Ah! That was helpful, Doug. While eliminating the & at the end didn't do anything, running the debug version of the command shows the following at the end of log.txt (attached):
set subjdir = $SUBJECTS_DIR/$subjid set subjdir = /home/hurry01/.gvfs/ebblvm$ on callunavm.psy.tufts.edu/projects/resdep/data/mri/resdep214 This is where the set message gets spit out. It's - for obvious reasons - not happy with that path. I'll work with IT over on this end as it likely has something to do with the way we're mounting the Windows shares on which data are stored and processed. Best, Heather On Wed, Aug 7, 2013 at 1:13 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > Hmm, not sure what is going on. > > First, run it without the ampersand on the end. > > If that still crashes, then run this and send me log.txt > > recon-all -debug -i > /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm -s resdep214 > -all |& tee log.txt > > doug > > > On 08/07/2013 12:47 PM, Heather L. Urry wrote: > > > > Ah, sorry-- that too: tcsh 6.18.01. > > > > (The command, which I just sent in a previous message, was as follows: > > > > recon-all -i /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm > > -s resdep214 -all & > > > > ) > > > > Heather > > > > > > On Wed, Aug 7, 2013 at 12:42 PM, Bruce Fischl > > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > > > and what shell are you using > > On Wed, 7 Aug 2013, Douglas N Greve wrote: > > > > > what is your command line? > > > > > > > > > > > > > > > On 08/07/2013 10:19 AM, Heather L. Urry wrote: > > >> Hi folks, > > >> > > >> When issuing a recon-all command, I'm seeing the following > message: > > >> > > >> set: Variable name must contain alphanumeric characters > > >> > > >> recon-all stalls and doesn't move forward (doesn't even create the > > >> subject directory). > > >> > > >> I'm using Freesurfer 5.3.0 > > >> (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu > > 12.04.2. > > >> In fact, we just upgraded to this version of Ubuntu from an older > > >> version of Mandriva and to this latest version of Freesurfer. > > >> recon-all did not produce this message before these two > > upgrades. Any > > >> help you can offer would be most appreciated! Thanks in advance. > > >> > > >> Best, > > >> > > >> Heather > > >> > > >> -- > > >> Heather L. Urry, Ph.D. > > >> Department of Psychology > > >> Tufts University > > >> 490 Boston Avenue > > >> Medford, MA 02155 > > >> > > >> email: heather.u...@tufts.edu <mailto:heather.u...@tufts.edu> > > <mailto:heather.u...@tufts.edu <mailto:heather.u...@tufts.edu>> > > >> phone: 617-627-3733 <tel:617-627-3733> > > >> fax: 617-627-3181 <tel:617-627-3181> > > >> > > >> http://ase.tufts.edu/psychology/ebbl > > >> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > 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. > > > > > > > > > > -- > > Heather L. Urry, Ph.D. > > Department of Psychology > > Tufts University > > 490 Boston Avenue > > Medford, MA 02155 > > > > email: heather.u...@tufts.edu <mailto:heather.u...@tufts.edu> > > phone: 617-627-3733 > > fax: 617-627-3181 > > > > http://ase.tufts.edu/psychology/ebbl > > > > > > _______________________________________________ > > 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 > -- Heather L. Urry, Ph.D. Department of Psychology Tufts University 490 Boston Avenue Medford, MA 02155 email: heather.u...@tufts.edu phone: 617-627-3733 fax: 617-627-3181 http://ase.tufts.edu/psychology/ebbl
set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 5 != 0 ) set flag = $argv[1] ; shift ; set flag = -i shift switch ( $flag ) switch ( -i ) if ( $#argv < 1 ) goto arg1err ; if ( 4 < 1 ) goto arg1err set InputVol = "$argv[1]" ; shift ; set InputVol = /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm shift if ( ! -e "$InputVol" ) then if ( ! -e /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm ) then if ( -d "$InputVol" ) then if ( -d /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm ) then if ( ! -r "$InputVol" ) then if ( ! -r /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm ) then set InVolDir = `dirname "$InputVol"` ; set InVolDir = `dirname "$InputVol"` dirname /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm set InVolBase = `basename "$InputVol"` ; set InVolBase = `basename "$InputVol"` basename /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm pushd $InVolDir > /dev/null pushd /home/hurry01/r/resdep_mri_data/resdep014 set InVolDir = `pwd` ; set InVolDir = `pwd` pwd popd > /dev/null popd set InputVol = "$InVolDir/$InVolBase" ; set InputVol = /home/hurry01/.gvfs/as-rsch-urry$ on rstore1.uit.tufts.edu/resdep_mri_data/resdep014/265000-10-1.dcm set InputList = ( $InputList "$InputVol" ) ; set InputList = ( /home/hurry01/.gvfs/as-rsch-urry$ on rstore1.uit.tufts.edu/resdep_mri_data/resdep014/265000-10-1.dcm ) set DoConvertInput = 1 ; set DoConvertInput = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 3 != 0 ) set flag = $argv[1] ; shift ; set flag = -s shift switch ( $flag ) switch ( -s ) if ( $#argv < 1 ) goto arg1err ; if ( 2 < 1 ) goto arg1err set subjid = $argv[1] ; shift ; set subjid = resdep214 shift set subjid = `basename $subjid` ; set subjid = `basename $subjid` basename resdep214 breaksw breaksw end end while ( $#argv != 0 ) while ( 1 != 0 ) set flag = $argv[1] ; shift ; set flag = -all shift switch ( $flag ) switch ( -all ) case "-autorecon-all": case -autorecon-all: set DoCreateBaseInput = 1 ; set DoCreateBaseInput = 1 set DoMotionCor = 1 ; set DoMotionCor = 1 set DoTalairach = 1 ; set DoTalairach = 1 set DoTalCheck = 1 ; set DoTalCheck = 1 set DoNuIntensityCor = 1 ; set DoNuIntensityCor = 1 set DoNormalization = 1 ; set DoNormalization = 1 set DoSkullStrip = 1 ; set DoSkullStrip = 1 set DoGCAReg = 1 ; set DoGCAReg = 1 set DoCARegInv = 1 ; set DoCARegInv = 1 set DoRemoveNeck = 1 ; set DoRemoveNeck = 1 set DoSkullLTA = 1 ; set DoSkullLTA = 1 set DoCANormalize = 1 ; set DoCANormalize = 1 set DoCAReg = 1 ; set DoCAReg = 1 set DoCALabel = 1 ; set DoCALabel = 1 set DoNormalization2 = 1 ; set DoNormalization2 = 1 set DoMaskBFS = 1 ; set DoMaskBFS = 1 set DoSegmentation = 1 ; set DoSegmentation = 1 set DoFill = 1 ; set DoFill = 1 set DoTessellate = 1 ; set DoTessellate = 1 set DoSmooth1 = 1 ; set DoSmooth1 = 1 set DoInflate1 = 1 ; set DoInflate1 = 1 set DoQSphere = 1 ; set DoQSphere = 1 set DoFix = 1 ; set DoFix = 1 set DoSmooth2 = 1 ; set DoSmooth2 = 1 set DoInflate2 = 1 ; set DoInflate2 = 1 set DoWhiteSurfs = 1 ; set DoWhiteSurfs = 1 set DoSphere = 1 ; set DoSphere = 1 set DoSurfReg = 1 ; set DoSurfReg = 1 set DoContraSurfReg = 0 ; set DoContraSurfReg = 0 set DoAvgCurv = 1 ; set DoAvgCurv = 1 set DoJacobianWhite = 1 ; set DoJacobianWhite = 1 set DoCortParc = 1 ; set DoCortParc = 1 set DoPialSurfs = 1 ; set DoPialSurfs = 1 set DoPctSurfCon = 1 ; set DoPctSurfCon = 1 set DoParcStats = 1 ; set DoParcStats = 1 set DoCortParc2 = 1 ; set DoCortParc2 = 1 set DoParcStats2 = 1 ; set DoParcStats2 = 1 set DoCortParc3 = 1 ; set DoCortParc3 = 1 set DoParcStats3 = 1 ; set DoParcStats3 = 1 set DoCortRibbonVolMask = 1 ; set DoCortRibbonVolMask = 1 set DoSegStats = 1 ; set DoSegStats = 1 set DoAParc2ASeg = 1 ; set DoAParc2ASeg = 1 set DoWMParc = 1 ; set DoWMParc = 1 set DoCurvStats = 1 ; set DoCurvStats = 1 set DoBaLabels = 1 ; set DoBaLabels = 1 set DoLabelExvivoEC = 1 ; set DoLabelExvivoEC = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( $DoT2pial && $DoFLAIRpial ) then if ( 0 && 0 ) then if ( $UseCuda || $GetCuda ) then if ( 0 || 0 ) then if ( ! $DoVersionsOnly ) then if ( ! 0 ) then if ( $#subjid != 1 ) then if ( 1 != 1 ) then if ( ! $?SUBJECTS_DIR ) then if ( ! 1 ) then if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /home/hurry01/w/projects/resdep/data/mri ) then pushd $SUBJECTS_DIR > /dev/null pushd /home/hurry01/w/projects/resdep/data/mri setenv SUBJECTS_DIR `$PWD` ; setenv SUBJECTS_DIR `$PWD` /bin/pwd popd > /dev/null popd set subjdir = $SUBJECTS_DIR/$subjid set subjdir = /home/hurry01/.gvfs/ebblvm$ on callunavm.psy.tufts.edu/projects/resdep/data/mri/resdep214 set: Variable name must contain alphanumeric characters.
_______________________________________________ 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.
