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
Fax: (312) 563-4660
Email: Douglas_Merkitch@rush.edu





On Nov 29, 2016, at 5:01 PM, Douglas N Greve <greve@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_Merkitch@rush.edu <mailto:Douglas_Merkitch@rush.edu>





On Nov 29, 2016, at 4:48 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@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_Merkitch@rush.edu <mailto:Douglas_Merkitch@rush.edu>
<mailto:Douglas_Merkitch@rush.edu>





On Nov 29, 2016, at 4:15 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@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_Merkitch@rush.edu
<mailto:Douglas_Merkitch@rush.edu> <mailto:Douglas_Merkitch@rush.edu>
<mailto:Douglas_Merkitch@rush.edu>





On Nov 29, 2016, at 3:36 PM, Z K <zkaufman@nmr.mgh.harvard.edu
<mailto:zkaufman@nmr.mgh.harvard.edu>
<mailto:zkaufman@nmr.mgh.harvard.edu>
<mailto:zkaufman@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_Merkitch@rush.edu <mailto:Douglas_Merkitch@rush.edu>
<mailto:Douglas_Merkitch@rush.edu>
<mailto:Douglas_Merkitch@rush.edu>
<mailto:Douglas_Merkitch@rush.edu>





On Nov 29, 2016, at 3:12 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@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_Merkitch@rush.edu
<mailto:Douglas_Merkitch@rush.edu>
<mailto:Douglas_Merkitch@rush.edu>
<mailto:Douglas_Merkitch@rush.edu>
<mailto:Douglas_Merkitch@rush.edu>
<mailto:Douglas_Merkitch@rush.edu>







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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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Fax: 617-726-7422

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_______________________________________________
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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=
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