Doug -- here's the output from the terminal....
kerryave:functionals $ selxavg3-sess -s ya24 -d /cluster/kuperberg/SemPrMM/MRI/functionals/ -analysis ya.ATLLoc.spm.sm8.lh -debug | & tee debug.log set echo = 1 ; breaksw breaksw
end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return
foreach grp ( $grpdefs ) foreach grp ( )
goto check_params ; goto check_params
if ( $#SessList == 0 ) then if ( 1 == 0 ) then
if ( $#SearchPathList == 0 ) then if ( 1 == 0 ) then
goto check_params_return ; goto check_params_return
set UniqueList = ( ) ; set UniqueList = ( ) foreach d ( $SearchPathList ) foreach d ( /cluster/kuperberg/SemPrMM/MRI/functionals/ ) if ( ! -e $d ) then if ( ! -e /cluster/kuperberg/SemPrMM/MRI/functionals/ ) then
set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ; if ( 1 ) set UniqueList = ( /cluster/kuperberg/SemPrMM/MRI/functionals/ ) set UniqueList = ( /cluster/kuperberg/SemPrMM/MRI/functionals/ ) end end
set SearchPathList = ( $UniqueList ) ; set SearchPathList = ( /cluster/kuperberg/SemPrMM/MRI/functionals/ )
set errs = 0 ; set errs = 0
set SessPath = ( ) ; set SessPath = ( ) foreach sess ( $SessList ) foreach sess ( ya24 ) set tmp = ( ) ; set tmp = ( ) foreach d ( $SearchPathList ) foreach d ( /cluster/kuperberg/SemPrMM/MRI/functionals/ ) set stst = $d/$sess set stst = /cluster/kuperberg/SemPrMM/MRI/functionals//ya24 if ( -d $stst ) then if ( -d /cluster/kuperberg/SemPrMM/MRI/functionals//ya24 ) then if ( ! -r $stst ) then if ( ! -r /cluster/kuperberg/SemPrMM/MRI/functionals//ya24 ) then pushd $stst > /dev/null ; pushd /cluster/kuperberg/SemPrMM/MRI/functionals//ya24 set tmp = ( $tmp `$PWDCMD` ) ; set tmp = ( `$PWDCMD` ) pwd popd > /dev/null ; popd endif endif end end set nfound = ( $#tmp ) ; set nfound = ( 1 ) if ( $nfound == 0 ) then if ( 1 == 0 ) then if ( $nfound > 1 ) then if ( 1 > 1 ) then set SessPath = ( $SessPath $tmp ) ; set SessPath = ( /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24 ) end end
set UniqueList = ( ) ; set UniqueList = ( ) foreach s ( $SessPath ) foreach s ( /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24 ) set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( ! $IsUnique && ! $AllowRedundant ) then if ( ! 1 && ! 0 ) then
set UniqueList = ( $UniqueList $s ) ; set UniqueList = ( /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24 ) endif endif end end
echo $SessPath echo /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24
exit $errs ; exit 0 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 ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#analysis == 0 && $flacfile == 0 ) then if ( 1 == 0 && == 0 ) then if ( $#analysis != 0 ) then if ( 1 != 0 ) then if ( ! -d $analysis ) then if ( ! -d ya.ATLLoc.spm.sm8.lh ) then if ( ! -e $analysis/analysis.info ) then if ( ! -e ya.ATLLoc.spm.sm8.lh/analysis.info ) then endif endif if ( $#flacfile != 0 ) then if ( 0 != 0 ) then if ( $perrun && $jkrun ) then if ( 0 && 0 ) then
if ( $UseOctave ) then if ( 0 ) then
goto check_params_return ; goto check_params_return
set StudyDir = `pwd` ; set StudyDir = `pwd` pwd
if ( $#analysis ) then if ( 1 ) then
set analysisname = $analysis set analysisname = ya.ATLLoc.spm.sm8.lh set fsd = `getana -a $analysis -t fsd` ; set fsd = `getana -a $analysis -t fsd` getana -a ya.ATLLoc.spm.sm8.lh -t fsd set IsNative = `getana -a $analysis -t IsNative` set IsNative = `getana -a $analysis -t IsNative` getana -a ya.ATLLoc.spm.sm8.lh -t IsNative set IsSurface = `getana -a $analysis -t IsSurface` set IsSurface = `getana -a $analysis -t IsSurface` getana -a ya.ATLLoc.spm.sm8.lh -t IsSurface if ( $IsSurface ) then if ( 1 ) then set subject = `getana -a $analysis -t subject` set subject = `getana -a $analysis -t subject` getana -a ya.ATLLoc.spm.sm8.lh -t subject set hemi = `getana -a $analysis -t hemi` set hemi = `getana -a $analysis -t hemi` getana -a ya.ATLLoc.spm.sm8.lh -t hemi echo "Surface data $subject $hemi" echo Surface data fsaverage lh Surface data fsaverage lh endif endif set dt = `getana -a $analysis -t designtype` set dt = `getana -a $analysis -t designtype` getana -a ya.ATLLoc.spm.sm8.lh -t designtype if ( $dt == "abblocked" ) set RequireContrasts = 0 ; if ( event-related == abblocked ) set RequireContrasts = 0 if ( $dt == "retinotopy" ) set RequireContrasts = 0 ; if ( event-related == retinotopy ) set RequireContrasts = 0 set contrasts = `getana -a $analysis -t contrasts` set contrasts = `getana -a $analysis -t contrasts` getana -a ya.ATLLoc.spm.sm8.lh -t contrasts if ( $#contrasts == 0 && $RequireContrasts ) then if ( 7 == 0 && 1 ) then endif endif
