Doug, can you do me a favor and check to see if this modified version of recon-all works on your data?
https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all On 11/30/2016 11:41 AM, Douglas Merkitch wrote: > Hmmm it is a dicom file. Could it be that the lack of file extension > gives it problems? > > Thanks, > > Doug > > Douglas Merkitch > Neurological Sciences > Rush University Medical Center > Phone: (312) 563-3853 <tel:%28312%29%20563-3853> > Fax: (312) 563-4660 <tel:%28312%29%20563-4660> > Email: douglas_merki...@rush.edu <mailto:douglas_merki...@rush.edu> > > > > > > On Nov 29, 2016, at 5:01 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > wrote: > >> It is not recognizing that the input is a dicom file. Is 4355-0005-00001 >> a dicom file? Or is it a folder? >> >> >> On 11/29/2016 05:51 PM, Douglas Merkitch wrote: >>> Here is the command/output with the -debug flag: >>> >>> recon-all -debug -i >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> -i >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> >>> >>> -s 1039_test >>> set echo = 1 ; >>> breaksw >>> breaksw >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 6 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = -i >>> shift >>> >>> switch ( $flag ) >>> switch ( -i ) >>> if ( $#argv < 1 ) goto arg1err ; >>> if ( 5 < 1 ) goto arg1err >>> set InputVol = "$argv[1]" ; shift ; >>> set InputVol = >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> shift >>> if ( ! -e "$InputVol" ) then >>> if ( ! -e >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> ) then >>> if ( -d "$InputVol" ) then >>> if ( -d >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> ) then >>> if ( ! -r "$InputVol" ) then >>> if ( ! -r >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> ) then >>> set InVolDir = `dirname "$InputVol"` ; >>> set InVolDir = `dirname "$InputVol"` >>> dirname >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> set InVolBase = `basename "$InputVol"` ; >>> set InVolBase = `basename "$InputVol"` >>> basename >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> pushd $InVolDir > /dev/null >>> pushd >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE >>> set InVolDir = `pwd` ; >>> set InVolDir = `pwd` >>> pwd >>> popd > /dev/null >>> popd >>> set InputVol = "$InVolDir/$InVolBase" ; >>> set InputVol = >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> set InputList = ( $InputList "$InputVol" ) ; >>> set InputList = ( >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> ) >>> set DoConvertInput = 1 ; >>> set DoConvertInput = 1 >>> breaksw >>> breaksw >>> end >>> end >>> while ( $#argv != 0 ) >>> while ( 4 != 0 ) >>> >>> set flag = $argv[1] ; shift ; >>> set flag = -i >>> shift >>> >>> switch ( $flag ) >>> switch ( -i ) >>> if ( $#argv < 1 ) goto arg1err ; >>> if ( 3 < 1 ) goto arg1err >>> set InputVol = "$argv[1]" ; shift ; >>> set InputVol = >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> shift >>> if ( ! -e "$InputVol" ) then >>> if ( ! -e >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> >>> >>> ) then >>> if ( -d "$InputVol" ) then >>> if ( -d >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> >>> >>> ) then >>> if ( ! -r "$InputVol" ) then >>> if ( ! -r >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> >>> >>> ) then >>> set InVolDir = `dirname "$InputVol"` ; >>> set InVolDir = `dirname "$InputVol"` >>> dirname >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> set InVolBase = `basename "$InputVol"` ; >>> set InVolBase = `basename "$InputVol"` >>> basename >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> pushd $InVolDir > /dev/null >>> pushd >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT >>> set InVolDir = `pwd` ; >>> set InVolDir = `pwd` >>> pwd >>> popd > /dev/null >>> popd >>> set InputVol = "$InVolDir/$InVolBase" ; >>> set InputVol = >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> set InputList = ( $InputList "$InputVol" ) ; >>> set InputList = ( >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> >>> >>> ) >>> set DoConvertInput = 1 ; >>> set DoConvertInput = 1 >>> 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 = 1039_test >>> shift >>> set subjid = `basename $subjid` ; >>> set subjid = `basename $subjid` >>> basename 1039_test >>> 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 ( $DoHippoSF_T1T2 || $DoHippoSF_T2 ) 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 /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ ) then >>> >>> >>> pushd $SUBJECTS_DIR > /dev/null >>> pushd /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/ >>> setenv SUBJECTS_DIR `$PWD` ; >>> setenv SUBJECTS_DIR `$PWD` >>> /bin/pwd >>> popd > /dev/null >>> popd >>> >>> set subjdir = $SUBJECTS_DIR/$subjid >>> set subjdir = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test >>> >>> 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 ( $longitudinal ) then >>> if ( 0 ) then >>> >>> >>> >>> set haslong = `echo $subjid | grep "\.long\."` >>> set haslong = `echo $subjid | grep "\.long\."` >>> grep \.long\. >>> echo 1039_test >>> set hasxhemi = `echo $subjid | grep xhemi` >>> set hasxhemi = `echo $subjid | grep xhemi` >>> grep xhemi >>> echo 1039_test >>> if ( "$haslong" != "" && "$hasxhemi" == "" ) then >>> if ( != && == ) then >>> >>> endif >>> endif >>> >>> >>> if ( ! $DoCreateBaseSubj ) then >>> if ( ! 