$ recon-all-old -autorecon-pial -debug -sd /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2 -s TB0029U2_T2TEST_FREESURFER

set echo = 1 ;
breaksw
breaksw
end
end

while ( $#argv != 0 )
while ( 4 != 0 )

set flag = $argv[1] ; shift ;
set flag = -sd
shift

switch ( $flag )
switch ( -sd )
if ( $#argv < 1 ) goto arg1err ;
if ( 3 < 1 ) goto arg1err
setenv SUBJECTS_DIR $argv[1] ; shift ;
setenv SUBJECTS_DIR /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )

set flag = $argv[1] ; shift ;
set flag = -s
shift

switch ( $flag )
switch ( -s )
if ( $#argv < 1 ) goto arg1err ;
if ( 1 < 1 ) goto arg1err
set subjid = $argv[1] ; shift ;
set subjid = TB0029U2_T2TEST_FREESURFER
shift
set subjid = `basename $subjid` ;
set subjid = `basename $subjid`
basename TB0029U2_T2TEST_FREESURFER
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 ( $DoT2pial && $DoFLAIRpial ) then
if ( 0 && 0 ) then

if ( ! $DoVersionsOnly ) then
if ( ! 0 ) then
if ( $#subjid != 1 ) then
if ( 1 != 1 ) then

if ( ! $?SUBJECTS_DIR ) then
if ( ! 1 ) then

if ( ! -e $SUBJECTS_DIR ) then
if ( ! -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2 ) then


pushd $SUBJECTS_DIR > /dev/null
pushd /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2
setenv SUBJECTS_DIR `$PWD` ;
setenv SUBJECTS_DIR `$PWD`
/bin/pwd
popd > /dev/null
popd

set subjdir = $SUBJECTS_DIR/$subjid
set subjdir = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER
set mdir = $subjdir/mri
set mdir = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/mri
set sdir = $subjdir/surf
set sdir = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/surf
set ldir = $subjdir/label
set ldir = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/label
set tdir = $subjdir/touch
set tdir = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/touch

if ( $TH3Flag ) set TH3Opt = "-th3"
if ( 1 ) set TH3Opt = -th3
set TH3Opt = -th3
if ( ! $TH3Flag ) set TH3Opt = "-no-th3"
if ( ! 1 ) set TH3Opt = -no-th3

if ( $DoConf2Hires ) then
if ( 0 ) then

set fname = $subjdir/scripts/DoConf2Hires
set fname = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/DoConf2Hires
if ( -e $fname && ! $DoConf2Hires && ( $DoPialSurfs || $DoT2pial || $DoFLAIRpial ) ) then
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/DoConf2Hires && ! 0 && ( 1 || 0 || 0 ) ) then


if ( $EMRegStrip == 0 ) set GCASkull = RB_all_withskull_2019_10_22.talxfm.mni305.gca
if ( 1 == 0 ) set GCASkull = RB_all_withskull_2019_10_22.talxfm.mni305.gca
if ( $EMRegAseg == 0 ) set GCA = RB_all_2019_10_25.talxfm.mni305.gca
if ( 1 == 0 ) set GCA = RB_all_2019_10_25.talxfm.mni305.gca

if ( $DoCreateBaseSubj && ( $DoT2pial || $DoFLAIRpial ) ) then
if ( 0 && ( 0 || 0 ) ) then


if ( $longitudinal || $LongSamseg ) then
if ( 0 || 0 ) then
if ( $longitudinal && ! $LongSamseg ) then
if ( 0 && ! 0 ) then



set haslong = `echo $subjid | grep "\.long\."`
set haslong = `echo $subjid | grep "\.long\."`
grep \.long\.
echo TB0029U2_T2TEST_FREESURFER
set hasxhemi = `echo $subjid | grep xhemi`
set hasxhemi = `echo $subjid | grep xhemi`
grep xhemi
echo TB0029U2_T2TEST_FREESURFER
if ( "$haslong" != "" && "$hasxhemi" == "" ) then
if (  !=  &&  ==  ) then

endif
endif


if ( ! $DoCreateBaseSubj ) then
if ( ! 0 ) then
if ( -e $subjdir/$BaseSubjsListFname ) then
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/base-tps ) then
endif
endif


if ( $DoCreateBaseSubj && -e $subjdir ) then
if ( 0 && -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER ) then

if ( $DoCreateBaseSubj ) then
if ( 0 ) then


if ( $#InputList == 0 ) then
if ( 0 == 0 ) then
if ( ! $DoCreateBaseSubj ) then
if ( ! 0 ) then
if ( $longitudinal ) mkdir -p ${subjdir}
if ( 0 ) mkdir -p /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER
if ( ! -e $subjdir ) then
if ( ! -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER ) then
if ( ! -w $subjdir ) then
if ( ! -w /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER ) then
endif
endif
else
else
else
else

if ( ! $?FREESURFER_HOME ) then
if ( ! 1 ) then

if ( ! -e $FREESURFER_HOME ) then
if ( ! -e /home/ns-zalewk/freesurfer ) then

if ( ! -e ${GCADIR}/$GCA ) then
if ( ! -e /home/ns-zalewk/freesurfer/average/RB_all_2020-01-02.gca ) then

if ( ! -e ${GCADIR}/$GCASkull && ( $DoSkullLTA || $DoSkullStrip ) ) then
if ( ! -e /home/ns-zalewk/freesurfer/average/RB_all_withskull_2020_01_02.gca && ( 0 || 0 ) ) then

