On 11/23/2018 11:26 AM, C.P.E. Rollins wrote:
> External Email - Use Caution
> Dear Freesurfer Developers,
> I have a 2-part question:
> 1) I was advised to use permutation to control for multiple
> comparisons in an LGI analysis, would you mind elaborating how to do
> this in command line (in terms of command and parameters)?
It is very similar to running with MCZ. See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
> 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache
> 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error
> (attached). I was wondering if you might have any advice? The file
> /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can
> view it in freeview.
I don't know what is going on there. Can you send me the result of
ls -Rl $FREESURFER_HOME/subjects/fsaverage
>
> Many thanks,
> 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
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
