Contrasts/PK-CONTROLE.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.example.10.glmd

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

cmdline mri_glmfit --debug --y lh.thickness.example.10.mgh --fsgd /home/vinicius/fsteste/example.fsgd --C /home/vinicius/fsteste/Contrasts/CONTROLE-PK.mtx --C /home/vinicius/fsteste/Contrasts/PK-CONTROLE.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.example.10.glmd

echo "" | tee -a $LF

echo 

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log



echo "DoSim = $DoSim" | tee -a $LF

echo DoSim = 0

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

DoSim = 0

echo "UseCache = $UseCache" | tee -a $LF

echo UseCache = 1

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

UseCache = 1

echo "DoPoll = $DoPoll" | tee -a $LF

echo DoPoll = 0

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

DoPoll = 0

echo "DoPBSubmit = $DoPBSubmit" | tee -a $LF

echo DoPBSubmit = 0

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

DoPBSubmit = 0

echo "DoBackground = $DoBackground" | tee -a $LF

echo DoBackground = 0

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

DoBackground = 0

echo "DiagCluster = $DiagCluster" | tee -a $LF

echo DiagCluster = 0

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

DiagCluster = 0

echo "gd2mtx = $gd2mtx" | tee -a $LF

echo gd2mtx = dods

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

gd2mtx = dods

if ( $#Seed ) echo "Seed = $Seed" | tee -a $LF

if ( 0 ) echo Seed = 

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

echo "fwhm = $fwhm" | tee -a $LF

echo fwhm = 11.273509

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

fwhm = 11.273509

if ( $#fwhmOverride ) then

if ( 0 ) then



if ( $UseCache ) then

if ( 1 ) then



set fwhmStr = `perl -e "printf('"'%02d'"',int ( $fwhm+0.5+$fwhmAdd ) ) "`

set fwhmStr = `perl -e "printf('"'%02d'"',int ( $fwhm+0.5+$fwhmAdd ) ) "`

perl -e printf('%02d',int ( 11.273509+0.5+0 ) ) 

if ( $fwhmStr == 00 ) set fwhmStr = 01 ;

if ( 11 == 00 ) set fwhmStr = 01

set threshStr = `perl -e "print 10*$thresh"` ;

set threshStr = `perl -e "print 10*$thresh"`

perl -e print 10*1.3

set csdCache = $CacheDir/$subject/$hemi/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd

set csdCache = /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd

if ( ! -e $csdCache ) then

if ( ! -e /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd ) then

echo CSD $csdCache | tee -a $LF

echo CSD /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

CSD /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd

if ( $#csdbase == 0 ) set csdbase = cache.th$threshStr.$simsign

if ( 0 == 0 ) set csdbase = cache.th13.pos

set csdbase = cache.th13.pos

endif

endif



if ( $DoSim ) then

if ( 0 ) then



if ( $DoPBSubmit ) then

if ( 0 ) then





foreach conname ( $conlist )

foreach conname ( CONTROLE-PK PK-CONTROLE )

if ( $UseTable ) continue ;

if ( 0 ) continue



set csdlist = ( ) ;

set csdlist = ( )

if ( ! $UseGRF ) then

if ( ! 0 ) then

if ( $UseCache ) then

if ( 1 ) then

set csdfiles = ( $csdCache )

set csdfiles = ( /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd )

else

else



set csdlist = ( ) ;

set csdlist = ( )

foreach csd ( $csdfiles )

foreach csd ( /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd )

set csdlist = ( $csdlist --csd $csd ) ;

set csdlist = ( --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd )

