Hi Doug, I've attached the output from running fieldsign-sess. Thanks for all your help. Michelle
On Mon, Oct 3, 2011 at 12:59 PM, Douglas N Greve <[email protected]>wrote: > Michelle, before you do that, can you run the offending program with -debug > and send me the (copious) terminal output? Your anat should not have to be > re-run. > > doug > > Michelle Umali wrote: > >> Hi Bruce, >> Will this undo my wm and pial edits? >> >> Thanks. >> Michelle >> >> On Sat, Oct 1, 2011 at 3:37 PM, Bruce Fischl >> <[email protected]<mailto: >> [email protected].**harvard.edu <[email protected]>>> wrote: >> >> try running >> >> >> recon-all -s subject -make all >> >> and leave the -dontrun off. It should bring everything up to date >> >> Bruce >> >> >> >> On Sat, 1 Oct 2011, Michelle Umali wrote: >> >> Dear Freesurfers, >> I'm still getting a MRISripZeros() and MRIScopyMRI Surf/src >> mismatch error >> when running fieldsign-sess. You suggested that this problem >> was due to the >> surfaces being out of synch. When I ran recon-all -s subject >> -make all >> -dontrun, I saw that several steps had not run. The data >> looked alright and >> the number of vertices matched when I ran -vno-check. >> >> The mismatch error is still occurring, and I don't know how to >> proceed. >> >> Please suggest steps that I should take. >> >> Thanks. >> Michelle >> >> >> >> >> >> 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<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. >> >> >> ------------------------------**------------------------------** >> ------------ >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >
fieldsign-sess -a rtopy.self.lh -occip -s sj12 -debug set echo = 1 ; breaksw breaksw 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 ( 0 == 0 ) then set SearchPathList = "." ; set SearchPathList = . endif endif goto check_params_return ; goto check_params_return set UniqueList = ( ) ; set UniqueList = ( ) foreach d ( $SearchPathList ) foreach d ( . ) if ( ! -e $d ) then if ( ! -e . ) then set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ; if ( 1 ) set UniqueList = ( . ) set UniqueList = ( . ) end end set SearchPathList = ( $UniqueList ) ; set SearchPathList = ( . ) set errs = 0 ; set errs = 0 set SessPath = ( ) ; set SessPath = ( ) foreach sess ( $SessList ) foreach sess ( sj12 ) set tmp = ( ) ; set tmp = ( ) foreach d ( $SearchPathList ) foreach d ( . ) set stst = $d/$sess set stst = ./sj12 if ( -d $stst ) then if ( -d ./sj12 ) then if ( ! -r $stst ) then if ( ! -r ./sj12 ) then pushd $stst > /dev/null ; pushd ./sj12 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 = ( /usr/local/freesurfer/subjects/retinotopy/sj12 ) end end set UniqueList = ( ) ; set UniqueList = ( ) foreach s ( $SessPath ) foreach s ( /usr/local/freesurfer/subjects/retinotopy/sj12 ) 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 = ( /usr/local/freesurfer/subjects/retinotopy/sj12 ) endif endif end end echo $SessPath echo /usr/local/freesurfer/subjects/retinotopy/sj12 exit $errs ; exit 0 set echo = 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 ( $#analysis == 0 ) then if ( 1 == 0 ) then if ( $#patch == 0 && $UseSphere == 0 ) then if ( 1 == 0 && 0 == 0 ) then if ( $#patch && $UseSphere ) then if ( 1 && 0 ) then set IsRet = `getana -a $analysis -t IsRetinotopy` set IsRet = `getana -a $analysis -t IsRetinotopy` getana -a rtopy.self.lh -t IsRetinotopy if ( ! $IsRet ) then if ( ! 1 ) then set IsMNI305Ana = `getana -a $analysis -t IsMNI305` set IsMNI305Ana = `getana -a $analysis -t IsMNI305` getana -a rtopy.self.lh -t IsMNI305 if ( $IsMNI305Ana ) then if ( 0 ) then set IsSurfAna = `getana -a $analysis -t IsSurface` set IsSurfAna = `getana -a $analysis -t IsSurface` getana -a rtopy.self.lh -t IsSurface if ( $IsSurfAna ) then if ( 1 ) then set anasubject = `getana -a $analysis -t subject` set anasubject = `getana -a $analysis -t subject` getana -a rtopy.self.lh -t subject set hemilist = `getana -a $analysis -t hemi` set hemilist = `getana -a $analysis -t hemi` getana -a rtopy.self.lh -t hemi endif endif set IsNativeAna = `getana -a $analysis -t IsNative` set IsNativeAna = `getana -a $analysis -t IsNative` getana -a rtopy.self.lh -t IsNative if ( $IsNativeAna ) then if ( 0 ) then if ( $#regfile == 0 ) set regfile = register.dof$RegDOF.dat if ( 0 == 0 ) set regfile = register.dof6.dat set regfile = register.dof6.dat set fsd = `getana -a $analysis -t fsd` ; set fsd = `getana -a $analysis -t fsd` getana -a rtopy.self.lh -t fsd if ( ! $UseLog ) set LF = /dev/null if ( ! 