set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 3 != 0 ) set flag = $argv[1] ; shift ; set flag = -all shift switch ( $flag ) switch ( -all ) case "-autorecon-all": case -autorecon-all: set DoCreateBaseInput = 1 ; set DoCreateBaseInput = 1 set DoMotionCor = 1 ; set DoMotionCor = 1 set DoTalairach = 1 ; set DoTalairach = 1 set DoTalCheck = 1 ; set DoTalCheck = 1 set DoNuIntensityCor = 1 ; set DoNuIntensityCor = 1 set DoNormalization = 1 ; set DoNormalization = 1 set DoSkullStrip = 1 ; set DoSkullStrip = 1 set DoGCAReg = 1 ; set DoGCAReg = 1 set DoCARegInv = 1 ; set DoCARegInv = 1 set DoRemoveNeck = 1 ; set DoRemoveNeck = 1 set DoSkullLTA = 1 ; set DoSkullLTA = 1 set DoCANormalize = 1 ; set DoCANormalize = 1 set DoCAReg = 1 ; set DoCAReg = 1 set DoCALabel = 1 ; set DoCALabel = 1 set DoNormalization2 = 1 ; set DoNormalization2 = 1 set DoMaskBFS = 1 ; set DoMaskBFS = 1 set DoSegmentation = 1 ; set DoSegmentation = 1 set DoFill = 1 ; set DoFill = 1 set DoTessellate = 1 ; set DoTessellate = 1 set DoSmooth1 = 1 ; set DoSmooth1 = 1 set DoInflate1 = 1 ; set DoInflate1 = 1 set DoQSphere = 1 ; set DoQSphere = 1 set DoFix = 1 ; set DoFix = 1 set DoSmooth2 = 1 ; set DoSmooth2 = 1 set DoInflate2 = 1 ; set DoInflate2 = 1 set DoWhiteSurfs = 1 ; set DoWhiteSurfs = 1 set DoSphere = 1 ; set DoSphere = 1 set DoSurfReg = 1 ; set DoSurfReg = 1 set DoContraSurfReg = 0 ; set DoContraSurfReg = 0 set DoAvgCurv = 1 ; set DoAvgCurv = 1 set DoJacobianWhite = 1 ; set DoJacobianWhite = 1 set DoCortParc = 1 ; set DoCortParc = 1 set DoPialSurfs = 1 ; set DoPialSurfs = 1 set DoPctSurfCon = 1 ; set DoPctSurfCon = 1 set DoParcStats = 1 ; set DoParcStats = 1 set DoCortParc2 = 1 ; set DoCortParc2 = 1 set DoParcStats2 = 1 ; set DoParcStats2 = 1 set DoCortParc3 = 1 ; set DoCortParc3 = 1 set DoParcStats3 = 1 ; set DoParcStats3 = 1 set DoCortRibbonVolMask = 1 ; set DoCortRibbonVolMask = 1 set DoSegStats = 1 ; set DoSegStats = 1 set DoAParc2ASeg = 1 ; set DoAParc2ASeg = 1 set DoWMParc = 1 ; set DoWMParc = 1 set DoCurvStats = 1 ; set DoCurvStats = 1 set DoBaLabels = 1 ; set DoBaLabels = 1 set DoLabelExvivoEC = 1 ; set DoLabelExvivoEC = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 ) set flag = $argv[1] ; shift ; set flag = -subjid shift switch ( $flag ) switch ( -subjid ) case "-sid": case -sid: case "-s": case -s: if ( $#argv < 1 ) goto arg1err ; if ( 1 < 1 ) goto arg1err set subjid = $argv[1] ; shift ; set subjid = CAA_022_struc shift set subjid = `basename $subjid` ; set subjid = `basename $subjid` basename CAA_022_struc 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 ( $UseCuda || $GetCuda ) 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 /cluster/ichresearch/Petechial/MEG ) then pushd $SUBJECTS_DIR > /dev/null pushd /cluster/ichresearch/Petechial/MEG setenv SUBJECTS_DIR `$PWD` ; setenv SUBJECTS_DIR `$PWD` /bin/pwd popd > /dev/null popd set subjdir = $SUBJECTS_DIR/$subjid set subjdir = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc if ( $longitudinal ) then if ( 0 ) then set haslong = `echo $subjid | grep "\.long\."` set haslong = `echo $subjid | grep "\.long\."` grep \.long\. echo CAA_022_struc if ( "$haslong" != "" ) then if ( != ) then endif endif if ( ! $DoCreateBaseSubj ) then if ( ! 0 ) then if ( -e $subjdir/$BaseSubjsListFname ) then if ( -e /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/base-tps ) then endif endif if ( $#InputList == 0 ) then if ( 0 == 0 ) then if ( ! $DoCreateBaseSubj ) then if ( ! 0 ) then if ( $longitudinal ) mkdir -p ${subjdir} if ( 0 ) mkdir -p /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc if ( ! -e $subjdir ) then if ( ! -e /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc ) then if ( ! -w $subjdir ) then if ( ! -w /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc ) then endif endif else else else else if ( ! $?FREESURFER_HOME ) then if ( ! 