Re: [Freesurfer] funcroi-table-sess error, "set: Variable name must begin with a letter" - Freesurfer

3 Sep 2013

      It is not finding what it needs in this folder
/srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh
Can you check that it exists and that it has the same files in it that the corresponding folders from other sessions has? If it does not, check that you have space and permissions there and then try rerunning selxavg3-sess
doug
On 09/03/2013 10:35 AM, Kathryn Devaney wrote:
...
Hi Doug,
Same error - here's the debug output (pasted below & in attached text 
file).
Thanks,
Katie
kdevaney@frontal: [227] 
circlet/connectivity_average_labels/ROI_average_labels/ funcroi-sess 
-s 120723EC -d /srv/mind3/r2/users/fspace2 -roi ROI_rh_antTPJ.roi
-update    10:27am
/srv/mind3/r2/users/fspace2/120723EC
Tue Sep  3 10:27:48 EDT 2013
set: Variable name must begin with a letter.
kdevaney@frontal: [228] 
circlet/connectivity_average_labels/ROI_average_labels/ funcroi-sess 
-debug -s 120723EC -d /srv/mind3/r2/users/fspace2 -roi 
ROI_rh_antTPJ.roi -update
set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 7 != 0 )
set flag = $argv[1] ; shift ;
set flag = -s
shift
switch ( $flag )
switch ( -s )
if ( $#argv == 0 ) goto arg1err ;
if ( 6 == 0 ) goto arg1err
set SessList = ( $SessList $argv[1] ) ; shift ;
set SessList = ( 120723EC )
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 5 != 0 )
set flag = $argv[1] ; shift ;
set flag = -d
shift
switch ( $flag )
switch ( -d )
if ( $#argv == 0 ) goto arg1err ;
if ( 4 == 0 ) goto arg1err
if ( ! -d $argv[1] ) then
if ( ! -d /srv/mind3/r2/users/fspace2 ) then
if ( ! -r $argv[1] ) then
if ( ! -r /srv/mind3/r2/users/fspace2 ) then
set srchdir = $argv[1] ; shift ;
set srchdir = /srv/mind3/r2/users/fspace2
shift
set SearchPathList = ( $SearchPathList $srchdir ) ;
set SearchPathList = ( /srv/mind3/r2/users/fspace2 )
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 3 != 0 )
set flag = $argv[1] ; shift ;
set flag = -roi
shift
switch ( $flag )
switch ( -roi )
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = ROI_rh_antTPJ.roi
shift
switch ( $flag )
switch ( ROI_rh_antTPJ.roi )
end
end
while ( $#argv != 0 )
while ( 1 != 0 )
set flag = $argv[1] ; shift ;
set flag = -update
shift
switch ( $flag )
switch ( -update )
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 ( /srv/mind3/r2/users/fspace2 )
if ( ! -e $d ) then
if ( ! -e /srv/mind3/r2/users/fspace2 ) then
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
if ( 1 ) set UniqueList = ( /srv/mind3/r2/users/fspace2 )
set UniqueList = ( /srv/mind3/r2/users/fspace2 )
end
end
set SearchPathList = ( $UniqueList ) ;
set SearchPathList = ( /srv/mind3/r2/users/fspace2 )
set errs = 0 ;
set errs = 0
set SessPath = ( ) ;
set SessPath = ( )
foreach sess ( $SessList )
foreach sess ( 120723EC )
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( /srv/mind3/r2/users/fspace2 )
set stst = $d/$sess
set stst = /srv/mind3/r2/users/fspace2/120723EC
if ( -d $stst ) then
if ( -d /srv/mind3/r2/users/fspace2/120723EC ) then
if ( ! -r $stst ) then
if ( ! -r /srv/mind3/r2/users/fspace2/120723EC ) then
pushd $stst > /dev/null ;
pushd /srv/mind3/r2/users/fspace2/120723EC
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 = ( /srv/mind3/r2/users/fspace2/120723EC )
end
end
set UniqueList = ( ) ;
set UniqueList = ( )
foreach s ( $SessPath )
foreach s ( /srv/mind3/r2/users/fspace2/120723EC )
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 = ( /srv/mind3/r2/users/fspace2/120723EC )
endif
endif
end
end
echo $SessPath
echo /srv/mind3/r2/users/fspace2/120723EC
exit $errs ;
exit 0
set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 7 != 0 )
set flag = $argv[1] ; shift ;
set flag = -s
shift
switch ( $flag )
switch ( -s )
case "-sf":
case -sf:
case "-d":
case -d:
case "-df":
case -df:
shift ;
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 5 != 0 )
set flag = $argv[1] ; shift ;
set flag = -d
shift
switch ( $flag )
switch ( -d )
case "-df":
case -df:
shift ;
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 3 != 0 )
set flag = $argv[1] ; shift ;
set flag = -roi
shift
switch ( $flag )
switch ( -roi )
if ( $#argv < 1 ) goto arg1err ;
if ( 2 < 1 ) goto arg1err
set roicfg = $argv[1] ; shift ;
set roicfg = ROI_rh_antTPJ.roi
shift
if ( ! -e $roicfg ) then
if ( ! -e ROI_rh_antTPJ.roi ) then
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 1 != 0 )
set flag = $argv[1] ; shift ;
set flag = -update
shift
switch ( $flag )
switch ( -update )
set UpdateOnly = 1 ;
set UpdateOnly = 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 ( $#roicfg == 0 ) then
if ( 1 == 0 ) then
set roiname = `cat $roicfg | awk '{if($1 == "roiname") print $2}'`
set roiname = `cat $roicfg | awk '{if($1 == "roiname") print $2}'`
awk {if($1 == "roiname") print $2}
cat ROI_rh_antTPJ.roi
set label = `cat $roicfg | awk '{if($1 == "label") print $2}'`
set label = `cat $roicfg | awk '{if($1 == "label") print $2}'`
awk {if($1 == "label") print $2}
cat ROI_rh_antTPJ.roi
set annot = `cat $roicfg | awk '{if($1 == "annot") print $2}'`
