Re: [Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file

Sat, 08 Jul 2017 10:04:43 -0700 

Hi Doug!

Thank you for the reply! Re-ran w/ --debug as first option. Below is the
output. Not sure if this is helpful, but when I cd to
/Applications/freesurfer/average/mult-comp-cor/fsaverage
there are only directories for lh and rh, nothing for mni.

Thanks for the help!

Aly

 Alysons-iMac:~/analyses/EMOT_REG_FX_DISS] aneg% mri_glmfit-sim \  --debug \

  --glmdir
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
\

  --cache 1.3 abs \

  --cwp  0.05\

  --3spaces \?   --debug \

?   --glmdir
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
\

?   --cache 1.3 abs \

?   --cwp  0.05\

?   --3spaces \

?

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 =
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/

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 = abs

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 )

case "--cwpvalthresh":

case --cwpvalthresh:

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 = --3spaces

shift


switch ( $flag )

switch ( --3spaces )

set Bonferroni = 3 ;

set Bonferroni = 3

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


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


goto check_params_return ;

goto check_params_return


if ( ! -e $glmdir ) then

if ( ! -e
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
) then


set glmfitlog = $glmdir/mri_glmfit.log

set glmfitlog =
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log

if ( ! -e $glmfitlog ) then

if ( ! -e
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log
) then


set mask = `stem2fname $glmdir/mask`

set mask = `stem2fname $glmdir/mask`

stem2fname
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mask

if ( $status ) then

if ( 0 ) then


if ( $nulltype != perm ) then

if ( != perm ) then

set fwhmfile = $glmdir/fwhm.dat

set fwhmfile =
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat

if ( ! -e $fwhmfile ) then

if ( ! -e
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat
) then


set fwhm = `cat $fwhmfile` ;

set fwhm = `cat $fwhmfile`

cat
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//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
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log

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

if ( ! -e $glmfitcwd ) then

if ( ! -e /Users/aneg/analyses/EMOT_REG_FX_DISS ) then


set anattype = volume ;

set anattype = volume

set subject = ( ) ;

set subject = ( )

set hemi = ( ) ;

set hemi = ( )

set surf = "white" ;

set surf = white

set y = ( ) ;

set y = ( )

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
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//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
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log

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

set glmfitcmd = ( $glmfitcmd0 ) ;

set glmfitcmd = ( cmdline mri_glmfit --y
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz
--wls
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz
--osgm --glmdir
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
--nii.gz )

echo $glmfitcmd

echo cmdline mri_glmfit --y
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz
--wls
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz
--osgm --glmdir
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
--nii.gz

cmdline mri_glmfit --y
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz
--wls
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz
--osgm --glmdir
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
--nii.gz

set gd2mtx = dods

set gd2mtx = dods

set label = ( ) ;

set label = ( )

while ( $#glmfitcmd )

while ( 10 )

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

set flag = cmdline

shift glmfitcmd


switch ( $flag )

switch ( cmdline )

case "mri_glmfit"

case mri_glmfit

case "--osgm"

case --osgm

case "--prune"

case --prune

case "--no-prune"

case --no-prune

case "--pca"

case --pca

case "--synth"

case --synth

case "--allowsubjrep"

case --allowsubjrep

case "--illcond"

case --illcond

case "--debug"

case --debug

case "--synth"

case --synth

case "--cortex"

case --cortex

case "--kurtosis"

case --kurtosis

case "--nii"

case --nii

case "--nii.gz"

case --nii.gz

case "--rescale-x"

case --rescale-x

case "--no-rescale-x"

case --no-rescale-x

case "dods"

case dods

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 9 )

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

set flag = mri_glmfit

shift glmfitcmd


switch ( $flag )

switch ( mri_glmfit )

case "--osgm"

case --osgm

case "--prune"

case --prune

case "--no-prune"

case --no-prune

case "--pca"

case --pca

case "--synth"

case --synth

case "--allowsubjrep"

case --allowsubjrep

case "--illcond"

case --illcond

case "--debug"

case --debug

case "--synth"

case --synth

case "--cortex"

case --cortex

case "--kurtosis"

case --kurtosis

case "--nii"

case --nii

case "--nii.gz"

case --nii.gz

case "--rescale-x"

case --rescale-x

case "--no-rescale-x"

case --no-rescale-x

case "dods"

case dods

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 8 )

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

set flag = --y

shift glmfitcmd


switch ( $flag )

switch ( --y )

set y = $glmfitcwd/$glmfitcmd[1] ; shift glmfitcmd ;

set y =
/Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz

shift glmfitcmd

if ( ! -e $y ) then

if ( ! -e
/Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz
) then

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 6 )

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

set flag = --wls

shift glmfitcmd


switch ( $flag )

switch ( --wls )

set wls = $glmfitcwd/$glmfitcmd[1] ; shift glmfitcmd ;

set wls =
/Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz

shift glmfitcmd

if ( ! -e $wls ) then

if ( ! -e
/Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz
) then

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 4 )

