selxavg3-sess -s subj067_GROUP -a fc.lamgseed.surf.lh -debugset echo = 1 ;breakswbreaksw endendwhile ( $#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 ) thenif ( 1 == 0 ) then if ( $#SearchPathList == 0 ) thenif ( 0 == 0 ) thenset SearchPathList = "." ;set SearchPathList = .endifendif goto check_params_return ;goto check_params_return
set UniqueList = ( ) ;set UniqueList = ( )foreach d ( $SearchPathList )foreach d ( . )if ( ! -e $d ) thenif ( ! -e . ) then set IsUnique = 1 ;set IsUnique = 1foreach u ( $UniqueList )foreach u ( )if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;if ( 1 ) set UniqueList = ( . )set UniqueList = ( . )endend set SearchPathList = ( $UniqueList ) ;set SearchPathList = ( . ) set errs = 0 ;set errs = 0
set SessPath = ( ) ;set SessPath = ( )foreach sess ( $SessList )foreach sess ( subj067_GROUP )set tmp = ( ) ;set tmp = ( )foreach d ( $SearchPathList )foreach d ( . )set stst = $d/$sessset stst = ./subj067_GROUPif ( -d $stst ) thenif ( -d ./subj067_GROUP ) thenif ( ! -r $stst ) thenif ( ! -r ./subj067_GROUP ) thenpushd $stst > /dev/null ;pushd ./subj067_GROUPset tmp = ( $tmp `$PWDCMD` ) ;set tmp = ( `$PWDCMD` )pwdpopd > /dev/null ;popdendifendifendendset nfound = ( $#tmp ) ;set nfound = ( 1 )if ( $nfound == 0 ) thenif ( 1 == 0 ) thenif ( $nfound > 1 ) thenif ( 1 > 1 ) thenset SessPath = ( $SessPath $tmp ) ;set SessPath = ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP )endend
set UniqueList = ( ) ;set UniqueList = ( )foreach s ( $SessPath )foreach s ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP )set IsUnique = 1 ;set IsUnique = 1foreach u ( $UniqueList )foreach u ( )if ( ! $IsUnique && ! $AllowRedundant ) thenif ( ! 1 && ! 0 ) then set UniqueList = ( $UniqueList $s ) ;set UniqueList = ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP )endifendifendend
echo $SessPathecho /Applications/freesurfer/subjects/fMRI/subj067_GROUP exit $errs ;exit 0set echo = 1 ;breakswbreaksw endendwhile ( $#argv != 0 )while ( 0 != 0 ) goto parse_args_return ;goto parse_args_return goto check_params ;goto check_params if ( $#SessList == 0 ) thenif ( 1 == 0 ) thenif ( $#analysis == 0 && $flacfile == 0 ) thenif ( 1 == 0 && == 0 ) thenif ( $#analysis != 0 ) thenif ( 1 != 0 ) thenif ( ! -d $analysis ) thenif ( ! -d fc.lamgseed.surf.lh ) thenif ( ! -e $analysis/analysis.info ) thenif ( ! -e fc.lamgseed.surf.lh/analysis.info ) thenendifendifif ( $#flacfile != 0 ) thenif ( 0 != 0 ) thenif ( $perrun && $jkrun ) thenif ( 0 && 0 ) then if ( $UseOctave ) thenif ( 0 ) then if ( $#DoneFile ) thenif ( 0 ) then goto check_params_return ;goto check_params_return set StudyDir = `pwd` ;set StudyDir = `pwd`pwd if ( $#analysis ) thenif ( 1 ) then set analysisname = $analysisset analysisname = fc.lamgseed.surf.lhset fsd = `getana -a $analysis -t fsd` ;set fsd = `getana -a $analysis -t fsd`getana -a fc.lamgseed.surf.lh -t fsdset PerSession = `getana -a $analysis -t IsPerSession`set PerSession = `getana -a $analysis -t IsPerSession`getana -a fc.lamgseed.surf.lh -t IsPerSessionset IsNative = `getana -a $analysis -t IsNative`set IsNative = `getana -a $analysis -t IsNative`getana -a fc.lamgseed.surf.lh -t IsNativeset IsSurface = `getana -a $analysis -t IsSurface`set IsSurface = `getana -a $analysis -t IsSurface`getana -a fc.lamgseed.surf.lh -t IsSurfaceif ( $IsSurface ) thenif ( 1 ) thenset subject = `getana -a $analysis -t subject`set subject = `getana -a $analysis -t subject`getana -a fc.lamgseed.surf.lh -t subjectset hemi = `getana -a $analysis -t hemi`set hemi = `getana -a $analysis -t hemi`getana -a fc.lamgseed.surf.lh -t hemiecho "Surface data $subject $hemi"echo Surface data fsaverage lhSurface data fsaverage lhendifendifset dt = `getana -a $analysis -t designtype`set dt = `getana -a $analysis -t designtype`getana -a fc.lamgseed.surf.lh -t designtypeif ( $dt == "abblocked" ) set RequireContrasts = 0 ;if ( notask == abblocked ) set RequireContrasts = 0if ( $dt == "retinotopy" ) set RequireContrasts = 0 ;if ( notask == retinotopy ) set RequireContrasts = 0set contrasts = `getana -a $analysis -t contrasts`set contrasts = `getana -a $analysis -t contrasts`getana -a fc.lamgseed.surf.lh -t contrastsif ( $#contrasts == 0 && $RequireContrasts ) thenif ( 1 == 0 && 1 ) thenendifendif
