External Email - Use Caution
Hi,
We are trying to do % signal change within a ROI. However, when we run
funcroi-sess function (after funcroi-config), we get following output in
terminal
set: variable name must begin with a letter
When we run the function with -debug, we saw that the function cannot find
meanfunc file. This is because we do our analysis performed as per-run and
therefore meanfunc files are not in the following path
$SUBJECTS_DIR/<session_folder>/bold/<analysis_folder>/meanfunc but exists in
$SUBJECTS_DIR/<session_folder>/bold/<analysis_folder>/pr001/meanfunc for each
run.
Could you please help us with this problem? I add the -debug output as an
attachment.
FYI: We use version 7.2 but tried it also with 7.5, problem persists there
Best, Beyza
set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
foreach grp ( $grpdefs )
foreach grp ( )
goto check_params ;
goto check_params
if ( $#SessList == 0 ) then
if ( 1 == 0 ) then
if ( $#SearchPathList == 0 ) then
if ( 0 == 0 ) then
set SearchPathList = "." ;
set SearchPathList = .
endif
endif
goto check_params_return ;
goto check_params_return
set UniqueList = ( ) ;
set UniqueList = ( )
foreach d ( $SearchPathList )
foreach d ( . )
if ( ! -e $d ) then
if ( ! -e . ) then
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
if ( 1 ) set UniqueList = ( . )
set UniqueList = ( . )
end
end
set SearchPathList = ( $UniqueList ) ;
set SearchPathList = ( . )
set errs = 0 ;
set errs = 0
set SessPath = ( ) ;
set SessPath = ( )
foreach sess ( $SessList )
foreach sess ( sub-201_post-task )
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( . )
set stst = $d/$sess
set stst = ./sub-201_post-task
if ( -d $stst ) then
if ( -d ./sub-201_post-task ) then
if ( ! -r $stst ) then
if ( ! -r ./sub-201_post-task ) then
pushd $stst > /dev/null ;
pushd ./sub-201_post-task
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 = ( <subj-directory>/sub-201_post-task )
end
end
set UniqueList = ( ) ;
set UniqueList = ( )
foreach s ( $SessPath )
foreach s ( <subj-directory>/sub-201_post-task )
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 = ( <subj-directory>/sub-201_post-task )
endif
endif
end
end
echo $SessPath
echo <subj-directory>/sub-201_post-task
exit $errs ;
exit 0
set echo = 1 ;
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto check_params ;
goto check_params
if ( $#SessList == 0 ) then
if ( 1 == 0 ) then
if ( $#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 rh.V1
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 rh.V1
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 rh.V1
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 rh.V1
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 rh.V1
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 rh.V1
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 rh.V1
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 rh.V1
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 rh.V1
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 rh.V1
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 rh.V1
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 rh.V1
if ( ! -d $analysis ) then
if ( ! -d task ) 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 task -t fsd
set IsNative = `getana -a $analysis -t IsNative`
set IsNative = `getana -a $analysis -t IsNative`
getana -a task -t IsNative
set IsMNI305 = `getana -a $analysis -t IsMNI305`
set IsMNI305 = `getana -a $analysis -t IsMNI305`
getana -a task -t IsMNI305
set IsSurface = `getana -a $analysis -t IsSurface`
set IsSurface = `getana -a $analysis -t IsSurface`
getana -a task -t IsSurface
if ( $IsSurface ) then
if ( 1 ) then
set hemi = `getana -a $analysis -t hemi`
set hemi = `getana -a $analysis -t hemi`
getana -a task -t hemi
set anasubject = `getana -a $analysis -t subject`
set anasubject = `getana -a $analysis -t subject`
getana -a task -t subject
endif
endif
set RegDOF = `getana -a $analysis -t RegDOF`
set RegDOF = `getana -a $analysis -t RegDOF`
getana -a task -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 ( <subj-directory>/sub-201_post-task )
@ nthsess = $nthsess + 1 ;
@ nthsess = 0 + 1
set sessbase = `basename $sess` ;
set sessbase = `basename $sess`
basename <subj-directory>/sub-201_post-task
set sessdir = `dirname $sess` ;
set sessdir = `dirname $sess`
dirname <subj-directory>/sub-201_post-task
echo "-------------------------------------------"
echo -------------------------------------------
-------------------------------------------
echo "$sess "
echo <subj-directory>/sub-201_post-task
<subj-directory>/sub-201_post-task
date
date
Tue 06 Feb 2024 03:36:11 PM CET
set subject = `cat $sess/subjectname`
set subject = `cat $sess/subjectname`
cat <subj-directory>/sub-201_post-task/subjectname
set anadir = $sess/$fsd/$analysis
set anadir = <subj-directory>/sub-201_post-task/bold/task
if ( ! -e $anadir ) then
if ( ! -e <subj-directory>/sub-201_post-task/bold/task ) then
set ext = `stem2fmt $anadir/meanfunc`
set ext = `stem2fmt $anadir/meanfunc`
stem2fmt <subj-directory>/sub-201_post-task/bold/task/meanfunc
if ( $#label ) then
if ( 1 ) then
set labelfile = $SUBJECTS_DIR/$subject/label/$label
set labelfile = <subj-directory>//sub-201_ses-post.long.sub-201_main/label/rh.V1
if ( ! -e $labelfile ) then
if ( ! -e <subj-directory>//sub-201_ses-post.long.sub-201_main/label/rh.V1 )
then
set labelfile0 = $labelfile
set labelfile0 =
<subj-directory>//sub-201_ses-post.long.sub-201_main/label/rh.V1
set labelfile = $SUBJECTS_DIR/$subject/label/$label.label
set labelfile =
<subj-directory>//sub-201_ses-post.long.sub-201_main/label/rh.V1.label
if ( ! -e $labelfile ) then
if ( ! -e
<subj-directory>//sub-201_ses-post.long.sub-201_main/label/rh.V1.label ) then
endif
endif
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 = <subj-directory>/sub-201_post-task/bold/task/rh.V1.ERROR: could
not determine format for <subj-directory>/sub-201_post-task/bold/task/meanfunc
set: Variable name must begin with a letter._______________________________________________
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