foreach hemi ( $hemilist )
foreach hemi ( lh rh )
set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ;
set avgtif = /home/ns-zalewk/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
if ( ! -e $avgtif ) then
if ( ! -e /home/ns-zalewk/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ) then
set GCSHemi = ${GCSDIR}/$hemi.$GCS
set GCSHemi = /home/ns-zalewk/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
if ( ! -e $GCSHemi ) then
if ( ! -e /home/ns-zalewk/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then
set CPAtlas = ${GCSDIR}/$hemi.$GCS
set CPAtlas = /home/ns-zalewk/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
if ( ! -e $CPAtlas ) then
if ( ! -e /home/ns-zalewk/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then
end
end
set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ;
set avgtif = /home/ns-zalewk/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
if ( ! -e $avgtif ) then
if ( ! -e /home/ns-zalewk/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ) then
set GCSHemi = ${GCSDIR}/$hemi.$GCS
set GCSHemi = /home/ns-zalewk/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
if ( ! -e $GCSHemi ) then
if ( ! -e /home/ns-zalewk/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then
set CPAtlas = ${GCSDIR}/$hemi.$GCS
set CPAtlas = /home/ns-zalewk/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
if ( ! -e $CPAtlas ) then
if ( ! -e /home/ns-zalewk/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ) then
end
end

if ( $XOptsUse == 1 && $XOptsClean == 1 ) then
if ( 1 == 1 && 0 == 1 ) then

if ( $IsMPRAGE == 1 && $IsWashuMPRAGE == 1 ) then
if ( 1 == 1 && 0 == 1 ) then

mkdir -p $subjdir/scripts
mkdir -p /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts
set XOptsPreExist = $subjdir/scripts/expert-options
set XOptsPreExist = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/expert-options
if ( -e $XOptsPreExist ) then
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/expert-options ) then


if ( $#XOptsFile != 0 ) then
if ( 0 != 0 ) then
endif
endif

set GlobXOptsFile = $SUBJECTS_DIR/global-expert-options.txt
set GlobXOptsFile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/global-expert-options.txt
if ( -e $GlobXOptsFile ) then
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/global-expert-options.txt ) then

set GlobXOptsFile = ( )
set GlobXOptsFile = ( )
endif
endif

if ( $DoConf2Hires ) then
if ( 0 ) then

if ( $#NotifyFile != 0 ) then
if ( 0 != 0 ) then

if ( $#WaitForFile != 0 ) then
if ( 0 != 0 ) then

if ( ! $DoCleanTal && ! $DoCleanCP && ! $DoCleanBM && ! $DoConvertInput && ! $DoCleanASeg && ! $DoCleanWM && ! $DoCleanSeed && ! $DoCleanCW256 && ! $DoCortParc && ! $DoCortParc2 && ! $DoGCAReg && ! $DoMotionCor && ! $DoTalairach && ! $DoTalCheck && ! $DoCleanXopts && ! $DoNormalization && ! $DoNormalization2 && ! $DoParcStats && ! $DoParcStats2 && ! $DoVersionsOnly && ! $DoDeface && ! $DoCleanPFH && ! $DoSkullStrip && ! $DoSegmentation && ! $DoNuIntensityCor && ! $DoFill && ! $DoTessellate && ! $DoAParc2ASeg && ! $DoWMParc && ! $DoSmooth1 && ! $DoInflate1 && ! $DoQSphere && ! $DoRemoveNeck && ! $DoFix && ! $DoSmooth2 && ! $DoInflate2 && ! $DoSphere && ! $DoSkullLTA && ! $DoQdecCache && ! $DoVnoMatchCheck && ! $DoSurfReg && ! $DoAvgCurv && ! $DoSegStats && ! $DoMorphRGB && ! $DoAutoDetGWStats && ! $DoWhitePreAparc && ! $DoWhiteSurfs && ! $DoCortexLabel && ! $DoCortRibbonVolMask && ! $DoJacobianWhite && ! $DoJacobianDist0 && ! $DoCANormalize && ! $DoCAReg && ! $DoCALabel && ! $DoMaskBFS && ! $DoAParcASegStats && ! $DoLocalGyriIndex && ! $DoMakefile && ! $DoParallel && ! $DoRelabelHypos && ! $DoCurvHK && ! $DoSurfVolume && ! $DoASegMerge && ! $DoCCSeg && ! $DoCurvStats && ! $DoLabelV1 && ! $DoCreateBaseSubj && ! $DoBaLabels && ! $DoShowEdits && ! $DoLabelExvivoEC && ! $DoPialSurfs && ! $DoConf2Hires && ! $DoSubfields && ! $DoPctSurfCon && ! $DoT2pial && ! $DoFLAIRpial && ! $DoConvertT2Input && ! $DoConvertFlairInput && ! $DoSuperClean && ! $DoCortParc3 && ! $DoParcStats3 && ! $DoAPas2ASeg && ! $UseHighMyelin ) then
if ( ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 1 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 1 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 1 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 1 && ! 1 && ! 1 && ! 0 && ! 0 && ! 0 && ! 1 && ! 1 && ! 1 && ! 0 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 1 && ! 1 && ! 0 && ! 0 && ! 0 && ! 1 && ! 0 && ! 0 && ! 1 && ! 0 && ! 0 && ! 1 && ! 0 && ! 0 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 1 && ! 1 && ! 1 && ! 0 ) then