0 ) then >>> if ( -e $subjdir/$BaseSubjsListFname ) then >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/base-tps >>> ) then >>> endif >>> endif >>> >>> >>> if ( $DoCreateBaseSubj && -e $subjdir ) then >>> if ( 0 && -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test ) then >>> >>> >>> >>> if ( $#InputList == 0 ) then >>> if ( 2 == 0 ) then >>> >>> if ( -e $subjdir ) then >>> if ( -e /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test >>> ) then >>> mkdir -p $subjdir >>> mkdir -p /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test >>> endif >>> endif >>> else >>> else >>> >>> if ( ! $?FREESURFER_HOME ) then >>> if ( ! 1 ) then >>> >>> if ( ! -e $FREESURFER_HOME ) then >>> if ( ! -e /Applications/freesurfer_v6beta_16Nov2016 ) then >>> >>> if ( ! -e ${GCADIR}/$GCA ) then >>> if ( ! -e >>> /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2016-05-10.vc700.gca >>> >>> >>> ) then >>> >>> if ( ! -e ${GCADIR}/$GCASkull && ( $DoSkullLTA || $DoSkullStrip ) ) then >>> if ( ! -e >>> /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_withskull_2016-05-10.vc700.gca >>> >>> >>> && ( 0 || 0 ) ) then >>> >>> foreach hemi ( $hemilist ) >>> foreach hemi ( lh rh ) >>> set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; >>> set avgtif = >>> /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif >>> if ( ! -e $avgtif ) then >>> if ( ! -e >>> /Applications/freesurfer_v6beta_16Nov2016/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif >>> >>> >>> ) then >>> set GCSHemi = ${GCSDIR}/$hemi.$GCS >>> set GCSHemi = >>> /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs >>> if ( ! -e $GCSHemi ) then >>> if ( ! -e >>> /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs >>> >>> >>> ) then >>> set CPAtlas = ${GCSDIR}/$hemi.$GCS >>> set CPAtlas = >>> /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs >>> if ( ! -e $CPAtlas ) then >>> if ( ! -e >>> /Applications/freesurfer_v6beta_16Nov2016/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs >>> >>> >>> ) then >>> end >>> end >>> set avgtif = ${AvgCurvTifPath}/$hemi.${AvgCurvTif} ; >>> set avgtif = >>> /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif >>> if ( ! -e $avgtif ) then >>> if ( ! -e >>> /Applications/freesurfer_v6beta_16Nov2016/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif >>> >>> >>> ) then >>> set GCSHemi = ${GCSDIR}/$hemi.$GCS >>> set GCSHemi = >>> /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs >>> if ( ! -e $GCSHemi ) then >>> if ( ! -e >>> /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs >>> >>> >>> ) then >>> set CPAtlas = ${GCSDIR}/$hemi.$GCS >>> set CPAtlas = >>> /Applications/freesurfer_v6beta_16Nov2016/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs >>> if ( ! -e $CPAtlas ) then >>> if ( ! -e >>> /Applications/freesurfer_v6beta_16Nov2016/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 >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts >>> set XOptsPreExist = $subjdir/scripts/expert-options >>> set XOptsPreExist = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/expert-options >>> if ( -e $XOptsPreExist ) then >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/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 && ! >>> $DoParallel && ! $DoRelabelHypos && ! $DoCurvHK && ! $DoSurfVolume && >>> ! $DoASegMerge && ! $DoCurvStats && ! $DoLabelV1 && ! >>> $DoCreateBaseSubj && ! $DoBaLabels && ! $DoShowEdits && ! >>> $DoLabelExvivoEC && ! $DoPialSurfs && ! $DoHippoSF_T1 && ! >>> $DoHippoSF_T1T2 && ! $DoHippoSF_T2 && ! $DoBSsubst && ! $DoPctSurfCon >>> && ! $DoT2pial && ! $DoFLAIRpial && ! $DoConvertT2Input && ! >>> $DoConvertFlairInput && ! $DoSuperClean && ! $DoCortParc3 && ! >>> $DoParcStats3 && ! $DoAPas2ASeg ) then >>> if ( ! 0 && ! 0 && ! 0 && ! 1 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! >>> 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! >>> 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! >>> 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! >>> 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! >>> 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! >>> 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! >>> 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! 0 && ! >>> 0 && ! 0 && ! 0 && ! 0 && ! 0 ) then >>> >>> if ( $WSMore && $WSLess ) then >>> if ( 0 && 0 ) then >>> >>> if ( ( $WSMore || $WSLess ) && $WSPctPreFlood ) then >>> if ( ( 0 || 0 ) && ) then >>> >>> if ( $#SurfRegToSubj ) then >>> if ( 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 = >>> /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt >>> mkdir -p $SUBJECTS_DIR/$subjid/scripts >>> mkdir -p >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts >>> set bstampfile = $SUBJECTS_DIR/$subjid/scripts/build-stamp.txt >>> set bstampfile = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt >>> if ( -e $bstampfile0 ) then >>> if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then >>> if ( ! -e $bstampfile ) cp $bstampfile0 $bstampfile >>> if ( ! -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt >>> >>> >>> ) cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt >>> cp /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt >>> set bstamp0 = `cat $bstampfile0` >>> set bstamp0 = `cat $bstampfile0` >>> cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt >>> set bstamp = `cat $bstampfile` >>> set bstamp = `cat $bstampfile` >>> cat >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/build-stamp.txt >>> if ( "$bstamp0" != "$bstamp" ) then >>> if ( freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae != >>> freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae ) then >>> echo "Subject Stamp: $bstamp" >>> echo Subject Stamp: >>> freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae >>> Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae >>> echo "Current Stamp: $bstamp0" >>> echo Current Stamp: >>> freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae >>> Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae >>> endif >>> endif >>> rm -f $SUBJECTS_DIR/$subjid/scripts/patchdir.txt >>> rm -f >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/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 /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/lastcall.build-stamp.txt >>> >>> if ( $DoMakefile ) then >>> if ( 0 ) then >>> >>> if ( $DoTime ) then >>> if ( 0 ) then >>> >>> echo "INFO: SUBJECTS_DIR is $SUBJECTS_DIR" >>> echo INFO: SUBJECTS_DIR is >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T >>> INFO: SUBJECTS_DIR is >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T >>> >>> >>> pushd $FREESURFER_HOME > /dev/null >>> pushd /Applications/freesurfer_v6beta_16Nov2016 >>> 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 /Applications/freesurfer_v6beta_16Nov2016 >>> Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 >>> >>> 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 /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test >>> 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 = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/touch >>> >>> >>> if ( ! $DoVersionsOnly ) then >>> if ( ! 0 ) then >>> set CF = ( $subjdir/scripts/$CF_DEFAULT_NAME ) >>> set CF = ( >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/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 = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env >>> if ( -e $ENVF ) mv -f $ENVF $ENVF.bak >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env >>> >>> >>> ) mv -f >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env >>> >>> >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.env.bak >>> date >> $ENVF >>> date >>> echo "FREESURFER_HOME $FREESURFER_HOME" >> $ENVF >>> echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 >>> echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $ENVF >>> echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 >>> pwd >> $ENVF >>> pwd >>> echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $ENVF >>> echo setenv SUBJECTS_DIR >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T >>> echo $inputargs >> $ENVF >>> echo -debug -i >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> -i >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> >>> >>> -s 1039_test >>> 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 = ( >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log >>> >>> >>> ) >>> if ( -e $LF ) then >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log >>> >>> >>> ) then >>> else >>> else >>> skip_new_invo: >>> skip_new_invo: >>> >>> date >> $LF >>> date >>> $PWD >> $LF >>> /bin/pwd >>> echo $0 >> $LF >>> echo /Applications/freesurfer_v6beta_16Nov2016/bin/recon-all >>> echo $inputargs >> $LF >>> echo -debug -i >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> -i >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> >>> >>> -s 1039_test >>> >>> if ( $?RECONALL_MAKE_SUBJECT ) goto skip_all_info >>> if ( 0 ) goto skip_all_info >>> echo "subjid $subjid" >> $LF >>> echo subjid 1039_test >>> echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $LF >>> echo setenv SUBJECTS_DIR >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T >>> echo "FREESURFER_HOME $FREESURFER_HOME" >> $LF >>> echo FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 >>> echo "Actual FREESURFER_HOME $freesurfer_home_true" >> $LF >>> echo Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 >>> if ( -e $FREESURFER_HOME/build-stamp.txt ) then >>> if ( -e /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt ) then >>> echo "build-stamp.txt: `cat $FREESURFER_HOME/build-stamp.txt`" >> $LF >>> echo build-stamp.txt: `cat >>> /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt` >>> cat /Applications/freesurfer_v6beta_16Nov2016/build-stamp.txt >>> endif >>> endif >>> uname -a | tee -a $LF >>> uname -a >>> tee -a >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log >>> Darwin glenn-stebbins-computer.local 12.6.0 Darwin Kernel Version >>> 12.6.0: Wed Mar 18 16:23:48 PDT 2015; >>> root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 >>> limit >> $LF >>> limit >>> if ( -e /usr/bin/free ) then >>> if ( -e /usr/bin/free ) then >>> if ( "`uname -s`" == "Darwin" ) then >>> if ( `uname -s` == Darwin ) then >>> uname -s >>> echo "" >> $LF >>> echo >>> /usr/bin/top -l 1 | grep PhysMem >> $LF >>> /usr/bin/top -l 1 >>> dyld: DYLD_ environment variables being ignored because main >>> executable (/usr/bin/top) is setuid or setgid >>> grep PhysMem >>> echo "" >> $LF >>> echo >>> endif >>> endif >>> 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 $VERSION >> $LF >>> echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman 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 /Applications/freesurfer_v6beta_16Nov2016/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 >>> 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 >>> 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 >>> mri_relabel_hypointensities -all-info >> $LF >>> mri_relabel_hypointensities -all-info >>> >>> echo "#######################################" >> $LF >>> echo ####################################### >>> echo "GCADIR $GCADIR" >> $LF >>> echo GCADIR /Applications/freesurfer_v6beta_16Nov2016/average >>> echo "GCA $GCA" >> $LF >>> echo GCA RB_all_2016-05-10.vc700.gca >>> echo "GCASkull $GCASkull" >> $LF >>> echo GCASkull RB_all_withskull_2016-05-10.vc700.gca >>> echo "AvgCurvTif $AvgCurvTif" >> $LF >>> echo AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif >>> echo "GCSDIR $GCSDIR" >> $LF >>> echo GCSDIR /Applications/freesurfer_v6beta_16Nov2016/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 = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error >>> rm -f $ErrorFile >>> rm -f >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.error >>> >>> if ( $#DoneFile == 0 ) then >>> if ( 0 == 0 ) then >>> set DoneFile = $subjdir/scripts/recon-all.done >>> set DoneFile = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done >>> rm -f $DoneFile >>> rm -f >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.done >>> endif >>> endif >>> >>> >>> if ( $DoIsRunning ) then >>> if ( 1 ) then >>> set IsRunningLH = $subjdir/scripts/IsRunning.lh >>> set IsRunningLH = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh >>> set IsRunningRH = $subjdir/scripts/IsRunning.rh >>> set IsRunningRH = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh >>> set IsRunningLHRH = $subjdir/scripts/IsRunning.lh+rh >>> set IsRunningLHRH = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/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 = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh >>> if ( -e $IsRunningLH ) set bailfile = $IsRunningLH >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh >>> >>> >>> ) set bailfile = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh >>> if ( -e $IsRunningRH ) set bailfile = $IsRunningRH >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh >>> >>> >>> ) set bailfile = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.rh >>> endif >>> endif >>> if ( -e $IsRunningFile ) set bailfile = $IsRunningFile >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh >>> >>> >>> ) set bailfile = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/IsRunning.lh+rh >>> if ( $#bailfile ) then >>> if ( 0 ) then >>> echo "------------------------------" > $IsRunningFile >>> echo ------------------------------ >>> echo "SUBJECT $subjid" >> $IsRunningFile >>> echo SUBJECT 1039_test >>> echo "HEMI $hemilist" >> $IsRunningFile >>> echo HEMI lh rh >>> echo "DATE `date`" >> $IsRunningFile >>> echo DATE `date` >>> date >>> echo "USER $user" >> $IsRunningFile >>> echo USER glennstebbins >>> echo "HOST `hostname`" >> $IsRunningFile >>> echo HOST `hostname` >>> hostname >>> echo "PROCESSID $$ " >> $IsRunningFile >>> echo PROCESSID 33721 >>> 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 $VERSION >> $IsRunningFile >>> echo $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ >>> if ( $?PBS_JOBID ) then >>> if ( 0 ) then >>> endif >>> endif >>> >>> >>> set CSDF = $subjdir/scripts/csurfdir >>> set CSDF = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir >>> if ( $DoCleanCSDF ) rm -vf $CSDF >>> if ( 0 ) rm -vf >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir >>> if ( -e $CSDF ) then >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/csurfdir >>> >>> >>> ) then >>> >>> >>> if ( $#SF == 0 ) then >>> if ( 0 == 0 ) then >>> set SF = ( $subjdir/scripts/$SF_DEFAULT_NAME ) >>> set SF = ( >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log >>> >>> >>> ) >>> if ( -e $SF ) then >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all-status.log >>> >>> >>> ) then >>> 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 >>> >>> >>> >>> if ( $#WaitForFile != 0 ) then >>> if ( 0 != 0 ) then >>> >>> if ( ! $RunIt ) then >>> if ( ! 1 ) 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 = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat >>> if ( $#PonsSeedCRS ) then >>> if ( 0 ) then >>> if ( -e $seedfile ) set PonsSeedCRS = `cat $seedfile | grep -v \#` >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-pons.crs.man.dat >>> >>> >>> ) set PonsSeedCRS = `cat $seedfile | grep -v \#` >>> set seedfile = $subjdir/scripts/seed-cc.crs.man.dat >>> set seedfile = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat >>> if ( $#CCSeedCRS ) then >>> if ( 0 ) then >>> if ( -e $seedfile ) set CCSeedCRS = `cat $seedfile | grep -v \#` >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-cc.crs.man.dat >>> >>> >>> ) set CCSeedCRS = `cat $seedfile | grep -v \#` >>> set seedfile = $subjdir/scripts/seed-lh.crs.man.dat >>> set seedfile = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat >>> if ( $#LHSeedCRS ) then >>> if ( 0 ) then >>> if ( -e $seedfile ) set