1 ) then if ( ! -e $FREESURFER_HOME ) then if ( ! -e /usr/local/freesurfer/stable5_3_0 ) then if ( ! -e ${GCADIR}/$GCA ) then if ( ! -e /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca ) then if ( ! -e ${GCADIR}/$GCASkull ) then if ( ! -e /usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca ) then foreach hemi ( $hemilist ) foreach hemi ( lh rh ) set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif if ( ! -e $avgtif ) then if ( ! -e /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif ) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /usr/local/freesurfer/stable5_3_0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs if ( ! -e $GCSHemi ) then if ( ! -e /usr/local/freesurfer/stable5_3_0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /usr/local/freesurfer/stable5_3_0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs if ( ! -e $CPAtlas ) then if ( ! -e /usr/local/freesurfer/stable5_3_0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ) then end end set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; set avgtif = /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif if ( ! -e $avgtif ) then if ( ! -e /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif ) then set GCSHemi = ${GCSDIR}/$hemi.$GCS set GCSHemi = /usr/local/freesurfer/stable5_3_0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs if ( ! -e $GCSHemi ) then if ( ! -e /usr/local/freesurfer/stable5_3_0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ) then set CPAtlas = ${GCSDIR}/$hemi.$GCS set CPAtlas = /usr/local/freesurfer/stable5_3_0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs if ( ! -e $CPAtlas ) then if ( ! -e /usr/local/freesurfer/stable5_3_0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ) then end end if ( $XOptsUse == 1 && $XOptsClean == 1 ) then if ( 1 == 1 && 0 == 1 ) then if ( $IsMPRAGE == 1 && $IsWashuMPRAGE == 1 ) then if ( 0 == 1 && 0 == 1 ) then mkdir -p $subjdir/scripts mkdir -p /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts set XOptsPreExist = $subjdir/scripts/expert-options set XOptsPreExist = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/expert-options if ( -e $XOptsPreExist ) then if ( -e /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/expert-options ) then if ( $#XOptsFile != 0 ) then if ( 0 != 0 ) then endif endif 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 && ! $DoCARegInv && ! $DoMotionCor && ! $DoTalairach && ! $DoTalCheck && ! $DoCleanXopts && ! $DoNormalization && ! $#SurfRegToSubj && ! $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 && ! $DoContraSurfReg && ! $DoAvgCurv && ! $DoSegStats && ! $DoMorphRGB && ! $DoWhiteSurfs && ! $DoContraSurfRegWithinSubject && ! $DoCortRibbonVolMask && ! $DoJacobianWhite && ! $DoJacobianDist0 && ! $DoCANormalize && ! $DoCAReg && ! $DoCALabel && ! $DoMaskBFS && ! $DoAParcASegStats && ! $DoLocalGyriIndex && ! $DoMakefile && ! $DoAsegStatsDiff && ! $DoAparcStatsDiff && ! $DoSurfVolume && ! $DoASegMerge && ! $DoCurvStats && ! $DoLabelV1 && ! $DoCreateBaseSubj && ! $DoBaLabels && ! $DoShowEdits && ! $DoLabelExvivoEC && ! $DoSurfSegEdit && ! $DoPialSurfs && ! $DoGEMS && ! $DoPctSurfCon && ! $DoT2pial && ! $DoFLAIRpial && ! $DoConvertT2Input && ! $DoConvertFlairInput && ! $DoCortParc3 && ! $DoParcStats3 ) then if ( ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 0 && ! 1 && ! 0 && ! 1 && ! 1 && ! 1 && ! 0 && ! 0 && ! 0 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 1 && ! 0 && ! 0 && ! 1 && ! 0 && ! 1 && ! 1 && ! 0 && ! 1 && ! 0 && ! 1 && ! 1 && ! 0 && ! 1 && ! 1 && ! 1 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 1 && ! 0 && ! 0 && ! 1 && ! 0 && ! 1 && ! 0 && ! 1 && ! 0 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 1 && ! 1 ) then if ( $WSMore && $WSLess ) then if ( 0 && 0 ) then if ( ( $WSMore || $WSLess ) && $WSPctPreFlood ) then if ( ( 0 || 0 ) && ) then if ( $DoAsegStatsDiff ) then if ( 0 ) then if ( $DoAparcStatsDiff ) then if ( 0 ) then if ( $#SurfRegToSubj ) then if ( 0 ) 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 = /usr/local/freesurfer/stable5_3_0/build-stamp.txt mkdir -p $SUBJECTS_DIR/$subjid/scripts mkdir -p /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts set bstampfile = $SUBJECTS_DIR/$subjid/scripts/build-stamp.txt set bstampfile = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/build-stamp.txt if ( -e $bstampfile0 ) then if ( -e /usr/local/freesurfer/stable5_3_0/build-stamp.txt ) then if ( ! -e $bstampfile ) cp $bstampfile0 $bstampfile if ( ! -e /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/build-stamp.txt ) cp /usr/local/freesurfer/stable5_3_0/build-stamp.txt /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/build-stamp.txt set bstamp0 = `cat $bstampfile0` set bstamp0 = `cat $bstampfile0` cat /usr/local/freesurfer/stable5_3_0/build-stamp.txt set bstamp = `cat $bstampfile` set bstamp = `cat $bstampfile` cat /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/build-stamp.txt if ( "$bstamp0" != "$bstamp" ) then if ( freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 != freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 ) then echo "Subject Stamp: $bstamp" echo Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 echo "Current Stamp: $bstamp0" echo Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 endif endif if ( $DoMakefile ) then if ( 0 ) then if ( $DoTime ) then if ( 0 ) then echo "INFO: SUBJECTS_DIR is $SUBJECTS_DIR" echo INFO: SUBJECTS_DIR is /autofs/cluster/ichresearch/Petechial/MEG INFO: SUBJECTS_DIR is /autofs/cluster/ichresearch/Petechial/MEG pushd $FREESURFER_HOME > /dev/null pushd /usr/local/freesurfer/stable5_3_0 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 /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 set DateString = "`date '+%y%m%d%H%M'`" set DateString = `date '+%y%m%d%H%M'` date +%y%m%d%H%M cd $subjdir cd /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc mkdir -p mri scripts surf tmp label touch stats touch src trash bem mkdir -p mri scripts surf tmp label touch stats touch src trash bem mkdir -p mri/transforms mri/transforms/bak mri/orig mkdir -p mri/transforms mri/transforms/bak mri/orig set touchdir = $subjdir/touch set touchdir = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/touch if ( ! $DoVersionsOnly ) then if ( ! 0 ) then set CF = ( $subjdir/scripts/$CF_DEFAULT_NAME ) set CF = ( /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.cmd ) rm -f $CF rm -f /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.cmd set ENVF = $subjdir/scripts/recon-all.env set ENVF = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.env if ( -e $ENVF ) mv $ENVF $ENVF.bak if ( -e /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.env ) mv /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.env /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.env.bak mv /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.env /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.env.bak date >> $ENVF date echo "FREESURFER_HOME $FREESURFER_HOME" >> $ENVF echo FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $ENVF echo Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 pwd >> $ENVF pwd echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $ENVF echo setenv SUBJECTS_DIR /autofs/cluster/ichresearch/Petechial/MEG echo $inputargs >> $ENVF echo -debug -all -subjid CAA_022_struc 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 = ( /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.log ) if ( -e $LF ) then if ( -e /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.log ) then ls -l $LF ls -l /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.log -rw-rw-r-- 1 pfotiad smithich 16476 Aug 27 12:35 /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/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: date >> $LF date $PWD >> $LF /bin/pwd echo $0 >> $LF echo /usr/local/freesurfer/stable5_3_0/bin/recon-all echo $inputargs >> $LF echo -debug -all -subjid CAA_022_struc if ( $?RECONALL_MAKE_SUBJECT ) goto skip_all_info if ( 0 ) goto skip_all_info echo "subjid $subjid" >> $LF echo subjid CAA_022_struc echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $LF echo setenv SUBJECTS_DIR /autofs/cluster/ichresearch/Petechial/MEG echo "FREESURFER_HOME $FREESURFER_HOME" >> $LF echo FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $LF echo Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 if ( -e $FREESURFER_HOME/build-stamp.txt ) then if ( -e /usr/local/freesurfer/stable5_3_0/build-stamp.txt ) then echo "build-stamp.txt: `cat $FREESURFER_HOME/build-stamp.txt`" >> $LF echo build-stamp.txt: `cat /usr/local/freesurfer/stable5_3_0/build-stamp.txt` cat /usr/local/freesurfer/stable5_3_0/build-stamp.txt endif endif uname -a | tee -a $LF uname -a tee -a /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.log Linux eesmith 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 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 >> $LF /usr/bin/free echo "" >> $LF echo endif endif if ( "`uname -s`" == "Darwin" ) then if ( `uname -s` == Darwin ) then uname -s echo "########################################" >> $LF echo ######################################## echo "program versions used" >> $LF echo program versions used echo $VERSION >> $LF echo $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ mri_motion_correct.fsl -version >> $LF mri_motion_correct.fsl -version if ( -e $FREESURFER_HOME/bin/flirt.fsl ) flirt.fsl -version >> $LF if ( -e /usr/local/freesurfer/stable5_3_0/bin/flirt.fsl ) flirt.fsl -version flirt.fsl -version talairach_avi --version >> $LF talairach_avi --version tkregister2_cmdl --all-info >> $LF tkregister2_cmdl --all-info nu_correct -version >> $LF nu_correct -version mri_make_uchar -all-info >> $LF mri_make_uchar -all-info mri_normalize -all-info >> $LF mri_normalize -all-info mri_watershed -all-info >> $LF mri_watershed -all-info mri_gcut -all-info >> $LF mri_gcut -all-info mri_segment -all-info >> $LF mri_segment -all-info mri_label2label -all-info >> $LF mri_label2label -all-info mri_em_register -all-info >> $LF mri_em_register -all-info mri_ca_normalize -all-info >> $LF mri_ca_normalize -all-info mri_ca_register -all-info >> $LF mri_ca_register -all-info mri_ca_label -all-info >> $LF mri_ca_label -all-info mri_pretess -all-info >> $LF mri_pretess -all-info mri_fill -all-info >> $LF mri_fill -all-info mri_tessellate -all-info >> $LF mri_tessellate -all-info mri_concatenate_lta -all-info >> $LF mri_concatenate_lta -all-info mri_normalize_tp2 -all-info >> $LF mri_normalize_tp2 -all-info mris_smooth -all-info >> $LF mris_smooth -all-info mris_inflate -all-info >> $LF mris_inflate -all-info mris_curvature -all-info >> $LF mris_curvature -all-info mris_sphere -all-info >> $LF mris_sphere -all-info mris_fix_topology -all-info >> $LF mris_fix_topology -all-info mris_topo_fixer -all-info >> $LF mris_topo_fixer -all-info mris_ca_label -all-info >> $LF mris_ca_label -all-info mris_euler_number -all-info >> $LF mris_euler_number -all-info mris_make_surfaces -all-info >> $LF mris_make_surfaces -all-info mris_register -all-info >> $LF mris_register -all-info mris_volmask --all-info >> $LF mris_volmask --all-info mris_anatomical_stats -all-info >> $LF mris_anatomical_stats -all-info mrisp_paint -all-info >> $LF mrisp_paint -all-info mris_curvature_stats -all-info >> $LF mris_curvature_stats -all-info if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats if ( -e .xdebug_mris_curvature_stats ) rm -f .xdebug_mris_curvature_stats rm -f .xdebug_mris_curvature_stats mris_calc -all-info >> $LF mris_calc -all-info if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc if ( -e .xdebug_mris_calc ) rm -f .xdebug_mris_calc rm -f .xdebug_mris_calc mri_robust_register -all-info >> $LF mri_robust_register -all-info mri_robust_template -all-info >> $LF mri_robust_template -all-info mri_and -all-info >> $LF mri_and -all-info mri_or -all-info >> $LF mri_or -all-info mri_fuse_segmentations -all-info >> $LF mri_fuse_segmentations -all-info mri_segstats -all-info >> $LF mri_segstats -all-info echo "#######################################" >> $LF echo ####################################### echo "GCADIR $GCADIR" >> $LF echo GCADIR /usr/local/freesurfer/stable5_3_0/average echo "GCA $GCA" >> $LF echo GCA RB_all_2008-03-26.gca echo "GCASkull $GCASkull" >> $LF echo GCASkull RB_all_withskull_2008-03-26.gca echo "AvgCurvTif $AvgCurvTif" >> $LF echo AvgCurvTif average.curvature.filled.buckner40.tif echo "GCSDIR $GCSDIR" >> $LF echo GCSDIR /usr/local/freesurfer/stable5_3_0/average echo "GCS $GCS" >> $LF echo GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.