if ( $WSMore && $WSLess ) then
if ( 0 && 0 ) then

if ( ( $WSMore || $WSLess ) && $WSPctPreFlood ) then
if ( ( 0 || 0 ) && ) then

if ( $DoParallel == 1 && $#hemilist == 1 ) then
if ( 0 == 1 && 2 == 1 ) then


goto check_params_return ;
goto check_params_return

set StartTime = `date` ;
set StartTime = `date`
date
set tSecStart = `date '+%s'` ;
set tSecStart = `date '+%s'`
date +%s




if ( $?REQUIRE_FS_MATCH == 0 ) setenv REQUIRE_FS_MATCH 0
if ( 0 == 0 ) setenv REQUIRE_FS_MATCH 0
setenv REQUIRE_FS_MATCH 0

set bstampfile0 = $FREESURFER_HOME/build-stamp.txt
set bstampfile0 = /home/ns-zalewk/freesurfer/build-stamp.txt
mkdir -p $SUBJECTS_DIR/$subjid/scripts
mkdir -p /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts
set bstampfile = $SUBJECTS_DIR/$subjid/scripts/build-stamp.txt
set bstampfile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/build-stamp.txt
if ( -e $bstampfile0 ) then
if ( -e /home/ns-zalewk/freesurfer/build-stamp.txt ) then
if ( ! -e $bstampfile ) cp $bstampfile0 $bstampfile
if ( ! -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/build-stamp.txt ) cp /home/ns-zalewk/freesurfer/build-stamp.txt /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/build-stamp.txt
set bstamp0 = `cat $bstampfile0`
set bstamp0 = `cat $bstampfile0`
cat /home/ns-zalewk/freesurfer/build-stamp.txt
set bstamp = `cat $bstampfile`
set bstamp = `cat $bstampfile`
cat /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/build-stamp.txt
if ( "$bstamp0" != "$bstamp" ) then
if ( freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 != freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 ) then
echo "Subject Stamp: $bstamp"
echo Subject Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
Subject Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
echo "Current Stamp: $bstamp0"
echo Current Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
Current Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
endif
endif
rm -f $SUBJECTS_DIR/$subjid/scripts/patchdir.txt
rm -f /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/patchdir.txt
if ( $?PatchDir ) then
if ( 1 ) then
echo "$PatchDir" > $SUBJECTS_DIR/$subjid/scripts/patchdir.txt
echo
endif
endif
cp $bstampfile0 $SUBJECTS_DIR/$subjid/scripts/lastcall.build-stamp.txt
cp /home/ns-zalewk/freesurfer/build-stamp.txt /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/lastcall.build-stamp.txt

if ( $DoMakefile ) then
if ( 0 ) then

if ( $DoTime ) then
if ( 1 ) then
fs_time ls > & /dev/null
fs_time ls
if ( ! $status ) set fs_time= ( fs_time )
if ( ! 0 ) set fs_time= ( fs_time )
set fs_time= ( fs_time )
endif
endif

echo "INFO: SUBJECTS_DIR is $SUBJECTS_DIR"
echo INFO: SUBJECTS_DIR is /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2
INFO: SUBJECTS_DIR is /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2


pushd $FREESURFER_HOME > /dev/null
pushd /home/ns-zalewk/freesurfer
set freesurfer_home_true = `pwd` ;
set freesurfer_home_true = `pwd`
pwd
popd > /dev/null
popd
echo "Actual FREESURFER_HOME $freesurfer_home_true"
echo Actual FREESURFER_HOME /home/ns-zalewk/freesurfer
Actual FREESURFER_HOME /home/ns-zalewk/freesurfer

set DateString = "`date '+%y%m%d%H%M'`"
set DateString = `date '+%y%m%d%H%M'`
date +%y%m%d%H%M


if ( $DoSuperClean ) then
if ( 0 ) then

cd $subjdir
cd /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER
mkdir -p mri scripts surf tmp label touch stats touch trash
mkdir -p mri scripts surf tmp label touch stats touch trash
mkdir -p mri/transforms mri/transforms/bak mri/orig
mkdir -p mri/transforms mri/transforms/bak mri/orig
set touchdir = $subjdir/touch
set touchdir = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/touch





rm -f scripts/recon-config.yaml scripts/unknown-args.txt
rm -f scripts/recon-config.yaml scripts/unknown-args.txt
cat $tmp_config > scripts/recon-config.yaml
cat /tmp/tmp.nlZRGcRLFn
cat $tmp_unknown_args > scripts/unknown-args.txt
cat /tmp/tmp.tGbqLv1mvv
rm -f $tmp_config $tmp_unknown_args
rm -f /tmp/tmp.nlZRGcRLFn /tmp/tmp.tGbqLv1mvv


if ( ! $DoVersionsOnly ) then
if ( ! 0 ) then
set CF = ( $subjdir/scripts/$CF_DEFAULT_NAME )
set CF = ( /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.cmd )

echo "\n\n#---------------------------------" >> $CF
echo \n\n#---------------------------------
echo "# New invocation of recon-all `date` " >> $CF
echo # New invocation of recon-all `date`
date