LHSeedCRS = `cat $seedfile | grep -v \#` >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-lh.crs.man.dat >>> >>> >>> ) set LHSeedCRS = `cat $seedfile | grep -v \#` >>> set seedfile = $subjdir/scripts/seed-rh.crs.man.dat >>> set seedfile = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat >>> if ( $#RHSeedCRS ) then >>> if ( 0 ) then >>> if ( -e $seedfile ) set RHSeedCRS = `cat $seedfile | grep -v \#` >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-rh.crs.man.dat >>> >>> >>> ) set RHSeedCRS = `cat $seedfile | grep -v \#` >>> >>> set seedfile = $subjdir/scripts/seed-ws.crs.man.dat >>> set seedfile = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat >>> if ( $#WSSeedPoint ) then >>> if ( 0 ) then >>> if ( -e $seedfile ) set WSSeedPoint = `cat $seedfile | grep -v \#` >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/seed-ws.crs.man.dat >>> >>> >>> ) set WSSeedPoint = `cat $seedfile | grep -v \#` >>> >>> >>> set ControlPointsFile = $subjdir/tmp/control.dat >>> set ControlPointsFile = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat >>> if ( -e $ControlPointsFile ) then >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/control.dat >>> >>> >>> ) then >>> >>> >>> set DefaultTWMControlPointsFile = $subjdir/tmp/twm.dat >>> set DefaultTWMControlPointsFile = >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat >>> if ( $UseTWMControlPoints ) then >>> if ( 0 ) then >>> >>> if ( -e $DefaultTWMControlPointsFile ) then >>> if ( -e >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/tmp/twm.dat >>> >>> ) then >>> endif >>> endif >>> >>> >>> >>> >>> if ( $DoConformWidth256 ) then >>> if ( 0 ) then >>> >>> >>> >>> >>> >>> >>> if ( $DoShowEdits ) then >>> if ( 0 ) then >>> >>> >>> >>> >>> >>> >>> if ( $longitudinal ) then >>> if ( 0 ) then >>> >>> >>> >>> >>> >>> >>> if ( $#InputList != 0 ) then >>> if ( 2 != 0 ) then >>> @ nth = 1 ; >>> @ nth = 1 >>> foreach InputVol ( $InputList ) >>> foreach InputVol ( >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> >>> >>> ) >>> >>> >>> if ( $nth == 1 ) then >>> if ( 1 == 1 ) then >>> >>> set firstInput = ( $InputVol ) >>> set firstInput = ( >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> ) >>> set rows = `mri_info --nrows $InputVol |& tail -n 1` >>> set rows = `mri_info --nrows $InputVol |& tail -n 1` >>> mri_info --nrows >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> tail -n 1 >>> set cols = `mri_info --ncols $InputVol |& tail -n 1` >>> set cols = `mri_info --ncols $InputVol |& tail -n 1` >>> mri_info --ncols >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> tail -n 1 >>> set slices = `mri_info --nslices $InputVol |& tail -n 1` >>> set slices = `mri_info --nslices $InputVol |& tail -n 1` >>> mri_info --nslices >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> tail -n 1 >>> else >>> else >>> >>> set nthid = `printf %03d.mgz $nth` >>> set nthid = `printf %03d.mgz $nth` >>> printf %03d.mgz 1 >>> set cmd = ( mri_convert $InputVol $subjdir/mri/orig/$nthid ) >>> set cmd = ( mri_convert >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/mri/orig/001.mgz >>> >>> >>> ) >>> $PWD | & tee -a $LF >>> /bin/pwd >>> tee -a >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test >>> echo "\n $cmd \n" | & tee -a $LF | & tee -a $CF >>> tee -a >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log >>> echo \n mri_convert >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/mri/orig/001.mgz >>> >>> >>> \n >>> tee -a >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.cmd >>> \n mri_convert >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/mri/orig/001.mgz >>> >>> >>> \n >>> if ( $RunIt ) then >>> if ( 1 ) then >>> $fs_time $cmd | & tee -a $LF >>> mri_convert >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/mri/orig/001.mgz >>> tee -a >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/scripts/recon-all.log >>> mri_convert.bin >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/mri/orig/001.mgz >>> >>> >>> >>> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ >>> reading from >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001... >>> Starting DICOMRead2() >>> dcmfile = >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> dcmdir = >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE >>> Ref Series No = 5 >>> Found 138 files, checking for dicoms >>> Found 136 dicom files in series. >>> First Sorting >>> Computing Slice Direction >>> Vs: -1.2 0 0 >>> Vs: -1 0 0 >>> Second Sorting >>> IsDWI = 0, IsPhilipsDWI = 0 >>> Counting frames >>> nframes = 1 >>> nslices = 136 >>> ndcmfiles = 136 >>> PE Dir = ROW (dicom read) >>> Loading pixel data >>> TR=9.23, TE=3.72, TI=450.00, flip angle=13.00 >>> i_ras = (0, -1, 0) >>> j_ras = (0, 0, -1) >>> k_ras = (1, -0, 0) >>> writing to >>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039_test/mri/orig/001.mgz... >>> if ( $status ) goto error_exit ; >>> if ( 0 ) goto error_exit >>> endif >>> endif >>> @ nth = $nth + 1 ; >>> @ nth = 1 + 1 >>> end >>> end >>> >>> >>> if ( $nth == 1 ) then >>> if ( 2 == 1 ) then >>> >>> >>> set nrows = `mri_info --nrows $InputVol |& tail -n 1` >>> set nrows = `mri_info --nrows $InputVol |& tail -n 1` >>> mri_info --nrows >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> tail -n 1 >>> set ncols = `mri_info --ncols $InputVol |& tail -n 1` >>> set ncols = `mri_info --ncols $InputVol |& tail -n 1` >>> mri_info --ncols >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> tail -n 1 >>> set nslices = `mri_info --nslices $InputVol |& tail -n 1` >>> set nslices = `mri_info --nslices $InputVol |& tail -n 1` >>> mri_info --nslices >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> tail -n 1 >>> if ( ( $nrows != $rows ) || ( $ncols != $cols ) || ( $nslices != >>> $slices ) ) then >>> if ( ( mri_info: could not parse extension from >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> >>> >>> != mri_info: could not parse extension from >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> ) || ( mri_info: could not parse extension from >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> >>> >>> != mri_info: could not parse extension from >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> ) || ( mri_info: could not parse extension from >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>> >>> >>> != mri_info: could not parse extension from >>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>> >>> >>> ) ) then >>> if: Expression Syntax. >>> >>> >>> >>> Thanks, >>> >>> Doug >>> >>> Douglas Merkitch >>> Neurological Sciences >>> Rush University Medical Center >>> Phone: (312) 563-3853 <tel:%28312%29%20563-3853> >>> Fax: (312) 563-4660 <tel:%28312%29%20563-4660> >>> Email: douglas_merki...@rush.edu <mailto:douglas_merki...@rush.edu> >>> <mailto:douglas_merki...@rush.edu> >>> >>> >>> >>> >>> >>> On Nov 29, 2016, at 4:48 PM, Douglas N Greve >>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>>> Can you run it with -debug and send the terminal output? >>>> >>>> >>>> On 11/29/2016 05:39 PM, Douglas Merkitch wrote: >>>>> Hello Bruce & Doug, >>>>> >>>>> There are no spaces in the filenames (just a lot of underscores and >>>>> dashes!). >>>>> >>>>> I don't think it's a permissions issue because it is able to write the >>>>> first of the two files that I input (regardless of which one I feed it >>>>> first), but fails to write the second file (what would be 002.mgz). My >>>>> current work around is to set it up as two different subjects for the >>>>> dicom conversion and then copy and rename one of the T1 outputs to >>>>> 002.mgz. I am currently processing this subject through the recon-all >>>>> -all pipeline after employing this work around, which suggests to me >>>>> that it's not a permissions issue? >>>>> >>>>> Thanks, >>>>> >>>>> Doug >>>>> >>>>> Douglas Merkitch >>>>> Neurological Sciences >>>>> Rush University Medical Center >>>>> Phone: (312) 563-3853 <tel:%28312%29%20563-3853> >>>>> Fax: (312) 563-4660 <tel:%28312%29%20563-4660> >>>>> Email: douglas_merki...@rush.edu >>>>> <mailto:douglas_merki...@rush.edu> <mailto:douglas_merki...@rush.edu> >>>>> <mailto:douglas_merki...@rush.edu> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Nov 29, 2016, at 4:15 PM, Douglas N Greve >>>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>>> <mailto:gr...@nmr.mgh.harvard.edu>> >>>>> wrote: >>>>> >>>>>> Do you have write permission into that folder, ie, >>>>>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig >>>>>> ? Can >>>>>> you run it with -debug as the first argument and send the terminal >>>>>> output? >>>>>> >>>>>> >>>>>> On 11/29/2016 05:00 PM, Douglas Merkitch wrote: >>>>>>> Hello again, >>>>>>> >>>>>>> I did, in fact, encounter another error that resulted in only the >>>>>>> first mri/orig/001.mgz and not the mr/orig/002.mgz file to be >>>>>>> written. >>>>>>> Below is the command line and terminal output: >>>>>>> >>>>>>> >>>>>>> ======= >>>>>>> recon-all -i >>>>>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -i >>>>>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -s 1039 >>>>>>> Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae >>>>>>> Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae >>>>>>> INFO: SUBJECTS_DIR is >>>>>>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T >>>>>>> Actual FREESURFER_HOME /Applications/freesurfer_v6beta_16Nov2016 >>>>>>> Darwin glenn-stebbins-computer.local 12.6.0 Darwin Kernel Version >>>>>>> 12.6.0: Wed Mar 18 16:23:48 PDT 2015; >>>>>>> root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64 >>>>>>> dyld: DYLD_ environment variables being ignored because main >>>>>>> executable (/usr/bin/top) is setuid or setgid >>>>>>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039 >>>>>>> \n mri_convert >>>>>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> \n >>>>>>> mri_convert.bin >>>>>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ >>>>>>> reading from >>>>>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001... >>>>>>> Starting DICOMRead2() >>>>>>> dcmfile = >>>>>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>>>>>> dcmdir = >>>>>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE >>>>>>> Ref Series No = 5 >>>>>>> Found 138 files, checking for dicoms >>>>>>> Found 136 dicom files in series. >>>>>>> First Sorting >>>>>>> Computing Slice Direction >>>>>>> Vs: -1.2 0 0 >>>>>>> Vs: -1 0 0 >>>>>>> Second Sorting >>>>>>> IsDWI = 0, IsPhilipsDWI = 0 >>>>>>> Counting frames >>>>>>> nframes = 1 >>>>>>> nslices = 136 >>>>>>> ndcmfiles = 136 >>>>>>> PE Dir = ROW (dicom read) >>>>>>> Loading pixel data >>>>>>> TR=9.23, TE=3.72, TI=450.00, flip angle=13.00 >>>>>>> i_ras = (0, -1, 0) >>>>>>> j_ras = (0, 0, -1) >>>>>>> k_ras = (1, -0, 0) >>>>>>> writing to >>>>>>> /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig/001.mgz... >>>>>>> if: Expression Syntax. >>>>>>> ======= >>>>>>> >>>>>>> I did a quick search of the mail archives involving Mac and dyld >>>>>>> variables, and it seems like this may be something that you may >>>>>>> provide a fix for? >>>>>>> >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Doug >>>>>>> >>>>>>> Douglas Merkitch >>>>>>> Neurological Sciences >>>>>>> Rush University Medical Center >>>>>>> Phone: (312) 563-3853 <tel:%28312%29%20563-3853> >>>>>>> Fax: (312) 563-4660 <tel:%28312%29%20563-4660> >>>>>>> Email: douglas_merki...