if ( $#LF == 0 ) then if ( 0 == 0 ) then if ( $nolog ) then if ( 0 ) then
if ( $#OutParent == 0 ) then if ( 0 == 0 ) then set logdir = `pwd`/log ; set logdir = `pwd`/log pwd else else mkdir -p $logdir mkdir -p /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log if ( ! -e $logdir ) then if ( ! -e /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log ) then
set LF = $logdir/selxavg3-sess-$fsd-$analysis-$DateStr.log set LF = /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log if ( -e $LF ) mv $LF $LF.old if ( -e /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log ) mv /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log.old endif endif endif endif endif endif echo "--------------------------------------------------------------" echo -------------------------------------------------------------- -------------------------------------------------------------- echo "selxavg3-sess logfile is $LF" echo selxavg3-sess logfile is /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log selxavg3-sess logfile is /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log echo "--------------------------------------------------------------" echo -------------------------------------------------------------- --------------------------------------------------------------
echo "selxavg3-sess log file" >> $LF echo selxavg3-sess log file echo $0 >> $LF echo /usr/local/freesurfer/stable5_0_0/fsfast/bin/selxavg3-sess echo $inputargs >> $LF echo -s ya24 -d /cluster/kuperberg/SemPrMM/MRI/functionals/ -analysis ya.ATLLoc.spm.sm8.lh -debug echo $VERSION >> $LF echo $Id: selxavg3-sess,v 1.52.2.5 2010/08/25 19:07:37 greve Exp $ id >> $LF id pwd >> $LF pwd uname -a >> $LF uname -a date >> $LF date
set StartTime = `date` ; set StartTime = `date` date
if ( $SaveRes || $SaveResUnwhitened ) set MatlabSaveRes = 1 ; if ( 0 || 0 ) set MatlabSaveRes = 1
set funcstemspec = `getana -a $analysis -t funcstem-specified` set funcstemspec = `getana -a $analysis -t funcstem-specified` getana -a ya.ATLLoc.spm.sm8.lh -t funcstem-specified if ( $funcstemspec ) set DoPreProc = 0 ; if ( 1 ) set DoPreProc = 0 set DoPreProc = 0
if ( $DoPreProc ) then if ( 0 ) then
if ( $#MLF == 0 ) set MLF = /tmp/selxavg3-sess-$$.m if ( 0 == 0 ) set MLF = /tmp/selxavg3-sess-1405.m set MLF = /tmp/selxavg3-sess-1405.m rm -f $MLF rm -f /tmp/selxavg3-sess-1405.m echo "% `date` " >> $MLF echo % `date` date echo "% `pwd` " >> $MLF echo % `pwd` pwd echo "% $flacfile $analysis " >> $MLF echo % ya.ATLLoc.spm.sm8.lh echo " " >> $MLF echo echo " " >> $MLF echo
set okfile = /tmp/selxavg3-sess-$$.ok set okfile = /tmp/selxavg3-sess-1405.ok rm -f $okfile rm -f /tmp/selxavg3-sess-1405.ok
set parname = `getana -a $analysis -t parname` set parname = `getana -a $analysis -t parname` getana -a ya.ATLLoc.spm.sm8.lh -t parname set funcstem = `getana -a $analysis -t funcstem` set funcstem = `getana -a $analysis -t funcstem` getana -a ya.ATLLoc.spm.sm8.lh -t funcstem set rlf = `getana -a $analysis -t runlistfile` set rlf = `getana -a $analysis -t runlistfile` getana -a ya.ATLLoc.spm.sm8.lh -t runlistfile set ConList = `getana -a $analysis -t contrasts` set ConList = `getana -a $analysis -t contrasts` getana -a ya.ATLLoc.spm.sm8.lh -t contrasts
@ nthsess = 0 ; @ nthsess = 0 @ nprocs = 0 ; @ nprocs = 0 foreach sess ( $SessList ) foreach sess ( /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24 ) @ nthsess = $nthsess + 1 ; @ nthsess = 0 + 1 set sessbase = `basename $sess` ; set sessbase = `basename $sess` basename /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24 set sessdir = `dirname $sess` ; set sessdir = `dirname $sess` dirname /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24
echo "-------------------------------------------" | & tee -a $LF echo ------------------------------------------- tee -a /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log ------------------------------------------- echo "$sess " | & tee -a $LF echo /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24 tee -a /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24 date | & tee -a $LF date tee -a /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log Sun Apr 10 19:19:09 EDT 2011