set ENVF = $subjdir/scripts/recon-all.env
set ENVF = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.env
if ( -e $ENVF ) mv -f $ENVF $ENVF.bak
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.env ) mv -f /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.env /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.env.bak
mv -f /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.env /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.env.bak
date >> $ENVF
date
echo "FREESURFER_HOME $FREESURFER_HOME" >> $ENVF
echo FREESURFER_HOME /home/ns-zalewk/freesurfer
echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $ENVF
echo Actual FREESURFER_HOME /home/ns-zalewk/freesurfer
pwd >> $ENVF
pwd
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $ENVF
echo setenv SUBJECTS_DIR /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2
echo $inputargs >> $ENVF
echo -autorecon-pial -debug -sd /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2 -s TB0029U2_T2TEST_FREESURFER
uname -a >> $ENVF
uname -a
echo "" >> $ENVF
echo
limit >> $ENVF
limit
echo "" >> $ENVF
echo
printenv >> $ENVF
printenv
endif
endif

if ( $DoVersionsOnly ) then
if ( 0 ) then


if ( $#LF == 0 ) then
if ( 0 == 0 ) then
set LF = ( $subjdir/scripts/$LF_DEFAULT_NAME )
set LF = ( /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.log )
if ( -e $LF ) then
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.log ) then
ls -l $LF
ls -l /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.log
-rwxrwxrwx 1 nobody 4294967294 489308 Apr  8  2021 /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.log
if ( ! $AppendLog ) then
if ( ! 1 ) then


if ( $?RECONALL_MAKE_SUBJECT ) goto skip_new_invo
if ( 0 ) goto skip_new_invo
echo "\n\n" >> $LF
echo \n\n
echo "#New# invocation of recon-all " >> $LF
echo #New# invocation of recon-all
echo "\n\n" >> $LF
echo \n\n
endif
endif
endif
endif
else
else
skip_new_invo:
skip_new_invo:

echo "" >> $LF
echo
date >> $LF
date
echo "cd `$PWD`" >> $LF
echo cd `/bin/pwd`
/bin/pwd
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $LF
echo setenv SUBJECTS_DIR /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2
echo $0 $inputargs >> $LF
echo /home/ns-zalewk/freesurfer/bin/recon-all-old -autorecon-pial -debug -sd /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2 -s TB0029U2_T2TEST_FREESURFER
echo "" >> $LF
echo


if ( $?RECONALL_MAKE_SUBJECT ) goto skip_all_info
if ( 0 ) goto skip_all_info
echo "subjid $subjid" >> $LF
echo subjid TB0029U2_T2TEST_FREESURFER
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $LF
echo setenv SUBJECTS_DIR /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2
echo "FREESURFER_HOME $FREESURFER_HOME" >> $LF
echo FREESURFER_HOME /home/ns-zalewk/freesurfer
echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $LF
echo Actual FREESURFER_HOME /home/ns-zalewk/freesurfer
if ( -e $FREESURFER_HOME/build-stamp.txt ) then
if ( -e /home/ns-zalewk/freesurfer/build-stamp.txt ) then
echo "build-stamp.txt: `cat $FREESURFER_HOME/build-stamp.txt`" >> $LF
echo build-stamp.txt: `cat /home/ns-zalewk/freesurfer/build-stamp.txt`
cat /home/ns-zalewk/freesurfer/build-stamp.txt
endif
endif
uname -a | tee -a $LF
uname -a
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.log
Linux loki 4.15.0-112-generic #113-Ubuntu SMP Thu Jul 9 23:41:39 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
limit >> $LF
limit
if ( -e /usr/bin/free ) then
if ( -e /usr/bin/free ) then
echo "" >> $LF
echo
/usr/bin/free --human >> $LF
/usr/bin/free --human
echo "" >> $LF
echo
endif
endif
if ( "`uname -s`" == "Darwin" ) then
if ( `uname -s` == Darwin ) then
uname -s
if ( $?PBS_JOBID ) then
if ( 0 ) then



set cmd = ( which bc )
set cmd = ( which bc )
$cmd > & /dev/null
which bc
if ( $status ) then
if ( 0 ) then


echo "########################################" >> $LF
echo ########################################
echo "program versions used" >> $LF
echo program versions used
echo $FS_RECON_VERSION >> $LF
echo 7.1.1 (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551)
set allinfocmds = ( lta_convert mri_and mri_annotation2label mri_aparc2aseg mri_surf2volseg mri_binarize mri_ca_label mri_ca_normalize mri_ca_register mri_cc mri_compute_overlap mri_compute_seg_overlap mri_concat mri_concatenate_lta mri_convert mri_diff mri_edit_wm_with_aseg mri_em_register mri_fill mri_fuse_segmentations mri_fwhm mri_gcut mri_info mri_label2label mri_label2vol mri_log_likelihood mri_mask mri_matrix_multiply mri_normalize mri_normalize_tp2 mri_or mri_relabel_hypointensities mri_relabel_nonwm_hypos mri_remove_neck mri_robust_register mri_robust_template mris_anatomical_stats mris_ca_label mris_calc mris_convert mris_curvature mris_curvature_stats mris_diff mris_divide_parcellation mri_segment mri_segstats mris_euler_number mris_fix_topology mris_topo_fixer mris_jacobian mris_label2annot mris_left_right_register mris_place_surface mrisp_paint mris_register mris_smooth mris_sphere mris_surface_stats mri_stats2seg mris_thickness mris_thickness_diff mris_topo_fixer mri_surf2surf mri_surf2vol mri_surfcluster mris_volmask mri_tessellate mri_vol2surf mri_vol2vol mri_voldiff mri_watershed tkregister2_cmdl )
set allinfocmds = ( lta_convert mri_and mri_annotation2label mri_aparc2aseg mri_surf2volseg mri_binarize mri_ca_label mri_ca_normalize mri_ca_register mri_cc mri_compute_overlap mri_compute_seg_overlap mri_concat mri_concatenate_lta mri_convert mri_diff mri_edit_wm_with_aseg mri_em_register mri_fill mri_fuse_segmentations mri_fwhm mri_gcut mri_info mri_label2label mri_label2vol mri_log_likelihood mri_mask mri_matrix_multiply mri_normalize mri_normalize_tp2 mri_or mri_relabel_hypointensities mri_relabel_nonwm_hypos mri_remove_neck mri_robust_register mri_robust_template mris_anatomical_stats mris_ca_label mris_calc mris_convert mris_curvature mris_curvature_stats mris_diff mris_divide_parcellation mri_segment mri_segstats mris_euler_number mris_fix_topology mris_topo_fixer mris_jacobian mris_label2annot mris_left_right_register mris_place_surface mrisp_paint mris_register mris_smooth mris_sphere mris_surface_stats mri_stats2seg mris_thickness mris_thickness_diff mris_topo_fixer mri_surf2surf mri_surf2vol mri_surfcluster mris_volmask mri_tessellate mri_vol2surf mri_vol2vol mri_voldiff mri_watershed tkregister2_cmdl )



foreach cmd ( $allinfocmds )
foreach cmd ( lta_convert mri_and mri_annotation2label mri_aparc2aseg mri_surf2volseg mri_binarize mri_ca_label mri_ca_normalize mri_ca_register mri_cc mri_compute_overlap mri_compute_seg_overlap mri_concat mri_concatenate_lta mri_convert mri_diff mri_edit_wm_with_aseg mri_em_register mri_fill mri_fuse_segmentations mri_fwhm mri_gcut mri_info mri_label2label mri_label2vol mri_log_likelihood mri_mask mri_matrix_multiply mri_normalize mri_normalize_tp2 mri_or mri_relabel_hypointensities mri_relabel_nonwm_hypos mri_remove_neck mri_robust_register mri_robust_template mris_anatomical_stats mris_ca_label mris_calc mris_convert mris_curvature mris_curvature_stats mris_diff mris_divide_parcellation mri_segment mri_segstats mris_euler_number mris_fix_topology mris_topo_fixer mris_jacobian mris_label2annot mris_left_right_register mris_place_surface mrisp_paint mris_register mris_smooth mris_sphere mris_surface_stats mri_stats2seg mris_thickness mris_thickness_diff mris_topo_fixer mri_surf2surf mri_surf2vol mri_surfcluster mris_volmask mri_tessellate mri_vol2surf mri_vol2vol mri_voldiff mri_watershed tkregister2_cmdl )
$cmd -all-info >> $LF
lta_convert -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_and -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_annotation2label -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_aparc2aseg -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_surf2volseg -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_binarize -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_ca_label -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_ca_normalize -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_ca_register -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_cc -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_compute_overlap -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_compute_seg_overlap -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_concat -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_concatenate_lta -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_convert -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_diff -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_edit_wm_with_aseg -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_em_register -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_fill -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_fuse_segmentations -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_fwhm -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_gcut -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_info -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_label2label -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_label2vol -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_log_likelihood -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_mask -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_matrix_multiply -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_normalize -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_normalize_tp2 -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_or -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_relabel_hypointensities -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_relabel_nonwm_hypos -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_remove_neck -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_robust_register -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_robust_template -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_anatomical_stats -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_ca_label -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_calc -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_convert -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_curvature -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_curvature_stats -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_diff -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_divide_parcellation -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_segment -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_segstats -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_euler_number -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_fix_topology -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_topo_fixer -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_jacobian -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_label2annot -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_left_right_register -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_place_surface -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mrisp_paint -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_register -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_smooth -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_sphere -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_surface_stats -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_stats2seg -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_thickness -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_thickness_diff -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_topo_fixer -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_surf2surf -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_surf2vol -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_surfcluster -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mris_volmask -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_tessellate -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_vol2surf -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_vol2vol -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_voldiff -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
mri_watershed -all-info
if ( $status ) then
if ( 0 ) then
end
end
$cmd -all-info >> $LF
tkregister2_cmdl -all-info
if ( $status ) then
if ( 0 ) then
end
end
mri_motion_correct.fsl -version >> $LF
mri_motion_correct.fsl -version

nu_correct -version >> $LF
nu_correct -version


if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats
if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats
if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc
if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc


echo "#######################################" >> $LF
echo #######################################
echo "GCADIR $GCADIR" >> $LF
echo GCADIR /home/ns-zalewk/freesurfer/average
echo "GCA $GCA" >> $LF
echo GCA RB_all_2020-01-02.gca
echo "GCASkull $GCASkull" >> $LF
echo GCASkull RB_all_withskull_2020_01_02.gca
echo "AvgCurvTif $AvgCurvTif" >> $LF
echo AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
echo "GCSDIR $GCSDIR" >> $LF
echo GCSDIR /home/ns-zalewk/freesurfer/average
echo "GCS $GCS" >> $LF
echo GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
echo "#######################################" >> $LF
echo #######################################
skip_all_info:
skip_all_info:

