can you verify that /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and that you have read permission to it? Eg, can you load it with freeview -f /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white

On 11/20/18 8:25 AM, C.P.E. Rollins wrote: 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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