set annot = `cat $roicfg | awk '{if($1 == "annot") print $2}'`
awk {if($1 == "annot") print $2}
cat ROI_rh_antTPJ.roi
if ( $#annot ) then
if ( 0 ) then
set segvol = `cat $roicfg | awk '{if($1 == "seg") print $2}'`
set segvol = `cat $roicfg | awk '{if($1 == "seg") print $2}'`
awk {if($1 == "seg") print $2}
cat ROI_rh_antTPJ.roi
if ( $#segvol ) then
if ( 0 ) then
set fillthresh = `cat $roicfg | awk '{if($1 == "fillthresh") print $2}'`
set fillthresh = `cat $roicfg | awk '{if($1 == "fillthresh") print $2}'`
awk {if($1 == "fillthresh") print $2}
cat ROI_rh_antTPJ.roi
set analysis = `cat $roicfg | awk '{if($1 == "analysis") print $2}'`
set analysis = `cat $roicfg | awk '{if($1 == "analysis") print $2}'`
awk {if($1 == "analysis") print $2}
cat ROI_rh_antTPJ.roi
set contrast = `cat $roicfg | awk '{if($1 == "contrast") print $2}'`
set contrast = `cat $roicfg | awk '{if($1 == "contrast") print $2}'`
awk {if($1 == "contrast") print $2}
cat ROI_rh_antTPJ.roi
set sign = `cat $roicfg | awk '{if($1 == "sign") print $2}'`
set sign = `cat $roicfg | awk '{if($1 == "sign") print $2}'`
awk {if($1 == "sign") print $2}
cat ROI_rh_antTPJ.roi
set thresh = `cat $roicfg | awk '{if($1 == "thresh") print $2}'`
set thresh = `cat $roicfg | awk '{if($1 == "thresh") print $2}'`
awk {if($1 == "thresh") print $2}
cat ROI_rh_antTPJ.roi
set pct = `cat $roicfg | awk '{if($1 == "pct") print $2}'`
set pct = `cat $roicfg | awk '{if($1 == "pct") print $2}'`
awk {if($1 == "pct") print $2}
cat ROI_rh_antTPJ.roi
set map = `cat $roicfg | awk '{if($1 == "map") print $2}'`
set map = `cat $roicfg | awk '{if($1 == "map") print $2}'`
awk {if($1 == "map") print $2}
cat ROI_rh_antTPJ.roi
set frame = `cat $roicfg | awk '{if($1 == "frame") print $2}'`
set frame = `cat $roicfg | awk '{if($1 == "frame") print $2}'`
awk {if($1 == "frame") print $2}
cat ROI_rh_antTPJ.roi
if ( ! -d $analysis ) then
if ( ! -d circlet.fsaverage.sm3.mc.rh ) then
goto check_params_return ;
goto check_params_return
set fsd = `getana -a $analysis -t fsd`
set fsd = `getana -a $analysis -t fsd`
getana -a circlet.fsaverage.sm3.mc.rh -t fsd
set IsNative = `getana -a $analysis -t IsNative`
set IsNative = `getana -a $analysis -t IsNative`
getana -a circlet.fsaverage.sm3.mc.rh -t IsNative
set IsMNI305 = `getana -a $analysis -t IsMNI305`
set IsMNI305 = `getana -a $analysis -t IsMNI305`
getana -a circlet.fsaverage.sm3.mc.rh -t IsMNI305
set IsSurface = `getana -a $analysis -t IsSurface`
set IsSurface = `getana -a $analysis -t IsSurface`
getana -a circlet.fsaverage.sm3.mc.rh -t IsSurface
if ( $IsSurface ) then
if ( 1 ) then
set hemi = `getana -a $analysis -t hemi`
set hemi = `getana -a $analysis -t hemi`
getana -a circlet.fsaverage.sm3.mc.rh -t hemi
set anasubject = `getana -a $analysis -t subject`
set anasubject = `getana -a $analysis -t subject`
getana -a circlet.fsaverage.sm3.mc.rh -t subject
endif
endif
set RegDOF = `getana -a $analysis -t RegDOF`
set RegDOF = `getana -a $analysis -t RegDOF`
getana -a circlet.fsaverage.sm3.mc.rh -t RegDOF
set cvol = ( ) ;
set cvol = ( )
set labelfile = ( ) ;
set labelfile = ( )
set segfile = ( ) ;
set segfile = ( )
set annotfile = ( ) ;
set annotfile = ( )
@ nthsess = 0 ;
@ nthsess = 0
foreach sess ( $SessList )
foreach sess ( /srv/mind3/r2/users/fspace2/120723EC )
@ nthsess = $nthsess + 1 ;
@ nthsess = 0 + 1
set sessbase = `basename $sess` ;
set sessbase = `basename $sess`
basename /srv/mind3/r2/users/fspace2/120723EC
set sessdir = `dirname  $sess` ;
set sessdir = `dirname  $sess`
dirname /srv/mind3/r2/users/fspace2/120723EC
echo "-------------------------------------------"
echo -------------------------------------------

echo "$sess "
echo /srv/mind3/r2/users/fspace2/120723EC
/srv/mind3/r2/users/fspace2/120723EC
date
date
Tue Sep  3 10:27:59 EDT 2013
set subject = `cat $sess/subjectname`
set subject = `cat $sess/subjectname`
cat /srv/mind3/r2/users/fspace2/120723EC/subjectname
set anadir = $sess/$fsd/$analysis
set anadir = 
/srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh
if ( ! -e $anadir ) then
if ( ! -e 
/srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh 
) then
set ext = `stem2fmt $anadir/meanfunc`
set ext = `stem2fmt $anadir/meanfunc`
stem2fmt 
/srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh/meanfunc
if ( $#label ) then
if ( 1 ) then
set labelfile = $SUBJECTS_DIR/$subject/label/$label
set labelfile = 
/r2/users/fspace2/autorecon-subjects//ec51/label/allsubjs_rh_antTPJ.label
if ( ! -e $labelfile ) then
if ( ! -e 
/r2/users/fspace2/autorecon-subjects//ec51/label/allsubjs_rh_antTPJ.label 
) then
endif
endif
if ( $#segvol ) then
if ( 0 ) then
if ( $#annot ) then
if ( 0 ) then
if ( $#contrast ) then
if ( 0 ) then
set roivol = $anadir/$roiname.$ext
set roivol = 
/srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.ERROR: 
could not determine format for 
/srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh/meanfunc
set: Variable name must begin with a letter.
kdevaney@frontal: [229] 
circlet/connectivity_average_labels/ROI_average_labels/
On 9/3/13 10:11 AM, Douglas N Greve wrote:
...
