Attached. I took a quick look and it seems that I wrote the subject name 3 times, on new lines, to the subjectname file. I removed 2 of them and re-ran selxavg3-sess and it appears to be working.
Thanks for the help Doug. Matt ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2016 5:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error Can you run the command below and send me dng.log? register-sess -debug -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 -per-run -nolog -update |& tee dng.log On 07/14/2016 02:51 PM, Hibert, Matthew Louis wrote: > Hi All, > I'm running into an error analyzing some fMRI data with FS-FAST in > Freesurfer version 5.3. The analysis runs fine until it gets to the > register-sess part, which quits before actually starting to do any > registration. The last line of the log file, attached, is "if: > Expression syntax", but there are no other errors prior to that. The > command I'm using, analysis, and contrasts have all worked on several > other similar data sets. Has anyone encountered this problem before, > or know what's causing it? > > Thanks, > Matt > > Clinical Research Coordinator > Stufflebeam Lab > Athinoula A. Martinos Center > Massachusetts General Hospital > 149 13th Street, Room 1115S > Charlestown, MA 02129 > > > _______________________________________________ > 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
set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 11 != 0 ) set flag = $argv[1] ; shift ; set flag = -s shift switch ( $flag ) switch ( -s ) case "-sf": case -sf: case "-df": case -df: case "-d": case -d: case "-g": case -g: shift ; shift breaksw breaksw end end while ( $#argv != 0 ) while ( 9 != 0 ) set flag = $argv[1] ; shift ; set flag = -d shift switch ( $flag ) switch ( -d ) case "-g": case -g: shift ; shift breaksw breaksw end end while ( $#argv != 0 ) while ( 7 != 0 ) set flag = $argv[1] ; shift ; set flag = -fsd shift switch ( $flag ) switch ( -fsd ) if ( $#argv < 1 ) goto arg1err ; if ( 6 < 1 ) goto arg1err set fsd = $argv[1] ; shift ; set fsd = sycabs shift breaksw breaksw end end while ( $#argv != 0 ) while ( 5 != 0 ) set flag = $argv[1] ; shift ; set flag = -dof shift switch ( $flag ) switch ( -dof ) if ( $#argv < 1 ) goto arg1err ; if ( 4 < 1 ) goto arg1err set dof = $argv[1] ; shift ; set dof = 6 shift breaksw breaksw end end while ( $#argv != 0 ) while ( 3 != 0 ) set flag = $argv[1] ; shift ; set flag = -per-run shift switch ( $flag ) switch ( -per-run ) case "-perrun": case -perrun: set PerRun = 1 ; set PerRun = 1 set PerSess = 0 ; set PerSess = 0 breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 ) set flag = $argv[1] ; shift ; set flag = -nolog shift switch ( $flag ) switch ( -nolog ) set nolog = 1 ; set nolog = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 1 != 0 ) set flag = $argv[1] ; shift ; set flag = -update shift switch ( $flag ) switch ( -update ) set UpdateOnly = 1 ; set UpdateOnly = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return set SessList = `getsesspath $inputargs` ; set SessList = `getsesspath $inputargs` getsesspath -debug -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 -per-run -nolog -update set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 11 != 0 ) set flag = $argv[1] ; shift ; set flag = -s shift switch ( $flag ) switch ( -s ) if ( $#argv == 0 ) goto arg1err ; if ( 10 == 0 ) goto arg1err set SessList = ( $SessList $argv[1] ) ; shift ; set SessList = ( nmr00978 ) shift breaksw breaksw end end while ( $#argv != 0 ) while ( 9 != 0 ) set flag = $argv[1] ; shift ; set flag = -d shift switch ( $flag ) switch ( -d ) if ( $#argv == 0 ) goto arg1err ; if ( 8 == 0 ) goto arg1err if ( ! -d $argv[1] ) then if ( ! -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ) then if ( ! -r $argv[1] ) then if ( ! -r /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ) then set srchdir = $argv[1] ; shift ; set srchdir = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects shift set SearchPathList = ( $SearchPathList $srchdir ) ; set SearchPathList = ( /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ) breaksw breaksw end end while ( $#argv != 0 ) while ( 7 != 0 ) set flag = $argv[1] ; shift ; set flag = -fsd shift switch ( $flag ) switch ( -fsd ) end end while ( $#argv != 0 ) while ( 6 != 0 ) set flag = $argv[1] ; shift ; set flag = sycabs shift switch ( $flag ) switch ( sycabs ) end end while ( $#argv != 0 ) while ( 5 != 0 ) set flag = $argv[1] ; shift ; set flag = -dof shift switch ( $flag ) switch ( -dof ) end end while ( $#argv != 0 ) while ( 4 != 0 ) set flag = $argv[1] ; shift ; set flag = 6 shift switch ( $flag ) switch ( 6 ) end end while ( $#argv != 0 ) while ( 3 != 0 ) set flag = $argv[1] ; shift ; set flag = -per-run shift switch ( $flag ) switch ( -per-run ) end end while ( $#argv != 0 ) while ( 2 != 0 ) set flag = $argv[1] ; shift ; set flag = -nolog shift switch ( $flag ) switch ( -nolog ) end end while ( $#argv != 0 ) while ( 1 != 0 ) set flag = $argv[1] ; shift ; set flag = -update shift switch ( $flag ) switch ( -update ) end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return foreach grp ( $grpdefs ) foreach grp ( ) goto check_params ; goto check_params if ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#SearchPathList == 0 ) then if ( 1 == 0 ) then goto check_params_return ; goto check_params_return set UniqueList = ( ) ; set UniqueList = ( ) foreach d ( $SearchPathList ) foreach d ( /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ) if ( ! -e $d ) then if ( ! -e /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ) then set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ; if ( 1 ) set UniqueList = ( /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ) set UniqueList = ( /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ) end