External Email - Use Caution
Thanks Douglas, I've attached here the output from mri_glmfit-sim
--glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces
--debug
Could you clarify how to use permutation to correct for MC for LGI? (as
in what to enter for command line?). I don't quite understand from the
documentation.
Thanks very much,
Colleen
set echo = 1 ;
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
goto check_params_return ;
goto check_params_return
if ( ! -e $glmdir ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir ) then
set glmfitlog = $glmdir/mri_glmfit.log
set glmfitlog = lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
if ( ! -e $glmfitlog ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir/mri_glmfit.log ) then
if ( $nulltype != perm ) then
if ( != perm ) then
set fwhmfile = $glmdir/fwhm.dat
set fwhmfile = lh.5.lgi_MAN_new.glmdir/fwhm.dat
if ( ! -e $fwhmfile ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir/fwhm.dat ) then
set fwhm = `cat $fwhmfile` ;
set fwhm = `cat $fwhmfile`
cat lh.5.lgi_MAN_new.glmdir/fwhm.dat
else
else
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
awk {if($1 == "cwd") print $2}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
if ( 0 && ! -e $glmfitcwd ) then
if ( 0 && ! -e /home/cper2/BeneMin/Freesurfer ) 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.5.lgi_MAN_new.glmdir/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.5.lgi_MAN_new.glmdir/mri_glmfit.log
set glmfitcmd = ( $glmfitcmd0 ) ;
set glmfitcmd = ( cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd
FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C
contrast_dods.txt )
echo $glmfitcmd
echo cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt
dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods
--glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
set gd2mtx = dods
set gd2mtx = dods
set UseTable = 0 ;
set UseTable = 0
set label = ( ) ;
set label = ( )
while ( $#glmfitcmd )
while ( 14 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = cmdline
shift glmfitcmd
switch ( $flag )
switch ( cmdline )
case "mri_glmfit"
case mri_glmfit
case "--prune"
case --prune
case "--no-prune"
case --no-prune
case "--pca"
case --pca
case "--synth"
case --synth
case "--allowsubjrep"
case --allowsubjrep
case "--illcond"
case --illcond
case "--debug"
case --debug
case "--synth"
case --synth
case "--cortex"
case --cortex
case "--kurtosis"
case --kurtosis
case "--nii"
case --nii
case "--nii.gz"
case --nii.gz
case "--rescale-x"
case --rescale-x
case "--no-rescale-x"
case --no-rescale-x
case "--fisher"
case --fisher
case "--no-pcc"
case --no-pcc
case "dods"
case dods
case "mri_glmfit.bin"
case mri_glmfit.bin
case "--save-eres"
case --save-eres
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 13 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = mri_glmfit.bin
shift glmfitcmd
switch ( $flag )
switch ( mri_glmfit.bin )
case "--save-eres"
case --save-eres
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 12 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --y
shift glmfitcmd
switch ( $flag )
switch ( --y )
if ( $#y == 0 ) set y = $glmfitcmd[1] ;
if ( 0 == 0 ) set y = lh.5.lgi_MAN_new.mgh
set y = lh.5.lgi_MAN_new.mgh
shift glmfitcmd ;
shift glmfitcmd
if ( $DoClusterMean ) then
if ( 1 ) then
if ( ! -e $y ) then
if ( ! -e lh.5.lgi_MAN_new.mgh ) then
endif
endif
if ( "$flag" == "--table" ) set UseTable = 1 ;
if ( --y == --table ) set UseTable = 1
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 10 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --fsgd
shift glmfitcmd
switch ( $flag )
switch ( --fsgd )
shift glmfitcmd ;
shift glmfitcmd
if ( $#glmfitcmd > 0 ) then
if ( 8 > 0 ) then
if ( $glmfitcmd[1] == doss ) set gd2mtx = doss
if ( dods == doss ) set gd2mtx = doss
endif
endif
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 8 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = dods
shift glmfitcmd
switch ( $flag )
switch ( dods )
case "mri_glmfit.bin"
case mri_glmfit.bin
case "--save-eres"
case --save-eres
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 7 )
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 ( 5 )
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 ( 2 != 0 ) then
set c = `echo $glmfitcmd[1] | cut -c 1-2` ;
set c = `echo $glmfitcmd[1] | cut -c 1-2`
cut -c 1-2
echo --C
if ( "$c" != "--" ) then
if ( -- != -- ) then
endif
endif
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 2 )
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 ( 0 )
set mask = ( ) ;
set mask = ( )
if ( ! $UseTable ) then
if ( ! 0 ) then
set mask = `stem2fname $glmdir/mask`
set mask = `stem2fname $glmdir/mask`
stem2fname lh.5.lgi_MAN_new.glmdir/mask
if ( $status ) then
if ( 0 ) then
endif
endif
if ( 0 && $UseGRF && $anattype != volume ) then
if ( 0 && 0 && surface != volume ) then
if ( $UseGRF ) then
if ( 0 ) then
if ( $#subjectOverride ) set subject = $subjectOverride
if ( 0 ) set subject =
if ( $#subject != 0 ) then
if ( 1 != 0 ) then
if ( ! -e $SUBJECTS_DIR/$subject ) then
if ( ! -e /home/cper2/BeneMin/Freesurfer/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.5.lgi_MAN_new.glmdir/y.fsgd ) then
set FSGDhasCon = `cat $glmdir/y.fsgd | awk '{if($1 == "Contrast") print 1}' |
wc -l`
set FSGDhasCon = `cat $glmdir/y.fsgd | awk '{if($1 == "Contrast") print 1}' |
wc -l`
cat lh.5.lgi_MAN_new.glmdir/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.5.lgi_MAN_new.glmdir/tmp.mri_glmfit-sim-2084
set tmpdir = lh.5.lgi_MAN_new.glmdir/tmp.mri_glmfit-sim-2084
mkdir -p $tmpdir
mkdir -p lh.5.lgi_MAN_new.glmdir/tmp.mri_glmfit-sim-2084
set clist = ( $glmdir/*/C.dat )
set clist = ( lh.5.lgi_MAN_new.glmdir/*/C.dat )
if ( $status ) then
if ( 0 ) then
set clist2 = ( ) ;
set clist2 = ( )
set conlist = ( ) ;
set conlist = ( )
foreach c ( $clist )
foreach c ( lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/C.dat
