Actually, it is the lack of a dot (".") in the file name. This is a
short-coming of recon-all. I'm really surprised that it took this long
to manifest itself. The short-term fix is to convert the files to mgz,
then pass the mgz files to 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.
