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)? 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.
Many thanks, Colleen
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:
- 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/MultipleComparisonsV6.0...
- 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
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Hi Douglas,
Thanks a lot for your answers.
1) For the permutations, would you recommend using this for controlling for MC in cortical thickness analyses too? Why is it recommended to use permutation simulation as opposed to Z Monte Carlo simulation for an LGI analysis?
2) I've attached here the output from ls -Rl $FREESURFER_HOME/subjects/fsaverage.
Thanks again, Colleen
On 2018-11-23 16:26, C.P.E. Rollins wrote:
Dear Freesurfer Developers, I have a 2-part question:
- 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)? 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.
Many thanks, Colleen
On 11/27/2018 06:46 AM, C.P.E. Rollins wrote:
External Email - Use Caution Hi Douglas,
Thanks a lot for your answers.
- For the permutations, would you recommend using this for
controlling for MC in cortical thickness analyses too?
Yes
Why is it recommended to use permutation simulation as opposed to Z Monte Carlo simulation for an LGI analysis?
Because the spatial correlations are very high (which makes MCZ less accurate)
- I've attached here the output from ls -Rl
$FREESURFER_HOME/subjects/fsaverage.
It looks like there is a difference in where you think FREESURFER_HOME is. Below, you say it is in /home/cper2/BeneMin/Freesurfer, but the attached file says it is in /applications/freesurfer/freesurfer_6.0.0. Which one is it?
Thanks again, Colleen
On 2018-11-23 16:26, C.P.E. Rollins wrote:
Dear Freesurfer Developers, I have a 2-part question:
- 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)? 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.
Many thanks, Colleen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Freesurfer, I am also experiencing the same problem and everything regarding FREESURFER path looks ok just getting error that says: Reading source surface /storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white MRISread(): could not open file No such file or directory mri_surfcluster: could not read surface /storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white No such file or directory I wonder if you found the reason and solution?
Best regards, Amirhossein Manzouri
On Thu, Dec 6, 2018 at 6:57 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
On 11/27/2018 06:46 AM, C.P.E. Rollins wrote:
External Email - Use Caution Hi Douglas,
Thanks a lot for your answers.
- For the permutations, would you recommend using this for
controlling for MC in cortical thickness analyses too?
Yes
Why is it recommended to use permutation simulation as opposed to Z Monte Carlo simulation for an LGI analysis?
Because the spatial correlations are very high (which makes MCZ less accurate)
- I've attached here the output from ls -Rl
$FREESURFER_HOME/subjects/fsaverage.
It looks like there is a difference in where you think FREESURFER_HOME is. Below, you say it is in /home/cper2/BeneMin/Freesurfer, but the attached file says it is in /applications/freesurfer/freesurfer_6.0.0. Which one is it?
Thanks again, Colleen
On 2018-11-23 16:26, C.P.E. Rollins wrote:
Dear Freesurfer Developers, I have a 2-part question:
- 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)? 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.
Many thanks, Colleen
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
freesurfer@nmr.mgh.harvard.edu
-
amirhossein manzouri -
C.P.E. Rollins -
Greve, Douglas N.,Ph.D.