It looks like it is dying on this command. Can you run it? If you get 
the same error, run it with -debug as the first option and send me 
the terminal output
funcroi-sess -s 120723EC -d /srv/mind3/r2/users/fspace2 -roi 
ROI_rh_antTPJ.roi -update
On 08/30/2013 04:27 PM, Kathryn Devaney wrote:
...
Hi Doug,
The -debug output is below and also in the attached text file - the 
first line is the command.
Thanks!
Katie
kdevaney@frontal: [231] 
circlet/connectivity_average_labels/ROI_average_labels/ 
funcroi-table-sess -debug -o output.rh_antTPJ -roi ROI_rh_antTPJ.roi 
-a circlet.fsaverage.sm3.mc.rh -c 3v4 -sf sessid -df sesspar
set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 12 != 0 )
set flag = $argv[1] ; shift ;
set flag = -o
shift
switch ( $flag )
switch ( -o )
end
end
while ( $#argv != 0 )
while ( 11 != 0 )
set flag = $argv[1] ; shift ;
set flag = output.rh_antTPJ
shift
switch ( $flag )
switch ( output.rh_antTPJ )
end
end
while ( $#argv != 0 )
while ( 10 != 0 )
set flag = $argv[1] ; shift ;
set flag = -roi
shift
switch ( $flag )
switch ( -roi )
end
end
while ( $#argv != 0 )
while ( 9 != 0 )
set flag = $argv[1] ; shift ;
set flag = ROI_rh_antTPJ.roi
shift
switch ( $flag )
switch ( ROI_rh_antTPJ.roi )
end
end
while ( $#argv != 0 )
while ( 8 != 0 )
set flag = $argv[1] ; shift ;
set flag = -a
shift
switch ( $flag )
switch ( -a )
end
end
while ( $#argv != 0 )
while ( 7 != 0 )
set flag = $argv[1] ; shift ;
set flag = circlet.fsaverage.sm3.mc.rh
shift
switch ( $flag )
switch ( circlet.fsaverage.sm3.mc.rh )
end
end
while ( $#argv != 0 )
while ( 6 != 0 )
set flag = $argv[1] ; shift ;
set flag = -c
shift
switch ( $flag )
switch ( -c )
end
end
while ( $#argv != 0 )
while ( 5 != 0 )
set flag = $argv[1] ; shift ;
set flag = 3v4
shift
switch ( $flag )
switch ( 3v4 )
end
end
while ( $#argv != 0 )
while ( 4 != 0 )
set flag = $argv[1] ; shift ;
set flag = -sf
shift
switch ( $flag )
switch ( -sf )
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set grpdef = $argv[1] ; shift ;
set grpdef = sessid
shift
if ( ! -e $grpdef ) then
if ( ! -e sessid ) then
set grpdefs = ( $grpdefs $grpdef ) ;
set grpdefs = ( sessid )
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = -df
shift
switch ( $flag )
switch ( -df )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
if ( ! -e $argv[1] ) then
if ( ! -e sesspar ) then
set srchdirfile = $argv[1] ; shift ;
set srchdirfile = sesspar
shift
set SearchPathList = ( $SearchPathList `cat $srchdirfile` ) ;
set SearchPathList = ( `cat $srchdirfile` )
cat sesspar
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
foreach grp ( $grpdefs )
foreach grp ( sessid )
set SessList = ( $SessList `cat $grp` ) ;
set SessList = ( `cat $grp` )
cat sessid
end
end
goto check_params ;
goto check_params
if ( $#SessList == 0 ) then
if ( 6 == 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 ( /r2/users/fspace2/ )
if ( ! -e $d ) then
if ( ! -e /r2/users/fspace2/ ) then
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
if ( 1 ) set UniqueList = ( /r2/users/fspace2/ )
set UniqueList = ( /r2/users/fspace2/ )
end
end
set SearchPathList = ( $UniqueList ) ;
set SearchPathList = ( /r2/users/fspace2/ )
set errs = 0 ;
set errs = 0
set SessPath = ( ) ;
set SessPath = ( )
foreach sess ( $SessList )
foreach sess ( 120209UU 120314ST 120405CC_circlet 120723EC 120723NP 
120723QL )
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( /r2/users/fspace2/ )
set stst = $d/$sess
set stst = /r2/users/fspace2//120209UU
if ( -d $stst ) then
if ( -d /r2/users/fspace2//120209UU ) then
if ( ! -r $stst ) then
if ( ! -r /r2/users/fspace2//120209UU ) then
pushd $stst > /dev/null ;
pushd /r2/users/fspace2//120209UU
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 = ( /srv/mind3/r2/users/fspace2/120209UU )
end
end
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( /r2/users/fspace2/ )
set stst = $d/$sess
set stst = /r2/users/fspace2//120314ST
if ( -d $stst ) then
if ( -d /r2/users/fspace2//120314ST ) then
if ( ! -r $stst ) then
if ( ! -r /r2/users/fspace2//120314ST ) then
pushd $stst > /dev/null ;
pushd /r2/users/fspace2//120314ST
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 = ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST )
end
end
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( /r2/users/fspace2/ )
set stst = $d/$sess
set stst = /r2/users/fspace2//120405CC_circlet
if ( -d $stst ) then
if ( -d /r2/users/fspace2//120405CC_circlet ) then
if ( ! -r $stst ) then
if ( ! -r /r2/users/fspace2//120405CC_circlet ) then
pushd $stst > /dev/null ;
pushd /r2/users/fspace2//120405CC_circlet
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 = ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST 
/srv/mind3/r2/users/fspace2/120405CC_circlet )
end
end
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( /r2/users/fspace2/ )
set stst = $d/$sess
set stst = /r2/users/fspace2//120723EC
if ( -d $stst ) then
if ( -d /r2/users/fspace2//120723EC ) then
if ( ! -r $stst ) then
if ( ! -r /r2/users/fspace2//120723EC ) then
pushd $stst > /dev/null ;
pushd /r2/users/fspace2//120723EC
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 = ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST 
/srv/mind3/r2/users/fspace2/120405CC_circlet 
/srv/mind3/r2/users/fspace2/120723EC )
end
end
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( /r2/users/fspace2/ )
set stst = $d/$sess
set stst = /r2/users/fspace2//120723NP
if ( -d $stst ) then
if ( -d /r2/users/fspace2//120723NP ) then
if ( ! -r $stst ) then
if ( ! -r /r2/users/fspace2//120723NP ) then
pushd $stst > /dev/null ;
pushd /r2/users/fspace2//120723NP
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 = ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST 