if ( $#LF == 0 ) thenif ( 0 == 0 ) thenif ( $nolog ) thenif ( 0 ) then if ( $#OutParent == 0 ) thenif ( 0 == 0 ) thenset logdir = `pwd`/log ;set logdir = `pwd`/logpwdelseelsemkdir -p $logdirmkdir -p /Applications/freesurfer/subjects/fMRI/logif ( ! -e $logdir ) thenif ( ! -e /Applications/freesurfer/subjects/fMRI/log ) then set LF = $logdir/selxavg3-sess-$fsd-$analysis-$DateStr.logset LF = /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logif ( -e $LF ) mv $LF $LF.oldif ( -e /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log ) mv /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log.oldendifendifendifendifendifendifecho "--------------------------------------------------------------"echo ----------------------------------------------------------------------------------------------------------------------------echo "selxavg3-sess logfile is $LF"echo selxavg3-sess logfile is /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logselxavg3-sess logfile is /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logecho "--------------------------------------------------------------"echo ---------------------------------------------------------------------------------------------------------------------------- echo "selxavg3-sess log file" | tee -a $LFtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logecho selxavg3-sess log fileselxavg3-sess log fileecho $0 | tee -a $LFtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logecho /Applications/freesurfer/fsfast/bin/selxavg3-sess/Applications/freesurfer/fsfast/bin/selxavg3-sessecho $inputargs | tee -a $LFtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logecho -s subj067_GROUP -a fc.lamgseed.surf.lh -debug-s subj067_GROUP -a fc.lamgseed.surf.lh -debugecho $VERSION | tee -a $LFtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logecho $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $id | tee -a $LFidtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.loguid=501(Stefano) gid=20(staff) groups=20(staff),402(com.apple.sharepoint.group.1),12(everyone),61(localaccounts),79(_appserverusr),80(admin),81(_appserveradm),98(_lpadmin),33(_appstore),100(_lpoperator),204(_developer),395(com.apple.access_ftp),398(com.apple.access_screensharing),399(com.apple.access_ssh)pwd | tee -a $LFpwdtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log/Applications/freesurfer/subjects/fMRIuname -a | tee -a $LFuname -atee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logDarwin iMac-di-Stefano.local 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64date | tee -a $LFdatetee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logTue May 16 17:51:18 CEST 2017 set StartTime = `date` ;set StartTime = `date`date if ( $SaveRes || $SaveResUnwhitened ) set MatlabSaveRes = 1 ;if ( 0 || 0 ) set MatlabSaveRes = 1
set funcstemspec = `getana -a $analysis -t funcstem-specified`set funcstemspec = `getana -a $analysis -t funcstem-specified`getana -a fc.lamgseed.surf.lh -t funcstem-specifiedif ( $funcstemspec ) set DoPreProc = 0 ;if ( 0 ) set DoPreProc = 0
if ( $DoPreProc ) thenif ( 1 ) thenforeach sess ( $SessList )foreach sess ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP )set sessbase = `basename $sess` ;set sessbase = `basename $sess`basename /Applications/freesurfer/subjects/fMRI/subj067_GROUPset sessdir = `dirname $sess` ;set sessdir = `dirname $sess`dirname /Applications/freesurfer/subjects/fMRI/subj067_GROUPset cmd = ( preproc-sess -s $sessbase -d $sessdir -a $analysis -nolog ) ;set cmd = ( preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog ) echo $cmd | tee -a $LFtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.logecho preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nologpreproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog$cmd | tee -a $LFpreproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nologtee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log--------------------------------------------------------------preproc-sess logfile is /dev/null--------------------------------------------------------------$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $Stefanosetenv FREESURFER_HOME /Applications/freesurfersetenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_provaDarwin iMac-di-Stefano.local 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64/Applications/freesurfer/subjects/fMRI/Applications/freesurfer/fsfast/bin/preproc-sess-s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nologTue May 16 17:51:20 CEST 2017instem f mc 1 f fmcpr stc 0 fmcprsm 0 mask 1 brainsubj067_GROUP Template -----------------------------mktemplate-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -fsd rest -nolog -update Session: /Applications/freesurfer/subjects/fMRI/subj067_GROUP ----------------Tue May 16 17:51:20 CEST 2017Detected input format at niisubj067_GROUP Update not needed Run: 001 ---------------- