Is this for a volume analysis? If so, then you'll need to use the --grf option instead of using the mcz simulations (those are just for surface)
On 07/08/2017 01:03 PM, Aly Negreira wrote:
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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