end

end

endif

endif



set sig = `stem2fname $glmdir/$conname/sig`

set sig = `stem2fname $glmdir/$conname/sig`

stem2fname lh.thickness.example.10.glmd/CONTROLE-PK/sig

set ext = `fname2ext $sig`

set ext = `fname2ext $sig`

fname2ext lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh

set vwsig = $glmdir/$conname/$csdbase.sig.voxel.$ext

set vwsig = lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.mgh

set vwsigmax = $glmdir/$conname/$csdbase.sig.voxel.max.dat

set vwsigmax = lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.max.dat

set cwsig = $glmdir/$conname/$csdbase.sig.cluster.$ext

set cwsig = lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh

set msig = $glmdir/$conname/$csdbase.sig.masked.$ext

set msig = lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh

set ocn = $glmdir/$conname/$csdbase.sig.ocn.$ext

set ocn = lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh

set oannot = $glmdir/$conname/$csdbase.sig.ocn.annot

set oannot = lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.annot

set sum = $glmdir/$conname/$csdbase.sig.cluster.summary

set sum = lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary

set csdpdf = $glmdir/$conname/$csdbase.pdf.dat

set csdpdf = lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.pdf.dat



if ( $anattype == surface ) then

if ( surface == surface ) then

set cmd = ( mri_surfcluster --in $sig --mask $mask --cwsig $cwsig --sum $sum --ocn $ocn --annot $annot --cwpvalthresh $cwpvalthresh --o $msig --no-fixmni )

set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni )

set cmd = ( $cmd --csd-out $glmdir/csd/all.$csdbase-$conname.csd )

set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd )

if ( ! $UseGRF ) set cmd = ( $cmd $csdlist --csdpdf $csdpdf --vwsig $vwsig --vwsigmax $vwsigmax )

if ( ! 0 ) set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.max.dat )

set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.max.dat )

if ( $UseGRF ) set cmd = ( $cmd --fwhm $fwhm --hemi $hemi --subject $subject --thmin $thresh --sign $simsign )

if ( 0 ) set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.max.dat --fwhm 11.273509 --hemi lh --subject fsaverage --thmin 1.3 --sign pos )

if ( $PermNonStatCor ) set cmd = ( $cmd --fwhm-map $fwhmmap )

if ( 0 ) set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.max.dat --fwhm-map )

if ( $OutputAnnot ) set cmd = ( $cmd --oannot $oannot )

if ( 1 ) set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.annot )

set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.annot )

if ( $Bonferroni ) set cmd = ( $cmd --bonferroni $Bonferroni )

if ( 2 ) set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.annot --bonferroni 2 )

set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.annot --bonferroni 2 )

if ( $ReportCentroid ) set cmd = ( $cmd --centroid ) ;

if ( 0 ) set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.annot --bonferroni 2 --centroid )

set cmd = ( $cmd --surf $surf ) ;

set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.annot --bonferroni 2 --surf white )

echo $cmd | tee -a $LF

echo mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.annot --bonferroni 2 --surf white

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.annot --bonferroni 2 --surf white

$cmd | tee -a $LF

mri_surfcluster --in lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.annot --bonferroni 2 --surf white

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

Merging CSD files

ERROR: could not open lh.thickness.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd

Creating CDFs from CSD files

csd->threshsign = 1

thsign = pos, id = 1

version 7.1.0

hemi           = lh

srcid          = lh.thickness.example.10.glmd/CONTROLE-PK/sig.mgh 

srcsubjid      = fsaverage

srcsurf        = white

srcframe       = 0

thsign         = pos

thmin          = 1.3

thmax          = -1

fdr            = -1

minarea        = 0

Bonferroni      = 2

xfmfile        = talairach.xfm

nth         = -1

outid    = lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh MGH

ocnid    = lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh MGH

sumfile  = lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.summary

subjectsdir    = /home/vinicius/fsteste

FixMNI = 0

Found 148642 vertices in mask

Found 148642 vertices in mask

Found 148642 points in clabel.

------------- XFM matrix (RAS2RAS) ---------------

/home/vinicius/fsteste/fsaverage/mri/transforms/talairach.xfm

 1.00000   0.00000   0.00000   0.00000;

 0.00000   1.00000   0.00000   0.00000;

 0.00000   0.00000   1.00000   0.00000;

 0.00000   0.00000   0.00000   1.00000;

----------------------------------------------------

Reading source surface /home/vinicius/fsteste/fsaverage/surf/lh.white

Done reading source surface

Reading annotation /home/vinicius/fsteste/fsaverage/label/lh.aparc.annot

mri_surfcluster supposed to be reproducible but seed not set

reading colortable from annotation file...

colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

Computing metric properties

Loading source values

number of voxels in search space = 148642

Done loading source values (nvtxs = 163842)

overall max = 5.35589 at vertex 45910

overall min = -6.07087 at vertex 83640

surface nvertices 163842

metric props tot surface area 65417.000000

group_avg_vtxarea_loaded 1

masked surface area 75912.656250

Computing voxel-wise significance

CSDpvalMaxSigMap(): found 460/163842 above 0, max=1.01439

Adjusting threshold for 1-tailed test.