1 ) set LF = /dev/null goto check_params_return ; goto check_params_return foreach sess ( $SessList ) foreach sess ( /usr/local/freesurfer/subjects/retinotopy/sj12 ) set sessid = `basename $sess` ; set sessid = `basename $sess` basename /usr/local/freesurfer/subjects/retinotopy/sj12 if ( $UseLog ) then if ( 1 ) then mkdir -p $sess/log mkdir -p /usr/local/freesurfer/subjects/retinotopy/sj12/log set LF = $sess/log/fieldsign-sess.log set LF = /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log if ( -e $LF ) mv $LF $LF.old if ( -e /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log ) mv /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log.old mv /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log.old echo $LF echo /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log echo "fieldsign-sess log file" >> $LF echo fieldsign-sess log file echo $VERSION >> $LF echo $Id: fieldsign-sess,v 1.2 2010/05/04 22:00:18 greve Exp $ date >> $LF date uname -a >> $LF uname -a pwd >> $LF pwd echo $0 >> $LF echo /usr/local/freesurfer/fsfast/bin/fieldsign-sess echo $inputargs >> $LF echo -a rtopy.self.lh -occip -s sj12 -debug id >> $LF id endif endif set srcsubject = `cat $sess/subjectname` set srcsubject = `cat $sess/subjectname` cat /usr/local/freesurfer/subjects/retinotopy/sj12/subjectname set sd = $SUBJECTS_DIR/$srcsubject set sd = /usr/local/freesurfer/subjects/ld12 if ( ! -e $sd ) then if ( ! -e /usr/local/freesurfer/subjects/ld12 ) then set anadir = $sess/$fsd/$analysis set anadir = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh if ( ! -e $anadir ) then if ( ! -e /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh ) then set eccenreal = `stem2fname $anadir/eccen/real` ; set eccenreal = `stem2fname $anadir/eccen/real` stem2fname /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real set eccenimag = `stem2fname $anadir/eccen/imag` ; set eccenimag = `stem2fname $anadir/eccen/imag` stem2fname /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag set polarreal = `stem2fname $anadir/polar/real` ; set polarreal = `stem2fname $anadir/polar/real` stem2fname /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real set polarimag = `stem2fname $anadir/polar/imag` ; set polarimag = `stem2fname $anadir/polar/imag` stem2fname /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag if ( $IsNativeAna ) then if ( 0 ) then if ( $IsSurfAna ) then if ( 1 ) then if ( $anasubject == self ) set trgsubject = $srcsubject ; if ( self == self ) set trgsubject = ld12 set trgsubject = ld12 if ( $anasubject != self ) set trgsubject = $anasubject ; if ( self != self ) set trgsubject = self endif endif set outdir = $anadir/fieldsign set outdir = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign mkdir -p $outdir mkdir -p /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign foreach hemi ( $hemilist ) foreach hemi ( lh ) if ( $IsNativeAna ) then if ( 0 ) then if ( $IsNativeAna ) then if ( 0 ) then set fieldsign = $outdir/fieldsign.nii set fieldsign = /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii endif endif set cmd = ( mri_fieldsign --s $trgsubject --hemi $hemi --old --eccen $eccenreal $eccenimag --polar $polarreal $polarimag --fs $fieldsign ) set cmd = ( mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii ) if ( $#fwhm ) set cmd = ( $cmd --fwhm $fwhm ) ; if ( 0 ) set cmd = ( mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --fwhm ) if ( $#patch ) set cmd = ( $cmd --patch occip.patch.flat ) if ( 1 ) set cmd = ( mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat ) set cmd = ( mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat ) if ( $UseSphere ) set cmd = ( $cmd --sphere ) ; if ( 0 ) set cmd = ( mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat --sphere ) if ( $DoReverse ) set cmd = ( $cmd --rev ) ; if ( 0 ) set cmd = ( mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat --rev ) echo $cmd | tee -a $LF echo mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat tee -a /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat $cmd mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat $Id: mri_fieldsign.c,v 1.14 2011/03/02 00:04:15 nicks Exp $ cwd /usr/local/freesurfer/subjects/retinotopy cmdline mri_fieldsign --s ld12 --hemi lh --old --eccen /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii --polar /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii --fs /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii --patch occip.patch.flat sysname Linux hostname BOTANICA machine x86_64 user michelle eccen real /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/real.nii eccen imag /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/eccen/imag.nii polar real /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/real.nii polar imag /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/polar/imag.nii patch occip.patch.flat subject ld12 hemi lh fwhm -1.000000 nsmooth -1 fieldsign /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh/fieldsign/fieldsign.nii usenew 0 Reading /usr/local/freesurfer/subjects/ld12/surf/lh.sphere Reading /usr/local/freesurfer/subjects/ld12/surf/lh.occip.patch.flat Reading /usr/local/freesurfer/subjects/ld12/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Complex Ripping Zeros ERROR: MRISripZeros(): dimension mismatch ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. ERROR: MRIScopyMRI: Surf/Src dimension mismatch. Rot (rad): 0 0 surfer: compute_fieldsign() mri_fieldsign done end end end end echo "-------------------" | tee -a $LF echo ------------------- tee -a /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log ------------------- date | tee -a $LF date tee -a /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log Mon Oct 3 13:02:58 EDT 2011 echo "mkfieldsign-sess completed" | tee -a $LF echo mkfieldsign-sess completed tee -a /usr/local/freesurfer/subjects/retinotopy/sj12/log/fieldsign-sess.log mkfieldsign-sess completed echo " " echo exit 0 ; exit 0
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