/srv/mind3/r2/users/fspace2/120405CC_circlet 
/srv/mind3/r2/users/fspace2/120723EC 
/srv/mind3/r2/users/fspace2/120723NP )
end
end
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( /r2/users/fspace2/ )
set stst = $d/$sess
set stst = /r2/users/fspace2//120723QL
if ( -d $stst ) then
if ( -d /r2/users/fspace2//120723QL ) then
if ( ! -r $stst ) then
if ( ! -r /r2/users/fspace2//120723QL ) then
pushd $stst > /dev/null ;
pushd /r2/users/fspace2//120723QL
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 = ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST 
/srv/mind3/r2/users/fspace2/120405CC_circlet 
/srv/mind3/r2/users/fspace2/120723EC 
/srv/mind3/r2/users/fspace2/120723NP 
/srv/mind3/r2/users/fspace2/120723QL )
end
end
set UniqueList = ( ) ;
set UniqueList = ( )
foreach s ( $SessPath )
foreach s ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST 
/srv/mind3/r2/users/fspace2/120405CC_circlet 
/srv/mind3/r2/users/fspace2/120723EC 
/srv/mind3/r2/users/fspace2/120723NP 
/srv/mind3/r2/users/fspace2/120723QL )
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 = ( /srv/mind3/r2/users/fspace2/120209UU )
endif
endif
end
end
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( /srv/mind3/r2/users/fspace2/120209UU )
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120314ST == 
/srv/mind3/r2/users/fspace2/120209UU ) then
end
end
if ( ! $IsUnique && ! $AllowRedundant ) then
if ( ! 1 && ! 0 ) then
set UniqueList = ( $UniqueList $s ) ;
set UniqueList = ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST )
endif
endif
end
end
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST )
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120405CC_circlet == 
/srv/mind3/r2/users/fspace2/120209UU ) then
end
end
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120405CC_circlet == 
/srv/mind3/r2/users/fspace2/120314ST ) then
end
end
if ( ! $IsUnique && ! $AllowRedundant ) then
if ( ! 1 && ! 0 ) then
set UniqueList = ( $UniqueList $s ) ;
set UniqueList = ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST 
/srv/mind3/r2/users/fspace2/120405CC_circlet )
endif
endif
end
end
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST 
/srv/mind3/r2/users/fspace2/120405CC_circlet )
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120723EC == 
/srv/mind3/r2/users/fspace2/120209UU ) then
end
end
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120723EC == 
/srv/mind3/r2/users/fspace2/120314ST ) then
end
end
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120723EC == 
/srv/mind3/r2/users/fspace2/120405CC_circlet ) then
end
end
if ( ! $IsUnique && ! $AllowRedundant ) then
if ( ! 1 && ! 0 ) then
set UniqueList = ( $UniqueList $s ) ;
set UniqueList = ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST 
/srv/mind3/r2/users/fspace2/120405CC_circlet 
/srv/mind3/r2/users/fspace2/120723EC )
endif
endif
end
end
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST 
/srv/mind3/r2/users/fspace2/120405CC_circlet 
/srv/mind3/r2/users/fspace2/120723EC )
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120723NP == 
/srv/mind3/r2/users/fspace2/120209UU ) then
end
end
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120723NP == 
/srv/mind3/r2/users/fspace2/120314ST ) then
end
end
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120723NP == 
/srv/mind3/r2/users/fspace2/120405CC_circlet ) then
end
end
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120723NP == 
/srv/mind3/r2/users/fspace2/120723EC ) then
end
end
if ( ! $IsUnique && ! $AllowRedundant ) then
if ( ! 1 && ! 0 ) then
set UniqueList = ( $UniqueList $s ) ;
set UniqueList = ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST 
/srv/mind3/r2/users/fspace2/120405CC_circlet 
/srv/mind3/r2/users/fspace2/120723EC 
/srv/mind3/r2/users/fspace2/120723NP )
endif
endif
end
end
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST 
/srv/mind3/r2/users/fspace2/120405CC_circlet 
/srv/mind3/r2/users/fspace2/120723EC 
/srv/mind3/r2/users/fspace2/120723NP )
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120723QL == 
/srv/mind3/r2/users/fspace2/120209UU ) then
end
end
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120723QL == 
/srv/mind3/r2/users/fspace2/120314ST ) then
end
end
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120723QL == 
/srv/mind3/r2/users/fspace2/120405CC_circlet ) then
end
end
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120723QL == 
/srv/mind3/r2/users/fspace2/120723EC ) then
end
end
if ( $s == $u ) then
if ( /srv/mind3/r2/users/fspace2/120723QL == 
/srv/mind3/r2/users/fspace2/120723NP ) then
end
end
if ( ! $IsUnique && ! $AllowRedundant ) then
if ( ! 1 && ! 0 ) then
set UniqueList = ( $UniqueList $s ) ;
set UniqueList = ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST 
/srv/mind3/r2/users/fspace2/120405CC_circlet 
/srv/mind3/r2/users/fspace2/120723EC 
/srv/mind3/r2/users/fspace2/120723NP 
/srv/mind3/r2/users/fspace2/120723QL )
endif
endif
end
end
echo $SessPath
echo /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST 
/srv/mind3/r2/users/fspace2/120405CC_circlet 
/srv/mind3/r2/users/fspace2/120723EC 
/srv/mind3/r2/users/fspace2/120723NP 
/srv/mind3/r2/users/fspace2/120723QL
exit $errs ;
exit 0
set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 12 != 0 )
set flag = $argv[1] ; shift ;
set flag = -o
shift
switch ( $flag )
switch ( -o )
if ( $#argv < 1 ) goto arg1err ;
if ( 11 < 1 ) goto arg1err
set outtable = $argv[1] ; shift ;
set outtable = output.rh_antTPJ
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 10 != 0 )
set flag = $argv[1] ; shift ;
set flag = -roi
shift
switch ( $flag )