if ( $DoVersionsOnly ) exit 0 ;
if ( 0 ) exit 0


set ErrorFile = $subjdir/scripts/recon-all.error
set ErrorFile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.error
rm -f $ErrorFile
rm -f /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.error

if ( $#DoneFile == 0 ) then
if ( 0 == 0 ) then
set DoneFile = $subjdir/scripts/recon-all.done
set DoneFile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.done
rm -f $DoneFile
rm -f /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.done
endif
endif


if ( $DoIsRunning ) then
if ( 1 ) then
set IsRunningLH = $subjdir/scripts/IsRunning.lh
set IsRunningLH = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/IsRunning.lh
set IsRunningRH = $subjdir/scripts/IsRunning.rh
set IsRunningRH = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/IsRunning.rh
set IsRunningLHRH = $subjdir/scripts/IsRunning.lh+rh
set IsRunningLHRH = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/IsRunning.lh+rh
set bailfile = ( ) ;
set bailfile = ( )
if ( $#hemilist == 1 ) then
if ( 2 == 1 ) then

set IsRunningFile = $subjdir/scripts/IsRunning.lh+rh
set IsRunningFile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/IsRunning.lh+rh
if ( -e $IsRunningLH ) set bailfile = $IsRunningLH
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/IsRunning.lh ) set bailfile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/IsRunning.lh
if ( -e $IsRunningRH ) set bailfile = $IsRunningRH
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/IsRunning.rh ) set bailfile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/IsRunning.rh
endif
endif
if ( -e $IsRunningFile ) set bailfile = $IsRunningFile
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/IsRunning.lh+rh ) set bailfile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/IsRunning.lh+rh
if ( $#bailfile ) then
if ( 0 ) then
echo "------------------------------" > $IsRunningFile
echo ------------------------------
echo "SUBJECT $subjid" >> $IsRunningFile
echo SUBJECT TB0029U2_T2TEST_FREESURFER
echo "HEMI    $hemilist" >> $IsRunningFile
echo HEMI    lh rh
echo "DATE `date`" >> $IsRunningFile
echo DATE `date`
date
echo "USER $user" >> $IsRunningFile
echo USER ns-zalewk
echo "HOST `hostname`" >> $IsRunningFile
echo HOST `hostname`
hostname
echo "PROCESSID $$ " >> $IsRunningFile
echo PROCESSID 30899
echo "PROCESSOR `uname -m`" >> $IsRunningFile
echo PROCESSOR `uname -m`
uname -m
echo "OS `uname -s`" >> $IsRunningFile
echo OS `uname -s`
uname -s
uname -a >> $IsRunningFile
uname -a
echo $FS_RECON_VERSION >> $IsRunningFile
echo 7.1.1 (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551)
if ( $?PBS_JOBID ) then
if ( 0 ) then
endif
endif


set CSDF = $subjdir/scripts/csurfdir
set CSDF = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/csurfdir
if ( $DoCleanCSDF ) rm -vf $CSDF
if ( 0 ) rm -vf /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/csurfdir
if ( -e $CSDF ) then
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/csurfdir ) then


if ( $#SF == 0 ) then
if ( 0 == 0 ) then
set SF = ( $subjdir/scripts/$SF_DEFAULT_NAME )
set SF = ( /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all-status.log )
if ( -e $SF ) then
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all-status.log ) then
if ( ! $AppendStatus ) then
if ( ! 1 ) then

echo "\n\n" >> $SF
echo \n\n
echo "#New# invocation of recon-all " >> $SF
echo #New# invocation of recon-all
echo "\n\n" >> $SF
echo \n\n
endif
endif
endif
endif
else
else
echo "status file for recon-all" >> $SF
echo status file for recon-all
date >> $SF
date


if ( "`uname -s`" == "Linux" ) then
if ( `uname -s` == Linux ) then
uname -s
set FullProgName = `readlink -f $0` ;
set FullProgName = `readlink -f $0`
readlink -f /home/ns-zalewk/freesurfer/bin/recon-all-old
cp -vp $FullProgName $subjdir/scripts/recon-all.local-copy
cp -vp /home/ns-zalewk/freesurfer/bin/recon-all-old /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.local-copy
'/home/ns-zalewk/freesurfer/bin/recon-all-old' -> '/home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.local-copy'
endif
endif


if ( $#WaitForFile != 0 ) then
if ( 0 != 0 ) then

if ( ! $RunIt ) then
if ( ! 1 ) then

if ( $DoRestart ) then
if ( 0 ) then




if ( $DoCleanSeed ) then
if ( 0 ) then
if ( $DoCleanCW256 ) then
if ( 0 ) then
if ( $DoCleanTal ) then
if ( 0 ) then
if ( $DoCleanLta ) then
if ( 0 ) then
if ( $DoCleanPFH ) then
if ( 0 ) then
if ( $DoCleanBM ) then
if ( 0 ) then
if ( $DoCleanASeg ) then
if ( 0 ) then
if ( $DoCleanWM ) then
if ( 0 ) then
if ( $DoCleanCP ) then
if ( 0 ) then
if ( $DoCleanTWM ) then
if ( 0 ) then
if ( $DoCleanBFSE ) then
if ( 0 ) then
if ( $DoCleanXopts ) then
if ( 0 ) then
if ( $DoCleanT2 ) then
if ( 0 ) then
if ( $DoCleanFLAIR ) then
if ( 0 ) then