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

set flag = --osgm

shift glmfitcmd


switch ( $flag )

switch ( --osgm )

case "--prune"

case --prune

case "--no-prune"

case --no-prune

case "--pca"

case --pca

case "--synth"

case --synth

case "--allowsubjrep"

case --allowsubjrep

case "--illcond"

case --illcond

case "--debug"

case --debug

case "--synth"

case --synth

case "--cortex"

case --cortex

case "--kurtosis"

case --kurtosis

case "--nii"

case --nii

case "--nii.gz"

case --nii.gz

case "--rescale-x"

case --rescale-x

case "--no-rescale-x"

case --no-rescale-x

case "dods"

case dods

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 3 )

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

shift glmfitcmd ;

shift glmfitcmd

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 1 )

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

set flag = --nii.gz

shift glmfitcmd


switch ( $flag )

switch ( --nii.gz )

case "--rescale-x"

case --rescale-x

case "--no-rescale-x"

case --no-rescale-x

case "dods"

case dods

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 0 )


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

if ( 0 && volume != volume ) then

if ( $UseGRF ) then

if ( 0 ) then


if ( $#subjectOverride ) set subject = $subjectOverride

if ( 0 ) set subject =



if ( $#subject != 0 ) then

if ( 0 != 0 ) then



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

if ( 0 == 0 ) set tmpdir =
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128

set tmpdir =
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128

mkdir -p $tmpdir

mkdir -p
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128

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

set clist = (
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//*/C.dat
)

if ( $status ) then

if ( 0 ) then

set clist2 = ( ) ;

set clist2 = ( )

set conlist = ( ) ;

set conlist = ( )

foreach c ( $clist )

foreach c (
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat
)

set tmp = `dirname $c`

set tmp = `dirname $c`

dirname
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat

set conname = `basename $tmp`

set conname = `basename $tmp`

basename
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm

set conlist = ( $conlist $conname ) ;

set conlist = ( osgm )

set confile = $tmpdir/$conname.mtx

set confile =
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx

cp $c $confile

cp
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx

set clist2 = ( $clist2 --C $confile ) ;

set clist2 = ( --C
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx
)



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

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

stem2fname
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/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 =
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

endif

endif

rm -f $LF

rm -f
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

endif

endif

echo "log file is $LF"

echo log file is
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

log file is
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log


echo "" | tee -a $LF

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo


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

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo cd `pwd`

pwd

cd /Users/aneg/analyses/EMOT_REG_FX_DISS

echo $0 | tee -a $LF

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo /Applications/freesurfer/bin/mri_glmfit-sim

/Applications/freesurfer/bin/mri_glmfit-sim

echo $inputargs | tee -a $LF

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo --debug --glmdir
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
--cache 1.3 abs --cwp 0.05 --3spaces

--debug --glmdir
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
--cache 1.3 abs --cwp 0.05 --3spaces

echo "" | tee -a $LF

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo


echo $VERSION | tee -a $LF

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $

date | tee -a $LF

date

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

Sat Jul  8 12:57:27 EDT 2017

uname -a | tee -a $LF

uname -a

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

Darwin Alysons-iMac.local 15.6.0 Darwin Kernel Version 15.6.0: Tue Apr 11
16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64

echo $user | tee -a $LF

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo aneg

aneg

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

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo setenv SUBJECTS_DIR /Users/aneg/analyses/EMOT_REG_RECON_DISS

setenv SUBJECTS_DIR /Users/aneg/analyses/EMOT_REG_RECON_DISS

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

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo FREESURFER_HOME /Applications/freesurfer

FREESURFER_HOME /Applications/freesurfer

echo "" | tee -a $LF

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo


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

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo Original mri_glmfit command line:

Original mri_glmfit command line:

echo $glmfitcmd0 | tee -a $LF

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo cmdline mri_glmfit --y
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz
--wls
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz
--osgm --glmdir
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
--nii.gz

cmdline mri_glmfit --y
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz
--wls
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz
--osgm --glmdir
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/
--nii.gz

echo "" | tee -a $LF

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo


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

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DoSim = 0

DoSim = 0

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

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo UseCache = 1

UseCache = 1

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

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DoPoll = 0

DoPoll = 0

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

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DoPBSubmit = 0

DoPBSubmit = 0

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

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DoBackground = 0

DoBackground = 0

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

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DiagCluster = 0

DiagCluster = 0

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

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo gd2mtx = dods

gd2mtx = dods

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

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

if ( 0 ) echo Seed =

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

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo fwhm = 9.625207

fwhm = 9.625207

if ( $#fwhmOverride ) then

if ( 0 ) then


if ( $UseCache ) then

if ( 1 ) then

set fwhm = `cat $glmdir/fwhm.dat` ;

set fwhm = `cat $glmdir/fwhm.dat`

cat
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat

set fwhmStr = `perl -e "printf('"'%02d'"',int ( $fwhm+.5 ) ) "`

set fwhmStr = `perl -e "printf('"'%02d'"',int ( $fwhm+.5 ) ) "`

perl -e printf('%02d',int ( 9.625207+.5 ) )

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 =
/Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd

if ( ! -e $csdCache ) then

if ( ! -e
/Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd
) then

echo "ERROR: cannot find $csdCache" | tee -a $LF

tee -a
GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo ERROR: cannot find
/Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd

ERROR: cannot find
/Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd

exit 1 ;

exit 1

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