If the input is not a -log10(p) volume, re-run with --no-adjust.

thminadj = 0.99897

Searching for Clusters ...

thmin=1.300000 (0.998970), thmax=-1.000000 (-1), thsignid=1, minarea=0.000000

Found 51 clusters

Max cluster size 284.708252

Pruning by CW P-Value 0.05

Saving thresholded output to  lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.masked.mgh

Saving cluster numbers to lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh

Saving cluster pval lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh

Constructing output annotation

Writing annotation lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.annot

if ( $status ) exit 1 ;

if ( 0 ) exit 1

if ( $DoClusterMean ) then

if ( 1 ) then



set avgwf = $glmdir/$conname/$csdbase.y.ocn.dat

set avgwf = lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.y.ocn.dat

set cmd = ( mri_segstats --seg $ocn --exclude 0 --i $y --avgwf $avgwf --sum /tmp/mri_glmfit-sim.junk.$$ )

set cmd = ( mri_segstats --seg lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --exclude 0 --i lh.thickness.example.10.mgh --avgwf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.15727 )

echo $cmd | tee -a $LF

echo mri_segstats --seg lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --exclude 0 --i lh.thickness.example.10.mgh --avgwf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.15727

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

mri_segstats --seg lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --exclude 0 --i lh.thickness.example.10.mgh --avgwf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.15727

$cmd | tee -a $LF

mri_segstats --seg lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --exclude 0 --i lh.thickness.example.10.mgh --avgwf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.15727

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log



7.1.0

cwd 

cmdline mri_segstats --seg lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh --exclude 0 --i lh.thickness.example.10.mgh --avgwf lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.15727 

sysname  Linux

hostname vinicius-virtual-machine

machine  x86_64

user     vinicius

whitesurfname  white

UseRobust  0

Loading lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.ocn.mgh

Loading lh.thickness.example.10.mgh

Voxel Volume is 1 mm^3

Generating list of segmentation ids

Found   1 segmentations

Computing statistics for each segmentation



Reporting on   0 segmentations

Using PrintSegStat

Computing spatial average of each frame



Writing to lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.y.ocn.dat

mri_segstats done

if ( $status ) exit 1 ;

if ( 0 ) exit 1

rm -f /tmp/mri_glmfit-sim.junk.$$

rm -f /tmp/mri_glmfit-sim.junk.15727

endif

endif

endif

endif



if ( $anattype == volume ) then

if ( surface == volume ) then





set cmd = ( mri_convert $cwsig $cwsig --frame 0 )

set cmd = ( mri_convert lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --frame 0 )

echo $cmd | tee -a $LF

echo mri_convert lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --frame 0

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

mri_convert lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --frame 0

$cmd | tee -a $LF

mri_convert lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --frame 0

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

mri_convert lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh --frame 0 

reading from lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

keeping frame 0

writing to lh.thickness.example.10.glmd/CONTROLE-PK/cache.th13.pos.sig.cluster.mgh...

if ( $status ) exit 1 ;

if ( 0 ) exit 1



end

end

if ( $UseTable ) continue ;

if ( 0 ) continue



set csdlist = ( ) ;

set csdlist = ( )

if ( ! $UseGRF ) then

if ( ! 0 ) then

if ( $UseCache ) then

if ( 1 ) then

set csdfiles = ( $csdCache )

set csdfiles = ( /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd )

else

else



set csdlist = ( ) ;

set csdlist = ( )

foreach csd ( $csdfiles )

foreach csd ( /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd )

set csdlist = ( $csdlist --csd $csd ) ;

set csdlist = ( --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd )

end

end

endif

endif



set sig = `stem2fname $glmdir/$conname/sig`

set sig = `stem2fname $glmdir/$conname/sig`

stem2fname lh.thickness.example.10.glmd/PK-CONTROLE/sig

set ext = `fname2ext $sig`

set ext = `fname2ext $sig`

fname2ext lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh

set vwsig = $glmdir/$conname/$csdbase.sig.voxel.$ext

set vwsig = lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.mgh

set vwsigmax = $glmdir/$conname/$csdbase.sig.voxel.max.dat

set vwsigmax = lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.max.dat

set cwsig = $glmdir/$conname/$csdbase.sig.cluster.$ext

set cwsig = lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh

set msig = $glmdir/$conname/$csdbase.sig.masked.$ext

set msig = lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh

set ocn = $glmdir/$conname/$csdbase.sig.ocn.$ext

set ocn = lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh

set oannot = $glmdir/$conname/$csdbase.sig.ocn.annot

set oannot = lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.annot

set sum = $glmdir/$conname/$csdbase.sig.cluster.summary

set sum = lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary

set csdpdf = $glmdir/$conname/$csdbase.pdf.dat

set csdpdf = lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.pdf.dat



if ( $anattype == surface ) then

if ( surface == surface ) then

set cmd = ( mri_surfcluster --in $sig --mask $mask --cwsig $cwsig --sum $sum --ocn $ocn --annot $annot --cwpvalthresh $cwpvalthresh --o $msig --no-fixmni )

set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni )

set cmd = ( $cmd --csd-out $glmdir/csd/all.$csdbase-$conname.csd )

set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd )

if ( ! $UseGRF ) set cmd = ( $cmd $csdlist --csdpdf $csdpdf --vwsig $vwsig --vwsigmax $vwsigmax )

if ( ! 0 ) set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.max.dat )

set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.max.dat )

if ( $UseGRF ) set cmd = ( $cmd --fwhm $fwhm --hemi $hemi --subject $subject --thmin $thresh --sign $simsign )

if ( 0 ) set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.max.dat --fwhm 11.273509 --hemi lh --subject fsaverage --thmin 1.3 --sign pos )

if ( $PermNonStatCor ) set cmd = ( $cmd --fwhm-map $fwhmmap )

if ( 0 ) set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.max.dat --fwhm-map )

if ( $OutputAnnot ) set cmd = ( $cmd --oannot $oannot )

if ( 1 ) set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.annot )

set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.annot )

if ( $Bonferroni ) set cmd = ( $cmd --bonferroni $Bonferroni )

if ( 2 ) set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.annot --bonferroni 2 )

set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.annot --bonferroni 2 )

if ( $ReportCentroid ) set cmd = ( $cmd --centroid ) ;

if ( 0 ) set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.annot --bonferroni 2 --centroid )

set cmd = ( $cmd --surf $surf ) ;

set cmd = ( mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.annot --bonferroni 2 --surf white )

echo $cmd | tee -a $LF

echo mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.annot --bonferroni 2 --surf white

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.annot --bonferroni 2 --surf white

$cmd | tee -a $LF

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

mri_surfcluster --in lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh --mask lh.thickness.example.10.glmd/mask.mgh --cwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --sum lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary --ocn lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh --no-fixmni --csd-out lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm11/pos/th13/mc-z.csd --csdpdf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.pdf.dat --vwsig lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.mgh --vwsigmax lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.voxel.max.dat --oannot lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.annot --bonferroni 2 --surf white

Merging CSD files

ERROR: could not open lh.thickness.example.10.glmd/csd/all.cache.th13.pos-PK-CONTROLE.csd

Creating CDFs from CSD files

csd->threshsign = 1

thsign = pos, id = 1

version 7.1.0

hemi           = lh

srcid          = lh.thickness.example.10.glmd/PK-CONTROLE/sig.mgh 

srcsubjid      = fsaverage

srcsurf        = white

srcframe       = 0

thsign         = pos

thmin          = 1.3

thmax          = -1

fdr            = -1

minarea        = 0

Bonferroni      = 2

xfmfile        = talairach.xfm

nth         = -1

outid    = lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh MGH

ocnid    = lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh MGH

sumfile  = lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.summary

subjectsdir    = /home/vinicius/fsteste

FixMNI = 0

Found 148642 vertices in mask

Found 148642 vertices in mask

Found 148642 points in clabel.

------------- XFM matrix (RAS2RAS) ---------------

/home/vinicius/fsteste/fsaverage/mri/transforms/talairach.xfm

 1.00000   0.00000   0.00000   0.00000;

 0.00000   1.00000   0.00000   0.00000;

 0.00000   0.00000   1.00000   0.00000;

 0.00000   0.00000   0.00000   1.00000;

----------------------------------------------------

Reading source surface /home/vinicius/fsteste/fsaverage/surf/lh.white

Done reading source surface

Reading annotation /home/vinicius/fsteste/fsaverage/label/lh.aparc.annot

mri_surfcluster supposed to be reproducible but seed not set

reading colortable from annotation file...

colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

Computing metric properties

Loading source values

number of voxels in search space = 148642

Done loading source values (nvtxs = 163842)

overall max = 6.07087 at vertex 83640

overall min = -5.35589 at vertex 45910

surface nvertices 163842

metric props tot surface area 65417.000000

group_avg_vtxarea_loaded 1

masked surface area 75912.656250

Computing voxel-wise significance

CSDpvalMaxSigMap(): found 544/163842 above 0, max=1.36725

Adjusting threshold for 1-tailed test.