set seedfile = $subjdir/scripts/seed-pons.crs.man.dat
set seedfile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/seed-pons.crs.man.dat
if ( $#PonsSeedCRS ) then
if ( 0 ) then
if ( -e $seedfile ) set PonsSeedCRS = `cat $seedfile | grep -v \#`
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/seed-pons.crs.man.dat ) set PonsSeedCRS = `cat $seedfile | grep -v \#`
set seedfile = $subjdir/scripts/seed-cc.crs.man.dat
set seedfile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/seed-cc.crs.man.dat
if ( $#CCSeedCRS ) then
if ( 0 ) then
if ( -e $seedfile ) set CCSeedCRS = `cat $seedfile | grep -v \#`
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/seed-cc.crs.man.dat ) set CCSeedCRS = `cat $seedfile | grep -v \#`
set seedfile = $subjdir/scripts/seed-lh.crs.man.dat
set seedfile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/seed-lh.crs.man.dat
if ( $#LHSeedCRS ) then
if ( 0 ) then
if ( -e $seedfile ) set LHSeedCRS = `cat $seedfile | grep -v \#`
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/seed-lh.crs.man.dat ) set LHSeedCRS = `cat $seedfile | grep -v \#`
set seedfile = $subjdir/scripts/seed-rh.crs.man.dat
set seedfile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/seed-rh.crs.man.dat
if ( $#RHSeedCRS ) then
if ( 0 ) then
if ( -e $seedfile ) set RHSeedCRS = `cat $seedfile | grep -v \#`
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/seed-rh.crs.man.dat ) set RHSeedCRS = `cat $seedfile | grep -v \#`

set seedfile = $subjdir/scripts/seed-ws.crs.man.dat
set seedfile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/seed-ws.crs.man.dat
if ( $#WSSeedPoint ) then
if ( 0 ) then
if ( -e $seedfile ) set WSSeedPoint = `cat $seedfile | grep -v \#`
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/seed-ws.crs.man.dat ) set WSSeedPoint = `cat $seedfile | grep -v \#`


set ControlPointsFile = $subjdir/tmp/control.dat
set ControlPointsFile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/tmp/control.dat
if ( -e $ControlPointsFile ) then
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/tmp/control.dat ) then


set DefaultTWMControlPointsFile = $subjdir/tmp/twm.dat
set DefaultTWMControlPointsFile = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/tmp/twm.dat
if ( $UseTWMControlPoints ) then
if ( 0 ) then

if ( -e $DefaultTWMControlPointsFile ) then
if ( -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/tmp/twm.dat ) then
endif
endif




if ( $DoConformWidth256 ) then
if ( 0 ) then






if ( $DoShowEdits ) then
if ( 0 ) then






if ( $longitudinal && ! $LongSamseg ) then
if ( 0 && ! 0 ) then
if ( $longitudinal ) then
if ( 0 ) then





if ( $#InputList != 0 ) then
if ( 0 != 0 ) then





if ( $DoConvertT2Input || $DoConvertFlairInput ) then
if ( 0 || 0 ) then






if ( $DoCreateBaseInput && $DoCreateBaseSubj ) then
if ( 0 && 0 ) then









if ( $DoMotionCor ) then
if ( 0 ) then




if ( $#EMRegMaskArg != 0 ) then
if ( 0 != 0 ) then




if ( $DoDeface ) then
if ( 0 ) then




if ( $DoTalairach ) then
if ( 0 ) then

if ( $DoTalairach ) then
if ( 0 ) then


pushd $SUBJECTS_DIR/$subjid/mri/transforms
pushd /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/mri/transforms
~/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/mri/transforms ~/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER
if ( $EMRegStrip == 0 ) then
if ( 1 == 0 ) then
if ( $EMRegAseg == 0 ) then
if ( 1 == 0 ) then
popd
popd
~/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER


if ( $DoTalCheck ) then
if ( 0 ) then





if ( $DoNuIntensityCor ) then
if ( 0 ) then





if ( $DoNormalization ) then
if ( 0 ) then





if ( $DoSkullStrip ) then
if ( 0 ) then









if ( $DoGCAReg ) then
if ( 0 ) then





if ( $DoCANormalize ) then
if ( 0 ) then





if ( $DoCAReg ) then
if ( 0 ) then





if ( $DoRemoveNeck ) then
if ( 0 ) then





if ( $DoSkullLTA ) then
if ( 0 ) then





if ( $DoCALabel ) then
if ( 0 ) then


Restart:
Restart:

if ( $DoRestart ) then
if ( 0 ) then






if ( $DoCCSeg ) then
if ( 0 ) then






if ( $DoASegMerge ) then
if ( 0 ) then





if ( $DoNormalization2 ) then
if ( 0 ) then





if ( $DoMaskBFS ) then
if ( 1 ) then
echo "#--------------------------------------------" | & tee -a $LF | & tee -a $CF
echo #--------------------------------------------
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.cmd
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.log
#--------------------------------------------
echo "#@# Mask BFS `date`" | & tee -a $SF | & tee -a $LF | & tee -a $CF
echo #@# Mask BFS `date`
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all-status.log
date
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.log
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.cmd
#@# Mask BFS Thu Apr  8 14:45:15 PDT 2021
cd $subjdir/mri > /dev/null
cd /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/mri
set xopts = `fsr-getxopts mri_mask $XOptsFile $GlobXOptsFile` ;
set xopts = `fsr-getxopts mri_mask $XOptsFile $GlobXOptsFile`
fsr-getxopts mri_mask

set cmd = ( mri_mask -T 5 $xopts brain.mgz brainmask.mgz brain.finalsurfs.mgz )
set cmd = ( mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz )
$PWD | & tee -a $LF
/bin/pwd
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.log
/home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/mri
echo "\n $cmd \n" | & tee -a $LF | & tee -a $CF
echo \n mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz \n
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.log
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.cmd