if ( ! -d $sess ) then if ( ! -d /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24 ) then
set funcdir = $sess/$fsd set funcdir = /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc set anadir = $sess/$fsd/$analysisname set anadir = /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/ya.ATLLoc.spm.sm8.lh if ( $#OutParent == 0 ) then if ( 0 == 0 ) then set anadir = $sess/$fsd/$analysisname set anadir = /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/ya.ATLLoc.spm.sm8.lh else else echo anadir = $anadir | tee -a $LF echo anadir = /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/ya.ATLLoc.spm.sm8.lh tee -a /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log anadir = /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/ya.ATLLoc.spm.sm8.lh
set DoGLMFit = 0 ; set DoGLMFit = 0 if ( $Overwrite || $perrun ) set DoGLMFit = 1 ; if ( 0 || 0 ) set DoGLMFit = 1 set beta = `stem2fname $anadir/beta` set beta = `stem2fname $anadir/beta` stem2fname /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/ya.ATLLoc.spm.sm8.lh/beta if ( $status ) set DoGLMFit = 1 ; if ( 0 ) set DoGLMFit = 1 if ( $DoGLMFit == 0 ) then if ( 0 == 0 ) then
set deplist = ( $analysis/analysis.info ) ; set deplist = ( ya.ATLLoc.spm.sm8.lh/analysis.info ) set RunList = ( `getrunlist $sess/$fsd $rlf` ) ; set RunList = ( `getrunlist $sess/$fsd $rlf` ) getrunlist /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc rlf set funclist = ( ) set funclist = ( ) foreach Run ( $RunList ) foreach Run ( 007 ) set funcstempath = $sess/$fsd/$Run/$funcstem ; set funcstempath = /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz set func = `stem2fname $funcstempath` ; set func = `stem2fname $funcstempath` stem2fname /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz if ( $status ) then if ( 1 ) then echo "ERROR: cannot find $funcstempath" echo ERROR: cannot find /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz ERROR: cannot find /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz exit 1 ; exit 1
Scott, can you run
selxavg3-sess -analysis ya.ATLLoc.spm.sm8.lh -s ya24 -d /cluster/kuperberg/SemPrMM/MRI/functionals/ -debug |& tee debug.log
and send me debug.log?
doug
Scott Burns wrote:
Freesurfers --
Here's the output of my terminal...
kerryave:functionals $ cd /cluster/kuperberg/SemPrMM/MRI/functionals/ kerryave:functionals $ rm /cluster/kuperberg/SemPrMM/MRI/functionals/ya24/scripts/atlloc_fs-stats.log kerryave:functionals $ selxavg3-sess -analysis ya.ATLLoc.spm.sm8.lh -s ya24 -d /cluster/kuperberg/SemPrMM/MRI/functionals/ -svres -nolog
Surface data fsaverage lh
selxavg3-sess logfile is /dev/null
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24 Fri Apr 8 16:47:17 EDT 2011 anadir = /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/ya.ATLLoc.spm.sm8.lh ERROR: cannot find /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz kerryave:functionals $ ls -l ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz -rw-rw-r-- 1 sburns lingua 83660305 Apr 7 07:56 ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz
Does anyone know what's going on? Here's my analysis.info http://analysis.info for that analysis...
kerryave:functionals $ cd ya.ATLLoc.spm.sm8.lh/ kerryave:ya.ATLLoc.spm.sm8.lh $ cat analysis.info http://analysis.info # FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319 # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve Exp $ # MKACMD /usr/local/freesurfer/stable5_0_0/fsfast/bin/mkanalysis-sess -analysis ya.ATLLoc.spm.sm8.lh -fsd ATLLoc -rlf rlf -p atlloc.par -spmhrf 0 -refeventdur 2 -event-related -TR 2 -nconditions 4 -mcextreg -hpf 128 -funcstem fmcpr.odd.sm8.fsaverage.lh.nii.gz -surface fsaverage lh -force # DATE Fri Apr 8 08:31:01 EDT 2011
analysis ya.ATLLoc.spm.sm8.lh mcstem fmcpr funcstem fmcpr.odd.sm8.fsaverage.lh.nii.gz fsd ATLLoc runlistfile rlf TR 2 RegDOF 6 RawSpace surface fsaverage lh mask brain RawFWHM 0 RawSTC none inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 128 nconditions 4 parname atlloc.par RefEventDur 2 timewindow 40.000000 prestim 0 TER 0.050000 spmhrf 0 stimulusdelay 0 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 nuisreg mcprextreg 3
Thanks for the help.
Scott Burns Kuperberg Lab Martinos Center for Biomedical Imaging sburns@nmr.mgh.harvard.edu mailto:sburns@nmr.mgh.harvard.edu
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