@rush.edu <mailto:douglas_merki...@rush.edu> >>>>>>> <mailto:douglas_merki...@rush.edu> >>>>>>> <mailto:douglas_merki...@rush.edu> >>>>>>> <mailto:douglas_merki...@rush.edu> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Nov 29, 2016, at 3:36 PM, Z K <zkauf...@nmr.mgh.harvard.edu >>>>>>> <mailto:zkauf...@nmr.mgh.harvard.edu> >>>>>>> <mailto:zkauf...@nmr.mgh.harvard.edu> >>>>>>> <mailto:zkauf...@nmr.mgh.harvard.edu> >>>>>>> <mailto:zkauf...@nmr.mgh.harvard.edu>> >>>>>>> wrote: >>>>>>> >>>>>>>> Hello Douglas, >>>>>>>> >>>>>>>> Any chance you can upload the two data files >>>>>>>> 005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 and 4355-0006-00001: >>>>>>>> >>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_FtpFileExchange&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tZ1yGlSjLRqbYLtgmRPVoSSCpQd1kptkk2pxdtqLxSM&s=t6LIHJ4FymbrNntHP5rjaeG3EwBFHeEkINY_hAxr--w&e= >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Ide like to try and reproduce this. Thanks. >>>>>>>> >>>>>>>> -Zeke >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 11/29/2016 04:20 PM, Douglas Merkitch wrote: >>>>>>>>> Hello Doug, >>>>>>>>> >>>>>>>>> Command line & terminal output: >>>>>>>>> >>>>>>>>> recon-all -i >>>>>>>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-00001 >>>>>>>>> -i >>>>>>>>> /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-00001 >>>>>>>>> -s 1039 >>>>>>>>> ERROR: cannot find >>>>>>>>> /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca >>>>>>>>> >>>>>>>>> I do have the following similarly-named files in the v6 beta >>>>>>>>> average >>>>>>>>> directory: >>>>>>>>> RB_all_2008-03-26.mni152.2mm.lta >>>>>>>>> RB_all_2016-05-10.vc700.gca >>>>>>>>> RB_all_withskull_2016-05-10.vc700.gca >>>>>>>>> >>>>>>>>> Thanks for the prompt response! >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> >>>>>>>>> Doug >>>>>>>>> >>>>>>>>> Douglas Merkitch >>>>>>>>> Neurological Sciences >>>>>>>>> Rush University Medical Center >>>>>>>>> Email: douglas_merki...@rush.edu >>>>>>>>> <mailto:douglas_merki...@rush.edu> >>>>>>>>> <mailto:douglas_merki...@rush.edu> >>>>>>>>> <mailto:douglas_merki...@rush.edu> >>>>>>>>> <mailto:douglas_merki...@rush.edu> >>>>>>>>> <mailto:douglas_merki...@rush.edu> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Nov 29, 2016, at 3:12 PM, Douglas N Greve >>>>>>>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>>>>>>>> >>>>>>>>>> can you send your command line and full terminal output? >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 11/29/2016 04:10 PM, Douglas Merkitch wrote: >>>>>>>>>>> Hello experts, >>>>>>>>>>> >>>>>>>>>>> I was attempting to test out the freesurfer v6 beta and >>>>>>>>>>> encountered >>>>>>>>>>> the following error during dicom conversion: "ERROR: cannot find >>>>>>>>>>> /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca". >>>>>>>>>>> >>>>>>>>>>> I'm currently >>>>>>>>>>> running freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae on >>>>>>>>>>> a Mac >>>>>>>>>>> Pro (3.33 GHz 6-Core Intel Xeon) with OS X 10.8.5. >>>>>>>>>>> >>>>>>>>>>> Any help would be greatly appreciated! >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> >>>>>>>>>>> Doug >>>>>>>>>>> >>>>>>>>>>> Douglas Merkitch >>>>>>>>>>> Neurological Sciences >>>>>>>>>>> Rush University Medical Center >>>>>>>>>>> Phone: (312) 563-3853 <tel:%28312%29%20563-3853> >>>>>>>>>>> Fax: (312) 563-4660 <tel:%28312%29%20563-4660> >>>>>>>>>>> Email: douglas_merki...@rush.edu >>>>>>>>>>> <mailto:douglas_merki...@rush.edu> >>>>>>>>>>> <mailto:douglas_merki...@rush.edu> >>>>>>>>>>> <mailto:douglas_merki...@rush.edu> >>>>>>>>>>> <mailto:douglas_merki...@rush.edu> >>>>>>>>>>> <mailto:douglas_merki...@rush.edu> >>>>>>>>>>> <mailto:douglas_merki...@rush.edu> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=RYoN0GgWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=waImhwQq0O8LHAlIun2v95CPShQ-yUCVzQzvOhsqD9s&e= >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>> MGH-NMR Center >>>>>>>>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>>>>>>>> Phone Number: 617-724-2358 >>>>>>>>>> Fax: 617-726-7422 >>>>>>>>>> >>>>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>> FileDrop: >>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=RYoN0GgWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=5c8BG0jWHPLzpY6NB7Qaxm6jR1KlRb-uxt-ubzqrV9U&e= >>>>>>>>>> >>>>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> Outgoing: >>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=RYoN0GgWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=q36YAeWf40aDIu00LgaqEQKGoZ6iygWUhdUQLvWflDo&e= >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Freesurfer