fieldsign-sess -a rtopy.self.lh -occip -s sj12 -debug
set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return

foreach grp ( $grpdefs )
foreach grp ( )

goto check_params ;
goto check_params

if ( $#SessList == 0 ) then
if ( 1 == 0 ) then

if ( $#SearchPathList == 0 ) then
if ( 0 == 0 ) then
set SearchPathList = "." ;
set SearchPathList = .
endif
endif

goto check_params_return ;
goto check_params_return


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

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

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

set errs = 0 ;
set errs = 0


set SessPath = ( ) ;
set SessPath = ( )
foreach sess ( $SessList )
foreach sess ( sj12 )
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( . )
set stst = $d/$sess
set stst = ./sj12
if ( -d $stst ) then
if ( -d ./sj12 ) then
if ( ! -r $stst ) then
if ( ! -r ./sj12 ) then
pushd $stst > /dev/null ;
pushd ./sj12
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 = ( /usr/local/freesurfer/subjects/retinotopy/sj12 )
end
end


set UniqueList = ( ) ;
set UniqueList = ( )
foreach s ( $SessPath )
foreach s ( /usr/local/freesurfer/subjects/retinotopy/sj12 )
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 = ( /usr/local/freesurfer/subjects/retinotopy/sj12 )
endif
endif
end
end


echo $SessPath
echo /usr/local/freesurfer/subjects/retinotopy/sj12

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 ( $#analysis == 0 ) then
if ( 1 == 0 ) then
if ( $#patch == 0 && $UseSphere == 0 ) then
if ( 1 == 0 && 0 == 0 ) then
if ( $#patch && $UseSphere ) then
if ( 1 && 0 ) then

set IsRet = `getana -a $analysis -t IsRetinotopy`
set IsRet = `getana -a $analysis -t IsRetinotopy`
getana -a rtopy.self.lh -t IsRetinotopy
if ( ! $IsRet ) then
if ( ! 1 ) then

set IsMNI305Ana = `getana -a $analysis -t IsMNI305`
set IsMNI305Ana = `getana -a $analysis -t IsMNI305`
getana -a rtopy.self.lh -t IsMNI305
if ( $IsMNI305Ana ) then
if ( 0 ) then

set IsSurfAna = `getana -a $analysis -t IsSurface`
set IsSurfAna = `getana -a $analysis -t IsSurface`
getana -a rtopy.self.lh -t IsSurface
if ( $IsSurfAna ) then
if ( 1 ) then
set anasubject = `getana -a $analysis -t subject`
set anasubject = `getana -a $analysis -t subject`
getana -a rtopy.self.lh -t subject
set hemilist = `getana -a $analysis -t hemi`
set hemilist = `getana -a $analysis -t hemi`
getana -a rtopy.self.lh -t hemi
endif
endif

set IsNativeAna = `getana -a $analysis -t IsNative`
set IsNativeAna = `getana -a $analysis -t IsNative`
getana -a rtopy.self.lh -t IsNative
if ( $IsNativeAna ) then
if ( 0 ) then

if ( $#regfile == 0 ) set regfile = register.dof$RegDOF.dat
if ( 0 == 0 ) set regfile = register.dof6.dat
set regfile = register.dof6.dat

set fsd = `getana -a $analysis -t fsd` ;
set fsd = `getana -a $analysis -t fsd`
getana -a rtopy.self.lh -t fsd
if ( ! $UseLog ) set LF = /dev/null
if ( ! 1 ) set LF = /dev/null

goto check_params_return ;
goto check_params_return


foreach sess ( $SessList )
foreach sess ( /usr/local/freesurfer/subjects/retinotopy/sj12 )
set sessid = `basename $sess` ;
set sessid = `basename $sess`
basename /usr/local/freesurfer/subjects/retinotopy/sj12

if ( $UseLog ) then
if ( 1 ) then

mkdir -p $sess/log
mkdir -p /usr/local/freesurfer/subjects/retinotopy/sj12/log
set LF = $sess/log/fieldsign-sess.log
set LF = /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log
if ( -e $LF ) mv $LF $LF.old
if ( -e /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log ) mv /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log.old
mv /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log.old
echo $LF
echo /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log
/usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log
echo "fieldsign-sess log file" >> $LF
echo fieldsign-sess log file
echo $VERSION >> $LF
echo $Id: fieldsign-sess,v 1.2 2010/05/04 22:00:18 greve Exp $
date >> $LF
date
uname -a >> $LF
uname -a
pwd >> $LF
pwd
echo $0 >> $LF
echo /usr/local/freesurfer/fsfast/bin/fieldsign-sess
echo $inputargs >> $LF
echo -a rtopy.self.lh -occip -s sj12 -debug
id >> $LF
id
endif
endif