switch ( -roi )
if ( $#argv < 1 ) goto arg1err ;
if ( 9 < 1 ) goto arg1err
set roicfg = $argv[1] ; shift ;
set roicfg = ROI_rh_antTPJ.roi
shift
if ( ! -e $roicfg ) then
if ( ! -e ROI_rh_antTPJ.roi ) then
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 8 != 0 )
set flag = $argv[1] ; shift ;
set flag = -a
shift
switch ( $flag )
switch ( -a )
case "-analysis":
case -analysis:
if ( $#argv < 1 ) goto arg1err ;
if ( 7 < 1 ) goto arg1err
set analysis = $argv[1] ; shift ;
set analysis = circlet.fsaverage.sm3.mc.rh
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 6 != 0 )
set flag = $argv[1] ; shift ;
set flag = -c
shift
switch ( $flag )
switch ( -c )
case "-contrast":
case -contrast:
if ( $#argv < 1 ) goto arg1err ;
if ( 5 < 1 ) goto arg1err
set contrast = $argv[1] ; shift ;
set contrast = 3v4
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 4 != 0 )
set flag = $argv[1] ; shift ;
set flag = -sf
shift
switch ( $flag )
switch ( -sf )
case "-df":
case -df:
case "-d":
case -d:
set sessargs = ( $sessargs $flag $argv[1] ) ; shift ;
set sessargs = ( -sf sessid )
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = -df
shift
switch ( $flag )
switch ( -df )
case "-d":
case -d:
set sessargs = ( $sessargs $flag $argv[1] ) ; shift ;
set sessargs = ( -sf sessid -df sesspar )
shift
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 ( $#outtable == 0 ) then
if ( 1 == 0 ) then
if ( $#roicfg == 0 ) then
if ( 1 == 0 ) then
set ROIname = `cat $roicfg | awk '{if($1 == "roiname") print $2}'`
set ROIname = `cat $roicfg | awk '{if($1 == "roiname") print $2}'`
awk {if($1 == "roiname") print $2}
cat ROI_rh_antTPJ.roi
set ROIanalysis = `cat $roicfg | awk '{if($1 == "analysis") print $2}'`
set ROIanalysis = `cat $roicfg | awk '{if($1 == "analysis") print $2}'`
awk {if($1 == "analysis") print $2}
cat ROI_rh_antTPJ.roi
set ROIIsNative = `getana -a $ROIanalysis -t IsNative`
set ROIIsNative = `getana -a $ROIanalysis -t IsNative`
getana -a circlet.fsaverage.sm3.mc.rh -t IsNative
set ROIIsMNI305 = `getana -a $ROIanalysis -t IsMNI305`
set ROIIsMNI305 = `getana -a $ROIanalysis -t IsMNI305`
getana -a circlet.fsaverage.sm3.mc.rh -t IsMNI305
set ROIIsSurface = `getana -a $ROIanalysis -t IsSurface`
set ROIIsSurface = `getana -a $ROIanalysis -t IsSurface`
getana -a circlet.fsaverage.sm3.mc.rh -t IsSurface
set ROIhemi = ( ) ;
set ROIhemi = ( )
if ( $ROIIsSurface ) then
if ( 1 ) then
set ROIhemi = `getana -a $ROIanalysis -t hemi`
set ROIhemi = `getana -a $ROIanalysis -t hemi`
getana -a circlet.fsaverage.sm3.mc.rh -t hemi
endif
endif
set ROIfsd = `getana -a $ROIanalysis -t fsd`
set ROIfsd = `getana -a $ROIanalysis -t fsd`
getana -a circlet.fsaverage.sm3.mc.rh -t fsd
if ( $measure == volume && $#analysis ) then
if ( mean == volume && 1 ) then
if ( $measure == volume && $#contrast ) then
if ( mean == volume && 1 ) then
if ( $#analysis == 0 ) set analysis = $ROIanalysis
if ( 1 == 0 ) set analysis = circlet.fsaverage.sm3.mc.rh
if ( $#contrast == 0 && $#map != 0 ) then
if ( 1 == 0 && 0 != 0 ) then
if ( $#contrast ) then
if ( 1 ) then
set conlist = ( `getana -a $analysis -t contrasts` ) ;
set conlist = ( `getana -a $analysis -t contrasts` )
getana -a circlet.fsaverage.sm3.mc.rh -t contrasts
set ConFound = 0 ;
set ConFound = 0
foreach con ( $conlist )
foreach con ( 12v0 12v7 1v0 2v0 34v0 34v12 3v0 3v4 4v0 56v0 56v12 
56v34 5v0 6v0 7v0 )
if ( $con == $contrast ) set ConFound = 1 ;
if ( 12v0 == 3v4 ) set ConFound = 1
end
end
if ( $con == $contrast ) set ConFound = 1 ;
if ( 12v7 == 3v4 ) set ConFound = 1
end
end
if ( $con == $contrast ) set ConFound = 1 ;
if ( 1v0 == 3v4 ) set ConFound = 1
end
end
if ( $con == $contrast ) set ConFound = 1 ;
if ( 2v0 == 3v4 ) set ConFound = 1
end
end
if ( $con == $contrast ) set ConFound = 1 ;
if ( 34v0 == 3v4 ) set ConFound = 1
end
end
if ( $con == $contrast ) set ConFound = 1 ;
if ( 34v12 == 3v4 ) set ConFound = 1
end
end
if ( $con == $contrast ) set ConFound = 1 ;
if ( 3v0 == 3v4 ) set ConFound = 1
end
end
if ( $con == $contrast ) set ConFound = 1 ;
if ( 3v4 == 3v4 ) set ConFound = 1
set ConFound = 1
end
end
if ( $con == $contrast ) set ConFound = 1 ;
if ( 4v0 == 3v4 ) set ConFound = 1
end
end
if ( $con == $contrast ) set ConFound = 1 ;
if ( 56v0 == 3v4 ) set ConFound = 1
end
end
if ( $con == $contrast ) set ConFound = 1 ;
if ( 56v12 == 3v4 ) set ConFound = 1
end
end
if ( $con == $contrast ) set ConFound = 1 ;
if ( 56v34 == 3v4 ) set ConFound = 1
end
end
if ( $con == $contrast ) set ConFound = 1 ;
if ( 5v0 == 3v4 ) set ConFound = 1
end
end
if ( $con == $contrast ) set ConFound = 1 ;
if ( 6v0 == 3v4 ) set ConFound = 1
end
end
if ( $con == $contrast ) set ConFound = 1 ;
if ( 7v0 == 3v4 ) set ConFound = 1
end
end
if ( ! $ConFound ) then
if ( ! 1 ) then
if ( $#map == 0 ) set map = ces ;
if ( 0 == 0 ) set map = ces
set map = ces
endif
endif
set fsd = `getana -a $analysis -t fsd`
set fsd = `getana -a $analysis -t fsd`
getana -a circlet.fsaverage.sm3.mc.rh -t fsd
set IsNative = `getana -a $analysis -t IsNative`
set IsNative = `getana -a $analysis -t IsNative`
getana -a circlet.fsaverage.sm3.mc.rh -t IsNative
set IsMNI305 = `getana -a $analysis -t IsMNI305`
set IsMNI305 = `getana -a $analysis -t IsMNI305`
getana -a circlet.fsaverage.sm3.mc.rh -t IsMNI305
set IsSurface = `getana -a $analysis -t IsSurface`
set IsSurface = `getana -a $analysis -t IsSurface`
getana -a circlet.fsaverage.sm3.mc.rh -t IsSurface
set hemi = ( ) ;
set hemi = ( )
if ( $IsSurface ) then
if ( 1 ) then
set hemi = `getana -a $analysis -t hemi`
set hemi = `getana -a $analysis -t hemi`
getana -a circlet.fsaverage.sm3.mc.rh -t hemi
endif
endif
if ( ( $IsNative && ! $ROIIsNative ) || ( $IsMNI305 && ! 