end set SearchPathList = ( $UniqueList ) ; set SearchPathList = ( /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ) set errs = 0 ; set errs = 0 set SessPath = ( ) ; set SessPath = ( ) foreach sess ( $SessList ) foreach sess ( nmr00978 ) set tmp = ( ) ; set tmp = ( ) foreach d ( $SearchPathList ) foreach d ( /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ) set stst = $d/$sess set stst = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 if ( -d $stst ) then if ( -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 ) then if ( ! -r $stst ) then if ( ! -r /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 ) then pushd $stst > /dev/null ; pushd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 set tmp = ( $tmp `$PWDCMD` ) ; set tmp = ( `$PWDCMD` ) pwd popd > /dev/null ; popd endif endif end end set nfound = ( $#tmp ) ; set nfound = ( 1 ) if ( $nfound == 0 ) then if ( 1 == 0 ) then if ( $nfound > 1 ) then if ( 1 > 1 ) then set SessPath = ( $SessPath $tmp ) ; set SessPath = ( /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 ) end end set UniqueList = ( ) ; set UniqueList = ( ) foreach s ( $SessPath ) foreach s ( /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 ) set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( ! $IsUnique && ! $AllowRedundant ) then if ( ! 1 && ! 0 ) then set UniqueList = ( $UniqueList $s ) ; set UniqueList = ( /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 ) endif endif end end echo $SessPath echo /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 exit $errs ; exit 0 if ( $status || $#SessList == 0 ) then if ( 0 || 1 == 0 ) then goto check_params ; goto check_params if ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#FSLXOpts && $regmethod != fslregister ) then if ( 0 && bbregister != fslregister ) then if ( $#SPMXOpts && $regmethod != spmregister ) then if ( 0 && bbregister != spmregister ) then if ( $#BBRXOpts && $regmethod != bbregister ) then if ( 0 && bbregister != bbregister ) then if ( $DoPBSub && $regmethod == spmregister ) then if ( 0 && bbregister == spmregister ) then if ( $DoBackground && $DoPBSub ) then if ( 0 && 0 ) then if ( $PerRun == 0 && $PerSess == 0 ) then if ( 1 == 0 && 0 == 0 ) then if ( $#regfilename == 0 ) then if ( 0 == 0 ) then if ( ! $UseB0DC ) set regfilename = register.dof$RegDOF.dat if ( ! 0 ) set regfilename = register.dof6.dat set regfilename = register.dof6.dat if ( $UseB0DC ) set regfilename = register.dof$RegDOF.b0dc.dat if ( 0 ) set regfilename = register.dof6.b0dc.dat endif endif goto check_params_return ; goto check_params_return if ( $#LF == 0 ) then if ( 0 == 0 ) then if ( ! $nolog ) then if ( ! 1 ) then set LF = /dev/null set LF = /dev/null endif endif endif endif echo "--------------------------------------------------------------" echo -------------------------------------------------------------- -------------------------------------------------------------- echo "register-sess logfile is $LF" echo register-sess logfile is /dev/null register-sess logfile is /dev/null echo "--------------------------------------------------------------" echo -------------------------------------------------------------- -------------------------------------------------------------- echo "register-sess log file" >> $LF echo register-sess log file echo $VERSION >> $LF echo $Id: register-sess,v 1.13 2011/03/11 20:17:31 greve Exp $ date | tee -a $LF date tee -a /dev/null Mon Jul 18 17:27:43 EDT 2016 echo "" | tee -a $LF echo tee -a /dev/null echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF echo setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/tsc_pilot/subjects/ tee -a /dev/null setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/tsc_pilot/subjects/ echo "cd `pwd`" | tee -a $LF echo cd `pwd` tee -a /dev/null pwd cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast echo $0 $inputargs | tee -a $LF echo /usr/local/freesurfer/stable5_3_0/fsfast/bin/register-sess -debug -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 -per-run -nolog -update tee -a /dev/null /usr/local/freesurfer/stable5_3_0/fsfast/bin/register-sess -debug -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 -per-run -nolog -update echo "" | tee -a $LF echo tee -a /dev/null cat $FREESURFER_HOME/build-stamp.txt | tee -a $LF cat /usr/local/freesurfer/stable5_3_0/build-stamp.txt tee -a /dev/null cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or directory uname -a | tee -a $LF uname -a tee -a /dev/null Linux marcie 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux foreach sess ( $SessList ) foreach sess ( /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 ) set sessbase = `basename $sess` set sessbase = `basename $sess` basename /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 set sessdir = `dirname $sess` set sessdir = `dirname $sess` dirname /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 echo " " | & tee -a $LF echo tee -a /dev/null echo "Session: $sess ----------------" | & tee -a $LF echo Session: /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 ---------------- tee -a /dev/null Session: /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 ---------------- date | & tee -a $LF date tee -a /dev/null Mon Jul 18 17:27:43 EDT 2016 if ( ! -e $sess/subjectname ) then if ( ! -e /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/subjectname ) then set subject = `cat $sess/subjectname` ; set subject = `cat $sess/subjectname` cat /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/subjectname if ( $#subject == 0 ) then if ( 3 == 0 ) then if ( ! -e $SUBJECTS_DIR/$subject ) then if ( ! -e /cluster/neuromind/dwakeman/tsc_pilot/subjects//nmr00978 nmr00978 nmr00978 ) then if: Expression Syntax.
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