lh.5.lgi_MAN_new.glmdir/contrast_doss.txt/C.dat )
set tmp = `dirname $c`
set tmp = `dirname $c`
dirname lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/C.dat
set conname = `basename $tmp`
set conname = `basename $tmp`
basename lh.5.lgi_MAN_new.glmdir/contrast_dods.txt
set conlist = ( $conlist $conname ) ;
set conlist = ( contrast_dods.txt )
set confile = $tmpdir/$conname.mtx
set confile =
lh.5.lgi_MAN_new.glmdir/tmp.mri_glmfit-sim-2084/contrast_dods.txt.mtx
cp $c $confile
cp lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/C.dat
lh.5.lgi_MAN_new.glmdir/tmp.mri_glmfit-sim-2084/contrast_dods.txt.mtx
if ( $FSGDhasCon == 0 ) set clist2 = ( $clist2 --C $confile ) ;
if ( 0 == 0 ) set clist2 = ( --C
lh.5.lgi_MAN_new.glmdir/tmp.mri_glmfit-sim-2084/contrast_dods.txt.mtx )
set clist2 = ( --C
lh.5.lgi_MAN_new.glmdir/tmp.mri_glmfit-sim-2084/contrast_dods.txt.mtx )
set sig = `stem2fname $glmdir/$conname/sig`
set sig = `stem2fname $glmdir/$conname/sig`
stem2fname lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/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.5.lgi_MAN_new.glmdir/contrast_doss.txt/C.dat
set conname = `basename $tmp`
set conname = `basename $tmp`
basename lh.5.lgi_MAN_new.glmdir/contrast_doss.txt
set conlist = ( $conlist $conname ) ;
set conlist = ( contrast_dods.txt contrast_doss.txt )
set confile = $tmpdir/$conname.mtx
set confile =
lh.5.lgi_MAN_new.glmdir/tmp.mri_glmfit-sim-2084/contrast_doss.txt.mtx
cp $c $confile
cp lh.5.lgi_MAN_new.glmdir/contrast_doss.txt/C.dat
lh.5.lgi_MAN_new.glmdir/tmp.mri_glmfit-sim-2084/contrast_doss.txt.mtx
if ( $FSGDhasCon == 0 ) set clist2 = ( $clist2 --C $confile ) ;
if ( 0 == 0 ) set clist2 = ( --C
lh.5.lgi_MAN_new.glmdir/tmp.mri_glmfit-sim-2084/contrast_dods.txt.mtx --C
lh.5.lgi_MAN_new.glmdir/tmp.mri_glmfit-sim-2084/contrast_doss.txt.mtx )
set clist2 = ( --C
lh.5.lgi_MAN_new.glmdir/tmp.mri_glmfit-sim-2084/contrast_dods.txt.mtx --C
lh.5.lgi_MAN_new.glmdir/tmp.mri_glmfit-sim-2084/contrast_doss.txt.mtx )
set sig = `stem2fname $glmdir/$conname/sig`
set sig = `stem2fname $glmdir/$conname/sig`
stem2fname lh.5.lgi_MAN_new.glmdir/contrast_doss.txt/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.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
endif
endif
rm -f $LF
rm -f lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
endif
endif
echo "log file is $LF"
echo log file is lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
log file is lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
echo "" | tee -a $LF
echo
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
echo "cd `pwd`" | tee -a $LF
echo cd `pwd`
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
pwd
cd /home/cper2/BeneMin/Freesurfer
echo $0 | tee -a $LF
echo /applications/freesurfer/freesurfer_6.0.0/bin/mri_glmfit-sim
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
/applications/freesurfer/freesurfer_6.0.0/bin/mri_glmfit-sim
echo $inputargs | tee -a $LF
echo --glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces
--debug
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
--glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces --debug
echo "" | tee -a $LF
echo
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
echo $VERSION | tee -a $LF
echo $Id: mri_glmfit-sim,v 1.66 2016/11/16 20:52:22 greve Exp $
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
$Id: mri_glmfit-sim,v 1.66 2016/11/16 20:52:22 greve Exp $
date | tee -a $LF
date
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
Tue Nov 20 13:21:35 GMT 2018
uname -a | tee -a $LF
uname -a
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
Linux wbic-gate-1 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64
GNU/Linux
echo $user | tee -a $LF
echo cper2
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
cper2
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF
echo setenv SUBJECTS_DIR /home/cper2/BeneMin/Freesurfer
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
setenv SUBJECTS_DIR /home/cper2/BeneMin/Freesurfer
echo "FREESURFER_HOME $FREESURFER_HOME" | tee -a $LF
echo FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0
echo "" | tee -a $LF
echo
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
echo "Original mri_glmfit command line:" | tee -a $LF
echo Original mri_glmfit command line:
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
Original mri_glmfit command line:
echo $glmfitcmd0 | tee -a $LF
echo cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt
dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods
--glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
echo "" | tee -a $LF
echo
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
echo "DoSim = $DoSim" | tee -a $LF
echo DoSim = 0
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
DoSim = 0
echo "UseCache = $UseCache" | tee -a $LF
echo UseCache = 1
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
UseCache = 1
echo "DoPoll = $DoPoll" | tee -a $LF
echo DoPoll = 0
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
DoPoll = 0
echo "DoPBSubmit = $DoPBSubmit" | tee -a $LF
echo DoPBSubmit = 0
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
DoPBSubmit = 0
echo "DoBackground = $DoBackground" | tee -a $LF
echo DoBackground = 0
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
DoBackground = 0
echo "DiagCluster = $DiagCluster" | tee -a $LF
echo DiagCluster = 0
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
DiagCluster = 0
echo "gd2mtx = $gd2mtx" | tee -a $LF
echo gd2mtx = dods
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
gd2mtx = dods
if ( $#Seed ) echo "Seed = $Seed" | tee -a $LF
if ( 0 ) echo Seed =
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
echo "fwhm = $fwhm" | tee -a $LF
echo fwhm = 26.134985
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