$ROIIsMNI305 ) || ( $IsSurface && ! $ROIIsSurface ) ) then
if ( ( 0 && ! 0 ) || ( 0 && ! 0 ) || ( 1 && ! 1 ) ) then
if ( $IsSurface && $hemi != $ROIhemi ) then
if ( 1 && rh != rh ) then
goto check_params_return ;
goto check_params_return
if ( $#LF == 0 ) set LF = log/funcroi-table-sess.log
if ( 0 == 0 ) set LF = log/funcroi-table-sess.log
set LF = log/funcroi-table-sess.log
if ( -e $LF ) mv $LF $LF.old
if ( -e log/funcroi-table-sess.log ) mv log/funcroi-table-sess.log 
log/funcroi-table-sess.log.old
mv log/funcroi-table-sess.log log/funcroi-table-sess.log.old
echo $LF
echo log/funcroi-table-sess.log
log/funcroi-table-sess.log
echo "funcroi-table-sess log file" >> $LF
echo funcroi-table-sess log file
echo $VERSION >> $LF
echo $Id: funcroi-table-sess,v 1.3.2.3 2011/04/18 19:50:37 greve Exp $
date >> $LF
date
uname -a >> $LF
uname -a
pwd >> $LF
pwd
echo $0 >> $LF
echo 
/scratch/local/pkg/freesurfer/freesurfer-5.1.0/fsfast/bin/funcroi-table-sess
echo $inputargs >> $LF
echo -debug -o output.rh_antTPJ -roi ROI_rh_antTPJ.roi -a 
circlet.fsaverage.sm3.mc.rh -c 3v4 -sf sessid -df sesspar
id >> $LF
id
set StartTime = `date` ;
set StartTime = `date`
date
set tmpdir = /tmp/tmp.funcroi-table-sess.$$
set tmpdir = /tmp/tmp.funcroi-table-sess.4966
mkdir -p $tmpdir
mkdir -p /tmp/tmp.funcroi-table-sess.4966
set sess0list = ( ) ;
set sess0list = ( )
set sumlist = ( ) ;
set sumlist = ( )
set sessidlist = $tmpdir/sessid
set sessidlist = /tmp/tmp.funcroi-table-sess.4966/sessid
rm -f $sessidlist
rm -f /tmp/tmp.funcroi-table-sess.4966/sessid
echo "FirstRow" >> $sessidlist
echo FirstRow
foreach sess ( $SessList )
foreach sess ( /srv/mind3/r2/users/fspace2/120209UU 
/srv/mind3/r2/users/fspace2/120314ST 
/srv/mind3/r2/users/fspace2/120405CC_circlet 
/srv/mind3/r2/users/fspace2/120723EC 
/srv/mind3/r2/users/fspace2/120723NP 
/srv/mind3/r2/users/fspace2/120723QL )
set sessid = `basename $sess` ;
set sessid = `basename $sess`
basename /srv/mind3/r2/users/fspace2/120209UU
set sessdir = `dirname $sess` ;
set sessdir = `dirname $sess`
dirname /srv/mind3/r2/users/fspace2/120209UU
echo "$sessid" >> $sessidlist
echo 120209UU
set ROIanadir = $sess/$ROIfsd/$ROIanalysis
set ROIanadir = 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh
if ( ! -e $ROIanadir ) then
if ( ! -e 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh 
) then
set cmd = ( funcroi-sess -s $sessid -d $sessdir -roi $roicfg -update )
set cmd = ( funcroi-sess -s 120209UU -d /srv/mind3/r2/users/fspace2 
-roi ROI_rh_antTPJ.roi -update )
echo $cmd
echo funcroi-sess -s 120209UU -d /srv/mind3/r2/users/fspace2 -roi 
ROI_rh_antTPJ.roi -update
funcroi-sess -s 120209UU -d /srv/mind3/r2/users/fspace2 -roi 
ROI_rh_antTPJ.roi -update
$cmd
funcroi-sess -s 120209UU -d /srv/mind3/r2/users/fspace2 -roi 
ROI_rh_antTPJ.roi -update

/srv/mind3/r2/users/fspace2/120209UU
Fri Aug 30 16:23:55 EDT 2013
120209UU Update not needed
Ended   at Fri Aug 30 16:23:55 EDT 2013
funcroi-sess completed
if ( $status ) exit 1 ;
if ( 0 ) exit 1
set ROImask = `stem2fname $sess/$ROIfsd/$ROIanalysis/$ROIname`
set ROImask = `stem2fname $sess/$ROIfsd/$ROIanalysis/$ROIname`
stem2fname 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ
if ( $status ) then
if ( 0 ) then
set anadir = $sess/$fsd/$analysis
set anadir = 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh
if ( ! -e $anadir ) then
if ( ! -e 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh 
) then
if ( $#contrast ) then
if ( 1 ) then
set condir = $anadir/$contrast
set condir = 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4
set mapfile = `stem2fname $condir/$map` ;
set mapfile = `stem2fname $condir/$map`
stem2fname 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces
if ( $status ) then
if ( 0 ) then
else
else
set sumdir = $tmpdir/$sessid
set sumdir = /tmp/tmp.funcroi-table-sess.4966/120209UU
mkdir -p $sumdir
mkdir -p /tmp/tmp.funcroi-table-sess.4966/120209UU
set sum = $sumdir/$ROIname.$frame.dat
set sum = /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat
set cmd = ( mri_segstats --seg $ROImask --frame $frame --id 1 --i 
$mapfile --sum $sum )
set cmd = ( mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat )
echo $cmd
echo mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat
mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat
$cmd | tee -a $LF
mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat
tee -a log/funcroi-table-sess.log
$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
cwd
cmdline mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat
sysname  Linux
hostname frontal
machine  x86_64
user     kdevaney
Loading 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz
Loading 
/srv/mind3/r2/users/fspace2/120209UU/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0     1    809  809
Reporting on   1 segmentations
if ( $status ) exit 1 ;
if ( 0 ) exit 1
set ok = `grep -v # $sum | wc -l`
set ok = `grep -v # $sum | wc -l`
wc -l
grep -v # /tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat
if ( ! $ok ) then
if ( ! 1 ) then
set sumlist = ( $sumlist $sum )
set sumlist = ( 
/tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat )
end
end
set sessid = `basename $sess` ;