If the input is not a -log10(p) volume, re-run with --no-adjust.

thminadj = 0.99897

Searching for Clusters ...

thmin=1.300000 (0.998970), thmax=-1.000000 (-1), thsignid=1, minarea=0.000000

Found 45 clusters

Max cluster size 333.310638

Pruning by CW P-Value 0.05

Saving thresholded output to  lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.masked.mgh

Saving cluster numbers to lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh

Saving cluster pval lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh

Constructing output annotation

Writing annotation lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.annot

if ( $status ) exit 1 ;

if ( 0 ) exit 1

if ( $DoClusterMean ) then

if ( 1 ) then



set avgwf = $glmdir/$conname/$csdbase.y.ocn.dat

set avgwf = lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.y.ocn.dat

set cmd = ( mri_segstats --seg $ocn --exclude 0 --i $y --avgwf $avgwf --sum /tmp/mri_glmfit-sim.junk.$$ )

set cmd = ( mri_segstats --seg lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --exclude 0 --i lh.thickness.example.10.mgh --avgwf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.15727 )

echo $cmd | tee -a $LF

echo mri_segstats --seg lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --exclude 0 --i lh.thickness.example.10.mgh --avgwf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.15727

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

mri_segstats --seg lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --exclude 0 --i lh.thickness.example.10.mgh --avgwf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.15727

$cmd | tee -a $LF

mri_segstats --seg lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --exclude 0 --i lh.thickness.example.10.mgh --avgwf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.15727

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log



7.1.0

cwd 

cmdline mri_segstats --seg lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh --exclude 0 --i lh.thickness.example.10.mgh --avgwf lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.15727 

sysname  Linux

hostname vinicius-virtual-machine

machine  x86_64

user     vinicius

whitesurfname  white

UseRobust  0

Loading lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.ocn.mgh

Loading lh.thickness.example.10.mgh

Voxel Volume is 1 mm^3

Generating list of segmentation ids

Found   1 segmentations

Computing statistics for each segmentation



Reporting on   0 segmentations

Using PrintSegStat

Computing spatial average of each frame



Writing to lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.y.ocn.dat

mri_segstats done

if ( $status ) exit 1 ;

if ( 0 ) exit 1

rm -f /tmp/mri_glmfit-sim.junk.$$

rm -f /tmp/mri_glmfit-sim.junk.15727

endif

endif

endif

endif



if ( $anattype == volume ) then

if ( surface == volume ) then





set cmd = ( mri_convert $cwsig $cwsig --frame 0 )

set cmd = ( mri_convert lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --frame 0 )

echo $cmd | tee -a $LF

echo mri_convert lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --frame 0

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

mri_convert lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --frame 0

$cmd | tee -a $LF

mri_convert lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --frame 0

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

mri_convert lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh --frame 0 

reading from lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

keeping frame 0

writing to lh.thickness.example.10.glmd/PK-CONTROLE/cache.th13.pos.sig.cluster.mgh...

if ( $status ) exit 1 ;

if ( 0 ) exit 1



end

end



if ( $CleanUp ) rm -r $tmpdir

if ( 1 ) rm -r lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727

rm -r lh.thickness.example.10.glmd/tmp.mri_glmfit-sim-15727



if ( $#AllDoneFile ) touch $AllDoneFile

if ( 0 ) touch



echo $StartDate | tee -a $LF

echo seg ago 24 21:29:28 -03 2020

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

seg ago 24 21:29:28 -03 2020

date | tee -a $LF

date

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

seg ago 24 21:29:31 -03 2020

echo "mri_glmfit-sim done" | tee -a $LF

echo mri_glmfit-sim done

tee -a lh.thickness.example.10.glmd/cache.mri_glmfit-sim.log

mri_glmfit-sim done



exit 0

exit 0