Re: [Freesurfer] R: Re: selxavg3-sess error

Douglas Greve Tue, 16 May 2017 09:21:53 -0700

Does this file exist ?/Applications/freesurfer/subjects/fMRI/subj067_GROUP/001/masks/brain.e3.nii.gz

You can try deleting the/Applications/freesurfer/subjects/fMRI/subj067_GROUP/001/masks folderand re-running.



On 5/16/17 11:53 AM, std...@virgilio.it wrote:

selxavg3-sess -s subj067_GROUP -a fc.lamgseed.surf.lh -debug
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 ( 0 == 0 ) then
set SearchPathList = "." ;
set SearchPathList = .
endif
endif

goto check_params_return ;
goto check_params_return


set UniqueList = ( ) ;
set UniqueList = ( )
foreach d ( $SearchPathList )
foreach d ( . )
if ( ! -e $d ) then
if ( ! -e . ) then

set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
if ( 1 ) set UniqueList = ( . )
set UniqueList = ( . )
end
end

set SearchPathList = ( $UniqueList ) ;
set SearchPathList = ( . )

set errs = 0 ;
set errs = 0


set SessPath = ( ) ;
set SessPath = ( )
foreach sess ( $SessList )
foreach sess ( subj067_GROUP )
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( . )
set stst = $d/$sess
set stst = ./subj067_GROUP
if ( -d $stst ) then
if ( -d ./subj067_GROUP ) then
if ( ! -r $stst ) then
if ( ! -r ./subj067_GROUP ) then
pushd $stst > /dev/null ;
pushd ./subj067_GROUP
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 = ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP )
end
end


set UniqueList = ( ) ;
set UniqueList = ( )
foreach s ( $SessPath )
foreach s ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP )
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 = ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP )
endif
endif
end
end


echo $SessPath
echo /Applications/freesurfer/subjects/fMRI/subj067_GROUP

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 fc.lamgseed.surf.lh ) then
if ( ! -e $analysis/analysis.info ) then
if ( ! -e fc.lamgseed.surf.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

if ( $#DoneFile ) 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 = fc.lamgseed.surf.lh
set fsd = `getana -a $analysis -t fsd` ;
set fsd = `getana -a $analysis -t fsd`
getana -a fc.lamgseed.surf.lh -t fsd
set PerSession = `getana -a $analysis -t IsPerSession`
set PerSession = `getana -a $analysis -t IsPerSession`
getana -a fc.lamgseed.surf.lh -t IsPerSession
set IsNative = `getana -a $analysis -t IsNative`
set IsNative = `getana -a $analysis -t IsNative`
getana -a fc.lamgseed.surf.lh -t IsNative
set IsSurface = `getana -a $analysis -t IsSurface`
set IsSurface = `getana -a $analysis -t IsSurface`
getana -a fc.lamgseed.surf.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 fc.lamgseed.surf.lh -t subject
set hemi = `getana -a $analysis -t hemi`
set hemi = `getana -a $analysis -t hemi`
getana -a fc.lamgseed.surf.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 fc.lamgseed.surf.lh -t designtype
if ( $dt == "abblocked" ) set RequireContrasts = 0 ;
if ( notask == abblocked ) set RequireContrasts = 0
if ( $dt == "retinotopy" ) set RequireContrasts = 0 ;
if ( notask == retinotopy ) set RequireContrasts = 0
set contrasts = `getana -a $analysis -t contrasts`
set contrasts = `getana -a $analysis -t contrasts`
getana -a fc.lamgseed.surf.lh -t contrasts
if ( $#contrasts == 0 && $RequireContrasts ) then
if ( 1 == 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 /Applications/freesurfer/subjects/fMRI/log
if ( ! -e $logdir ) then
if ( ! -e /Applications/freesurfer/subjects/fMRI/log ) then

set LF = $logdir/selxavg3-sess-$fsd-$analysis-$DateStr.log

set LF =/Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log

if ( -e $LF ) mv $LF $LF.old

if ( -e/Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log) mv/Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log/Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log.old

endif
endif
endif
endif
endif
endif
echo "--------------------------------------------------------------"
echo --------------------------------------------------------------
--------------------------------------------------------------
echo "selxavg3-sess logfile is $LF"

echo selxavg3-sess logfile is/Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logselxavg3-sess logfile is/Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log

echo "--------------------------------------------------------------"
echo --------------------------------------------------------------
--------------------------------------------------------------

echo "selxavg3-sess log file" | tee -a $LF