set srcsubject = `cat $sess/subjectname`
set srcsubject = `cat $sess/subjectname`
cat /usr/local/freesurfer/subjects/retinotopy/sj12/subjectname
set sd = $SUBJECTS_DIR/$srcsubject
set sd = /usr/local/freesurfer/subjects/ld12
if ( ! -e $sd ) then
if ( ! -e /usr/local/freesurfer/subjects/ld12 ) then

set anadir = $sess/$fsd/$analysis
set anadir = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh
if ( ! -e $anadir ) then
if ( ! -e /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh ) then

set eccenreal = `stem2fname $anadir/eccen/real` ;
set eccenreal = `stem2fname $anadir/eccen/real`
stem2fname /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real
set eccenimag = `stem2fname $anadir/eccen/imag` ;
set eccenimag = `stem2fname $anadir/eccen/imag`
stem2fname /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag
set polarreal = `stem2fname $anadir/polar/real` ;
set polarreal = `stem2fname $anadir/polar/real`
stem2fname /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real
set polarimag = `stem2fname $anadir/polar/imag` ;
set polarimag = `stem2fname $anadir/polar/imag`
stem2fname /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag

if ( $IsNativeAna ) then
if ( 0 ) then
if ( $IsSurfAna ) then
if ( 1 ) then
if ( $anasubject == self ) set trgsubject = $srcsubject ;
if ( self == self ) set trgsubject = ld12
set trgsubject = ld12
if ( $anasubject != self ) set trgsubject = $anasubject ;
if ( self != self ) set trgsubject = self
endif
endif

set outdir = $anadir/fieldsign
set outdir = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign
mkdir -p $outdir
mkdir -p /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign

foreach hemi ( $hemilist )
foreach hemi ( lh )
if ( $IsNativeAna ) then
if ( 0 ) then

if ( $IsNativeAna ) then
if ( 0 ) then

set fieldsign = $outdir/fieldsign.nii
set fieldsign = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii
endif
endif

set cmd = ( mri_fieldsign --s $trgsubject --hemi $hemi --old --eccen $eccenreal $eccenimag --polar $polarreal $polarimag --fs $fieldsign )
set cmd = ( mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii )
if ( $#fwhm ) set cmd = ( $cmd --fwhm $fwhm ) ;
if ( 0 ) set cmd = ( mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --fwhm )
if ( $#patch ) set cmd = ( $cmd --patch occip.patch.flat )
if ( 1 ) set cmd = ( mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat )
set cmd = ( mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat )
if ( $UseSphere ) set cmd = ( $cmd --sphere ) ;
if ( 0 ) set cmd = ( mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat --sphere )
if ( $DoReverse ) set cmd = ( $cmd --rev ) ;
if ( 0 ) set cmd = ( mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat --rev )
echo $cmd | tee -a $LF
echo mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat
tee -a /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log
mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat
$cmd
mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat

$Id: mri_fieldsign.c,v 1.14 2011/03/02 00:04:15 nicks Exp $
cwd /usr/local/freesurfer/subjects/retinotopy
cmdline mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat 
sysname  Linux
hostname BOTANICA
machine  x86_64
user     michelle
eccen real  /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii
eccen imag  /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii
polar real  /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii
polar imag  /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii
patch     occip.patch.flat
subject     ld12
hemi        lh
fwhm        -1.000000
nsmooth     -1
fieldsign   /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii
usenew      0
Reading /usr/local/freesurfer/subjects/ld12/surf/lh.sphere
Reading /usr/local/freesurfer/subjects/ld12/surf/lh.occip.patch.flat
Reading /usr/local/freesurfer/subjects/ld12/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Complex
Ripping Zeros
ERROR: MRISripZeros(): dimension mismatch
ERROR: MRIScopyMRI: Surf/Src dimension mismatch.
ERROR: MRIScopyMRI: Surf/Src dimension mismatch.
ERROR: MRIScopyMRI: Surf/Src dimension mismatch.
ERROR: MRIScopyMRI: Surf/Src dimension mismatch.
Rot (rad): 0 0
surfer: compute_fieldsign()
mri_fieldsign done
end
end

end
end

echo "-------------------" | tee -a $LF
echo -------------------
tee -a /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log
-------------------
date | tee -a $LF
date
tee -a /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log
Mon Oct  3 13:02:58 EDT 2011
echo "mkfieldsign-sess completed" | tee -a $LF
echo mkfieldsign-sess completed
tee -a /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log
mkfieldsign-sess completed
echo " "
echo  
 

exit 0 ;
exit 0