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz

if ( $RunIt ) $fs_time $cmd | & tee -a $LF
if ( 1 ) fs_time mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.log
fs_time mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5
DoAbs = 0
Found 1496285 voxels in mask (pct=  8.92)
MRImask(): AllowDiffGeom = 1
Writing masked volume to brain.finalsurfs.mgz...done.
@#@FSTIME  2021:04:08:14:45:15 mri_mask N 5 e 1.39 S 0.02 U 1.30 P 95% M 74408 F 0 R 17277 W 0 c 15 w 84 I 0 O 2352 L 3.23 3.09 2.45
@#@FSLOADPOST 2021:04:08:14:45:16 mri_mask N 5 3.23 3.09 2.45
if ( $status ) goto error_exit ;
if ( 0 ) goto error_exit

if ( -e brain.finalsurfs.manedit.mgz ) then
if ( -e brain.finalsurfs.manedit.mgz ) then

set bfmanedit = ${SUBJECTS_DIR}/${tpNid}/mri/brain.finalsurfs.manedit.mgz
set bfmanedit = /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2//mri/brain.finalsurfs.manedit.mgz
if ( $longitudinal && -e $bfmanedit && ! $LongSamseg ) then
if ( 0 && -e /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2//mri/brain.finalsurfs.manedit.mgz && ! 0 ) then
endif
endif
endif
endif





if ( $DoSegmentation ) then
if ( 0 ) then




if ( $DoFill ) then
if ( 0 ) then































if ( $DoTessellate && ( ! $longitudinal ) ) then
if ( 0 && ( ! 0 ) ) then




if ( $DoSmooth1 && ( ! $longitudinal ) ) then
if ( 0 && ( ! 0 ) ) then




if ( $DoInflate1 && ( ! $longitudinal ) ) then
if ( 0 && ( ! 0 ) ) then




if ( $DoQSphere && ( ! $longitudinal ) ) then
if ( 0 && ( ! 0 ) ) then





if ( $DoFix && ( ! $longitudinal ) ) then
if ( 0 && ( ! 0 ) ) then



if ( $DoAutoDetGWStats ) then
if ( 1 ) then
cd $mdir
cd /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/mri
set bfs = brain.finalsurfs.mgz
set bfs = brain.finalsurfs.mgz
set wm = wm.mgz
set wm = wm.mgz
set aseg = aseg.presurf.mgz
set aseg = aseg.presurf.mgz
foreach hemi ( $hemilist )
foreach hemi ( lh rh )
echo "#--------------------------------------------" | & tee -a $LF | & tee -a $CF
echo #--------------------------------------------
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.log
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.cmd
#--------------------------------------------
echo "#@# AutoDetGWStats $hemi `date`" | & tee -a $LF | & tee -a $CF
echo #@# AutoDetGWStats lh `date`
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.log
date
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.cmd
#@# AutoDetGWStats lh Thu Apr  8 14:45:16 PDT 2021
set ads = ../surf/autodet.gw.stats.$hemi.dat
set ads = ../surf/autodet.gw.stats.lh.dat
set orig = ../surf/$hemi.orig
set orig = ../surf/lh.orig

if ( $DoRemesh && ! $longitudinal ) set orig = ../surf/$hemi.orig.premesh
if ( 1 && ! 0 ) set orig = ../surf/lh.orig.premesh
set orig = ../surf/lh.orig.premesh

set cmd = ( mris_autodet_gwstats --o $ads --i $bfs --wm $wm --surf $orig )
set cmd = ( mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh )
set xopts = `fsr-getxopts mris_autodet_gwstats $XOptsFile $GlobXOptsFile` ;
set xopts = `fsr-getxopts mris_autodet_gwstats $XOptsFile $GlobXOptsFile`
fsr-getxopts mris_autodet_gwstats
set cmd = ( $cmd $xopts )
set cmd = ( mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh )
echo "cd `$PWD`" | & tee -a $LF | & tee -a $CF
echo cd `/bin/pwd`
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.log
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.cmd
/bin/pwd
cd /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/mri
echo $cmd | & tee -a $LF | & tee -a $CF
echo mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.log
tee -a /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/scripts/recon-all.cmd
mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh
set ud = `UpdateNeeded $ads $bfs $wm $orig`
set ud = `UpdateNeeded $ads $bfs $wm $orig`
UpdateNeeded ../surf/autodet.gw.stats.lh.dat brain.finalsurfs.mgz wm.mgz ../surf/lh.orig.premesh
if ( $ud || $ForceUpdate ) then
if ( /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/mri mri mri_FREESURFER /home/ns-zalewk/Desktop/memorycube/EVOLVE10/TB0029U2/TB0029U2_T2TEST_FREESURFER/mri/mri_FREESURFER/stats 1 || 0 ) then
if: Expression Syntax.