mailing list >>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=RYoN0GgWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=waImhwQq0O8LHAlIun2v95CPShQ-yUCVzQzvOhsqD9s&e= >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>>>> whom >>>>>>>>>> it is >>>>>>>>>> addressed. If you believe this e-mail was sent to you in error >>>>>>>>>> and the >>>>>>>>>> e-mail >>>>>>>>>> contains patient information, please contact the Partners >>>>>>>>>> Compliance >>>>>>>>>> HelpLine at >>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=RYoN0GgWPi9MuiSoN-_tC7n3EM0X-3w27aQb4YV8g_0&s=l884SPU9n9FO1VCPEZEhUM1DdT4D5SDBf9KDe5zMylY&e= >>>>>>>>>> . If the e-mail was sent to you in error >>>>>>>>>> but does not contain patient information, please contact the >>>>>>>>>> sender >>>>>>>>>> and properly >>>>>>>>>> dispose of the e-mail. >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tZ1yGlSjLRqbYLtgmRPVoSSCpQd1kptkk2pxdtqLxSM&s=fgHm7WtEcDeIObTMf1ec6mcjDDifXpuQrECJ1EoQ7rE&e= >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tZ1yGlSjLRqbYLtgmRPVoSSCpQd1kptkk2pxdtqLxSM&s=fgHm7WtEcDeIObTMf1ec6mcjDDifXpuQrECJ1EoQ7rE&e= >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>> whom it is >>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>> the e-mail >>>>>>>> contains patient information, please contact the Partners >>>>>>>> Compliance >>>>>>>> HelpLine at >>>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=tZ1yGlSjLRqbYLtgmRPVoSSCpQd1kptkk2pxdtqLxSM&s=IpoDR5ajMtOI8sgDIeYFARbgI4SlYbCfivrUFYy4inM&e= >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> . If the e-mail was sent to you in error >>>>>>>> but does not contain patient information, please contact the sender >>>>>>>> and properly >>>>>>>> dispose of the e-mail. >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=Mf7oo_xqWDKrJzWtWF0FCpgZw95IM1WXgDfGiXrVYrM&s=4jwNum1N3NbFml_S3yJtQiONYIzboVQQcGGUWEbSkJg&e= >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> FileDrop: >>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=Mf7oo_xqWDKrJzWtWF0FCpgZw95IM1WXgDfGiXrVYrM&s=t9AhvRxW5R5eVdXbZf549gjnMjQntTg_3M6Olb_AYtk&e= >>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> Outgoing: >>>>>> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=Mf7oo_xqWDKrJzWtWF0FCpgZw95IM1WXgDfGiXrVYrM&s=3rTENbtNIhE4g6X5kSTMZvxN-V2nNLBN-rOwXWNIH7w&e= >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=Mf7oo_xqWDKrJzWtWF0FCpgZw95IM1WXgDfGiXrVYrM&s=4jwNum1N3NbFml_S3yJtQiONYIzboVQQcGGUWEbSkJg&e= >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to >>>>>> whom it is >>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>> the e-mail >>>>>> contains patient information, please contact the Partners Compliance >>>>>> HelpLine at >>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=Mf7oo_xqWDKrJzWtWF0FCpgZw95IM1WXgDfGiXrVYrM&s=n6OAqPVdKFImlasv9Vgs5X6L8s-9bcBLbgOfmleS-Fc&e= >>>>>> >>>>>> >>>>>> >>>>>> . If the e-mail was sent to you in error >>>>>> but does not contain patient information, please contact the sender >>>>>> and properly >>>>>> dispose of the e-mail. >>>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=OOgLwUOMizMCtyPwVSIlYeCcUfFqc-pTRZpqyfLqn5U&s=5rBQRHJqxqYwhX34XzobMD0UuIK3X6J8NxM1Kzx-UnA&e= >>>>> >>>>> >>>>> >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=OOgLwUOMizMCtyPwVSIlYeCcUfFqc-pTRZpqyfLqn5U&s=uL2rYBH_OT2yVa2b-LKJv_u2cVHnCIoR-3SGLe3i5E8&e= >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: >>>> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=OOgLwUOMizMCtyPwVSIlYeCcUfFqc-pTRZpqyfLqn5U&s=DzZhDxhAwLGuusTKxelhzBTZkx5U2dETAlrP-COwB0w&e= >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=OOgLwUOMizMCtyPwVSIlYeCcUfFqc-pTRZpqyfLqn5U&s=5rBQRHJqxqYwhX34XzobMD0UuIK3X6J8NxM1Kzx-UnA&e= >>>> >>>> >>>> >>>> >>>> >>>> The information in this e-mail is intended only for the person to >>>> whom it is >>>> addressed. If you believe this e-mail was sent to you in error and >>>> the e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=OOgLwUOMizMCtyPwVSIlYeCcUfFqc-pTRZpqyfLqn5U&s=XU07oC1bxYFxHQbY0EodPEC6xx4m82Dwj49jh2Sv01U&e= >>>> >>>> >>>> . If the e-mail was sent to you in error >>>> but does not contain patient information, please contact the sender >>>> and properly >>>> dispose of the e-mail. >>>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=cWNq4x_Gc_8IqjX_rgOK7RzmrrWGFEHerIMX2-VP_xo&s=OQEkejGkoKZQrQrBwJFUJ00aZVPiOYZzvt9F851pHlg&e= >>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: >> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=cWNq4x_Gc_8IqjX_rgOK7RzmrrWGFEHerIMX2-VP_xo&s=atNA3FqyvrlNbpX0BdfOfJz1ySv6DvbHgj6oOrBA18E&e= >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=cWNq4x_Gc_8IqjX_rgOK7RzmrrWGFEHerIMX2-VP_xo&s=08Rak8IOG70fTGPFiD3kSs4-9onVK-ARVMJKc7XNYzo&e= >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=cWNq4x_Gc_8IqjX_rgOK7RzmrrWGFEHerIMX2-VP_xo&s=OQEkejGkoKZQrQrBwJFUJ00aZVPiOYZzvt9F851pHlg&e= >> >> >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DgIBAg&c=XxU8ngzB_WPJXKyiin_6iQ&r=GRn28rC6ssBi3WYtpTHXUZZiKgdhzFrFkzz7_Ref9iw&m=cWNq4x_Gc_8IqjX_rgOK7RzmrrWGFEHerIMX2-VP_xo&s=5RSBTPL6x99n0UrBaJubeIYDoOpEkFwqWDJ9EJ0ZIaA&e= >> >> . If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.