set sessid = `basename $sess`
basename /srv/mind3/r2/users/fspace2/120314ST
set sessdir = `dirname $sess` ;
set sessdir = `dirname $sess`
dirname /srv/mind3/r2/users/fspace2/120314ST
echo "$sessid" >> $sessidlist
echo 120314ST
set ROIanadir = $sess/$ROIfsd/$ROIanalysis
set ROIanadir = 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh
if ( ! -e $ROIanadir ) then
if ( ! -e 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh 
) then
set cmd = ( funcroi-sess -s $sessid -d $sessdir -roi $roicfg -update )
set cmd = ( funcroi-sess -s 120314ST -d /srv/mind3/r2/users/fspace2 
-roi ROI_rh_antTPJ.roi -update )
echo $cmd
echo funcroi-sess -s 120314ST -d /srv/mind3/r2/users/fspace2 -roi 
ROI_rh_antTPJ.roi -update
funcroi-sess -s 120314ST -d /srv/mind3/r2/users/fspace2 -roi 
ROI_rh_antTPJ.roi -update
$cmd
funcroi-sess -s 120314ST -d /srv/mind3/r2/users/fspace2 -roi 
ROI_rh_antTPJ.roi -update

/srv/mind3/r2/users/fspace2/120314ST
Fri Aug 30 16:23:55 EDT 2013
120314ST Update not needed
Ended   at Fri Aug 30 16:23:55 EDT 2013
funcroi-sess completed
if ( $status ) exit 1 ;
if ( 0 ) exit 1
set ROImask = `stem2fname $sess/$ROIfsd/$ROIanalysis/$ROIname`
set ROImask = `stem2fname $sess/$ROIfsd/$ROIanalysis/$ROIname`
stem2fname 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ
if ( $status ) then
if ( 0 ) then
set anadir = $sess/$fsd/$analysis
set anadir = 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh
if ( ! -e $anadir ) then
if ( ! -e 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh 
) then
if ( $#contrast ) then
if ( 1 ) then
set condir = $anadir/$contrast
set condir = 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4
set mapfile = `stem2fname $condir/$map` ;
set mapfile = `stem2fname $condir/$map`
stem2fname 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces
if ( $status ) then
if ( 0 ) then
else
else
set sumdir = $tmpdir/$sessid
set sumdir = /tmp/tmp.funcroi-table-sess.4966/120314ST
mkdir -p $sumdir
mkdir -p /tmp/tmp.funcroi-table-sess.4966/120314ST
set sum = $sumdir/$ROIname.$frame.dat
set sum = /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat
set cmd = ( mri_segstats --seg $ROImask --frame $frame --id 1 --i 
$mapfile --sum $sum )
set cmd = ( mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat )
echo $cmd
echo mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat
mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat
$cmd | tee -a $LF
mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat
tee -a log/funcroi-table-sess.log
$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
cwd
cmdline mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat
sysname  Linux
hostname frontal
machine  x86_64
user     kdevaney
Loading 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz
Loading 
/srv/mind3/r2/users/fspace2/120314ST/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0     1    784  784
Reporting on   1 segmentations
if ( $status ) exit 1 ;
if ( 0 ) exit 1
set ok = `grep -v # $sum | wc -l`
set ok = `grep -v # $sum | wc -l`
wc -l
grep -v # /tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat
if ( ! $ok ) then
if ( ! 1 ) then
set sumlist = ( $sumlist $sum )
set sumlist = ( 
/tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat 
/tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat )
end
end
set sessid = `basename $sess` ;
set sessid = `basename $sess`
basename /srv/mind3/r2/users/fspace2/120405CC_circlet
set sessdir = `dirname $sess` ;
set sessdir = `dirname $sess`
dirname /srv/mind3/r2/users/fspace2/120405CC_circlet
echo "$sessid" >> $sessidlist
echo 120405CC_circlet
set ROIanadir = $sess/$ROIfsd/$ROIanalysis
set ROIanadir = 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh
if ( ! -e $ROIanadir ) then
if ( ! -e 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh 
) then
set cmd = ( funcroi-sess -s $sessid -d $sessdir -roi $roicfg -update )
set cmd = ( funcroi-sess -s 120405CC_circlet -d 
/srv/mind3/r2/users/fspace2 -roi ROI_rh_antTPJ.roi -update )
echo $cmd
echo funcroi-sess -s 120405CC_circlet -d /srv/mind3/r2/users/fspace2 
-roi ROI_rh_antTPJ.roi -update
funcroi-sess -s 120405CC_circlet -d /srv/mind3/r2/users/fspace2 -roi 
ROI_rh_antTPJ.roi -update
$cmd
funcroi-sess -s 120405CC_circlet -d /srv/mind3/r2/users/fspace2 -roi 
ROI_rh_antTPJ.roi -update

/srv/mind3/r2/users/fspace2/120405CC_circlet
Fri Aug 30 16:23:55 EDT 2013
120405CC_circlet Update not needed
Ended   at Fri Aug 30 16:23:55 EDT 2013
funcroi-sess completed
if ( $status ) exit 1 ;
if ( 0 ) exit 1
set ROImask = `stem2fname $sess/$ROIfsd/$ROIanalysis/$ROIname`
set ROImask = `stem2fname $sess/$ROIfsd/$ROIanalysis/$ROIname`
stem2fname 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ
if ( $status ) then
if ( 0 ) then
set anadir = $sess/$fsd/$analysis
set anadir = 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh
if ( ! -e $anadir ) then
if ( ! -e 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh 
) then
if ( $#contrast ) then
if ( 1 ) then
set condir = $anadir/$contrast
set condir = 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4
set mapfile = `stem2fname $condir/$map` ;
set mapfile = `stem2fname $condir/$map`