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 = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.error rm -f $ErrorFile rm -f /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.error set DoneFile = $subjdir/scripts/recon-all.done set DoneFile = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.done rm -f $DoneFile rm -f /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/recon-all.done if ( $DoIsRunning ) then if ( 1 ) then set IsRunningLH = $subjdir/scripts/IsRunning.lh set IsRunningLH = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.lh set IsRunningRH = $subjdir/scripts/IsRunning.rh set IsRunningRH = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.rh set IsRunningLHRH = $subjdir/scripts/IsRunning.lh+rh set IsRunningLHRH = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/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 = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.lh+rh if ( -e $IsRunningLH ) set bailfile = $IsRunningLH if ( -e /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.lh ) set bailfile = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.lh if ( -e $IsRunningRH ) set bailfile = $IsRunningRH if ( -e /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.rh ) set bailfile = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.rh endif endif if ( -e $IsRunningFile ) set bailfile = $IsRunningFile if ( -e /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.lh+rh ) set bailfile = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.lh+rh set bailfile = /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.lh+rh if ( $#bailfile ) then if ( 1 ) then echo "" echo echo "ERROR: it appears that recon-all is already running" echo ERROR: it appears that recon-all is already running ERROR: it appears that recon-all is already running echo "for $subjid based on the presence of $bailfile. It could" echo for CAA_022_struc based on the presence of /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.lh+rh. It could for CAA_022_struc based on the presence of /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.lh+rh. It could echo "also be that recon-all was running at one point but" echo also be that recon-all was running at one point but also be that recon-all was running at one point but echo "died in an unexpected way. If it is the case that there" echo died in an unexpected way. If it is the case that there died in an unexpected way. If it is the case that there echo "is a process running, you can kill it and start over or" echo is a process running, you can kill it and start over or is a process running, you can kill it and start over or echo "just let it run. If the process has died, you should type:" echo just let it run. If the process has died, you should type: just let it run. If the process has died, you should type: echo "" echo echo "rm $bailfile" echo rm /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.lh+rh rm /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.lh+rh echo "" echo echo "and re-run. Or you can add -no-isrunning to the recon-all" echo and re-run. Or you can add -no-isrunning to the recon-all and re-run. Or you can add -no-isrunning to the recon-all echo "command-line. The contents of this file are:" echo command-line. The contents of this file are: command-line. The contents of this file are: echo "----------------------------------------------------------" echo ---------------------------------------------------------- ---------------------------------------------------------- cat $bailfile cat /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/scripts/IsRunning.lh+rh ------------------------------ SUBJECT CAA_022_struc HEMI lh rh DATE Tue Aug 27 12:35:01 EDT 2013 USER pfotiad HOST eesmith PROCESSID 3653 PROCESSOR x86_64 OS Linux Linux eesmith 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ echo "----------------------------------------------------------" echo ---------------------------------------------------------- ---------------------------------------------------------- exit 1 ; exit 1 Exit 1