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