fwhm = 26.134985
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 ( 26.134985+0.5+0 ) )
if ( $fwhmStr == 00 ) set fwhmStr = 01 ;
if ( 26 == 00 ) set fwhmStr = 01
set threshStr = `perl -e "print 10*$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 =
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
if ( ! -e $csdCache ) then
if ( ! -e
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
) then
echo CSD $csdCache | tee -a $LF
echo CSD
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
CSD
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/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 ( contrast_dods.txt contrast_doss.txt )
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 = (
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
)
else
else
set csdlist = ( ) ;
set csdlist = ( )
foreach csd ( $csdfiles )
foreach csd (
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
)
set csdlist = ( $csdlist --csd $csd ) ;
set csdlist = ( --csd
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
)
end
end
endif
endif
set sig = `stem2fname $glmdir/$conname/sig`
set sig = `stem2fname $glmdir/$conname/sig`
stem2fname lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig
set ext = `fname2ext $sig`
set ext = `fname2ext $sig`
fname2ext lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh
set vwsig = $glmdir/$conname/$csdbase.sig.voxel.$ext
set vwsig =
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.mgh
set vwsigmax = $glmdir/$conname/$csdbase.sig.voxel.max.dat
set vwsigmax =
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.max.dat
set cwsig = $glmdir/$conname/$csdbase.sig.cluster.$ext
set cwsig =
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.mgh
set msig = $glmdir/$conname/$csdbase.sig.masked.$ext
set msig =
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh
set ocn = $glmdir/$conname/$csdbase.sig.ocn.$ext
set ocn = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
set oannot = $glmdir/$conname/$csdbase.sig.ocn.annot
set oannot =
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.annot
set sum = $glmdir/$conname/$csdbase.sig.cluster.summary
set sum =
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
set csdpdf = $glmdir/$conname/$csdbase.pdf.dat
set csdpdf = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/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.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask
lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.mgh --sum
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
--ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh
--no-fixmni )
if ( ! $UseGRF ) set cmd = ( $cmd $csdlist --csdpdf $csdpdf --vwsig $vwsig
--vwsigmax $vwsigmax )
if ( ! 0 ) set cmd = ( mri_surfcluster --in
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask
lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.mgh --sum
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
--ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh
--no-fixmni --csd
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
--csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.pdf.dat
--vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.mgh
--vwsigmax
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.max.dat )
set cmd = ( mri_surfcluster --in
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask
lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.mgh --sum
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
--ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh
--no-fixmni --csd
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
--csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.pdf.dat
--vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.mgh
--vwsigmax
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/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.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask
lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.mgh --sum
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
--ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh
--no-fixmni --csd
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
--csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.pdf.dat
--vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.mgh
--vwsigmax
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.max.dat
--fwhm 26.134985 --hemi lh --subject fsaverage --thmin 1.3 --sign pos )
if ( $OutputAnnot ) set cmd = ( $cmd --oannot $oannot )
if ( 1 ) set cmd = ( mri_surfcluster --in
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask
lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.mgh --sum
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
--ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh
--no-fixmni --csd
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
--csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.pdf.dat
--vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.mgh
--vwsigmax
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.max.dat
--oannot lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.annot
)
set cmd = ( mri_surfcluster --in
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask
lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.mgh --sum
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
--ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh
--no-fixmni --csd
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
--csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.pdf.dat
--vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.mgh
--vwsigmax
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.max.dat
--oannot lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.annot
)
if ( $Bonferroni ) set cmd = ( $cmd --bonferroni $Bonferroni )
if ( 2 ) set cmd = ( mri_surfcluster --in
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask
lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.mgh --sum
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
--ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh
--no-fixmni --csd
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
--csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.pdf.dat
--vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.mgh
--vwsigmax
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.max.dat
--oannot lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.annot
--bonferroni 2 )
set cmd = ( mri_surfcluster --in
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask
lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.mgh --sum
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
--ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh
--no-fixmni --csd
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
--csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.pdf.dat
--vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.mgh
--vwsigmax
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.max.dat
--oannot lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.annot
--bonferroni 2 )
if ( $ReportCentroid ) set cmd = ( $cmd --centroid ) ;
if ( 0 ) set cmd = ( mri_surfcluster --in
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask
lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.mgh --sum
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
--ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh
--no-fixmni --csd
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
--csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.pdf.dat
--vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.mgh
--vwsigmax
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.max.dat
--oannot lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.annot
--bonferroni 2 --centroid )
set cmd = ( $cmd --surf $surf ) ;
set cmd = ( mri_surfcluster --in
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask
lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.mgh --sum
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
--ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh
--no-fixmni --csd
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
--csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.pdf.dat
--vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.mgh
--vwsigmax
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.max.dat
--oannot lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.annot
--bonferroni 2 --surf white )
echo $cmd | tee -a $LF
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
echo mri_surfcluster --in lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh
--mask lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.mgh --sum
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
--ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh
--no-fixmni --csd
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
--csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.pdf.dat
--vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.mgh
--vwsigmax
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.max.dat
--oannot lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.annot
--bonferroni 2 --surf white
mri_surfcluster --in lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask
lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.mgh --sum
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
--ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh
--no-fixmni --csd
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
--csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.pdf.dat
--vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.mgh
--vwsigmax
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.max.dat
--oannot lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.annot
--bonferroni 2 --surf white
$cmd | tee -a $LF
tee -a lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
mri_surfcluster --in lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask
lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.mgh --sum
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
--ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh
--no-fixmni --csd
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/pos/th13/mc-z.csd
--csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.pdf.dat
--vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.mgh
--vwsigmax
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.voxel.max.dat
--oannot lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.annot
--bonferroni 2 --surf white
Creating CDFs from CSD files
csd->threshsign = 1
thsign = pos, id = 1
version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $
hemi = lh
srcid = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/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.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.masked.mgh MGH
ocnid = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.ocn.mgh
MGH
sumfile =
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th13.pos.sig.cluster.summary
subjectsdir = /home/cper2/BeneMin/Freesurfer
FixMNI = 0
Found 149955 vertices in mask
Found 149955 vertices in mask
Found 149955 points in clabel.
------------- XFM matrix (RAS2RAS) ---------------
/home/cper2/BeneMin/Freesurfer/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;
MRISread(): could not open file
No such file or directory
----------------------------------------------------
Reading source surface /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
mri_surfcluster.bin: could not read surface
/home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
No such file or directory
if ( $status ) exit 1 ;
if ( 255 ) exit 1
exit 1_______________________________________________
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