stem2fname 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces
if ( $status ) then
if ( 0 ) then
else
else
set sumdir = $tmpdir/$sessid
set sumdir = /tmp/tmp.funcroi-table-sess.4966/120405CC_circlet
mkdir -p $sumdir
mkdir -p /tmp/tmp.funcroi-table-sess.4966/120405CC_circlet
set sum = $sumdir/$ROIname.$frame.dat
set sum = 
/tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat
set cmd = ( mri_segstats --seg $ROImask --frame $frame --id 1 --i 
$mapfile --sum $sum )
set cmd = ( mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum 
/tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat )
echo $cmd
echo mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum 
/tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat
mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum 
/tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat
$cmd | tee -a $LF
mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum 
/tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat
tee -a log/funcroi-table-sess.log
$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
cwd
cmdline mri_segstats --seg 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz 
--frame 0 --id 1 --i 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz 
--sum 
/tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat
sysname  Linux
hostname frontal
machine  x86_64
user     kdevaney
Loading 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/ROI_rh_antTPJ.nii.gz
Loading 
/srv/mind3/r2/users/fspace2/120405CC_circlet/bold_nopace/circlet.fsaverage.sm3.mc.rh/3v4/ces.nii.gz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0     1    801  801
Reporting on   1 segmentations
if ( $status ) exit 1 ;
if ( 0 ) exit 1
set ok = `grep -v # $sum | wc -l`
set ok = `grep -v # $sum | wc -l`
wc -l
grep -v # 
/tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat
if ( ! $ok ) then
if ( ! 1 ) then
set sumlist = ( $sumlist $sum )
set sumlist = ( 
/tmp/tmp.funcroi-table-sess.4966/120209UU/ROI_rh_antTPJ.0.dat 
/tmp/tmp.funcroi-table-sess.4966/120314ST/ROI_rh_antTPJ.0.dat 
/tmp/tmp.funcroi-table-sess.4966/120405CC_circlet/ROI_rh_antTPJ.0.dat )
end
end
set sessid = `basename $sess` ;
set sessid = `basename $sess`
basename /srv/mind3/r2/users/fspace2/120723EC
set sessdir = `dirname $sess` ;
set sessdir = `dirname $sess`
dirname /srv/mind3/r2/users/fspace2/120723EC
echo "$sessid" >> $sessidlist
echo 120723EC
set ROIanadir = $sess/$ROIfsd/$ROIanalysis
set ROIanadir = 
/srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh
if ( ! -e $ROIanadir ) then
if ( ! -e 
/srv/mind3/r2/users/fspace2/120723EC/bold_nopace/circlet.fsaverage.sm3.mc.rh 
) then
set cmd = ( funcroi-sess -s $sessid -d $sessdir -roi $roicfg -update )
set cmd = ( funcroi-sess -s 120723EC -d /srv/mind3/r2/users/fspace2 
-roi ROI_rh_antTPJ.roi -update )
echo $cmd
echo funcroi-sess -s 120723EC -d /srv/mind3/r2/users/fspace2 -roi 
ROI_rh_antTPJ.roi -update
funcroi-sess -s 120723EC -d /srv/mind3/r2/users/fspace2 -roi 
ROI_rh_antTPJ.roi -update
$cmd
funcroi-sess -s 120723EC -d /srv/mind3/r2/users/fspace2 -roi 
ROI_rh_antTPJ.roi -update

/srv/mind3/r2/users/fspace2/120723EC
Fri Aug 30 16:23:56 EDT 2013
set: Variable name must begin with a letter.
if ( $status ) exit 1 ;
if ( 1 ) exit 1
exit 1
On 8/30/13 2:09 PM, Douglas N Greve wrote:
...
Hi Katie, can you run it with -debug as the first arg and send me the
copious terminal output?
doug
On 08/30/2013 01:53 PM, Kathryn Devaney wrote:
...
Hi Doug&  Surfers,
I'm having this same issue.  I'm running funcroi-table-sess on two
analyses (lh and rh). There was no 'log' folder in my working 
directory,
so I created it.  Everythingran fine for the lh, but when I try to 
run
it in the rh I get
set: Variable name must begin with a letter
Here's the output of 'bugr' on my machine:

FREESURFER_HOME: /scratch/local/pkg/freesurfer/freesurfer-5.1.0
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
RedHat release: Fedora release 17 (Beefy Miracle)
Kernel info: Linux 3.6.3-1.fc17.x86_64 x86_64

Let me know if you'd like me to send the terminal output of
funcroi-table-sess -debug
Thanks!
Katie
On 8/19/13 4:05 PM, Douglas N Greve wrote:
...
Is there a folder called "log" in the directly you are running it 
from?
If not, try creating one. If so, then
run it with -debug as the first arg and send me the terminal output.
doug
On 08/19/2013 02:07 PM, Joseph Andreano wrote:
> Hi All,
>
> I'm trying to use funcroi-table-sess, but whenever I send this 
> command:
>
> funcroi-table-sess -roi l_amyg_test -analysis habit_concat.mni305
> -contrast neg1Vfix -sf subjects.lst -o l_amyg_neg1Vfix.dat
>
> I get this error:
>
> set: Variable name must begin with a letter
>
> So far as I can tell, all the variables in that command begin 
> with a
> letter.  Any idea what the problem might be?
>
>
> _________________________________
>
> Joseph M. Andreano, PhD
> Postdoctoral Researcher
> Interdisciplinary Affective
>        Science Laboratory
> Massachusetts General Hospital
> _________________________________
> _______________________________________________
> 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
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/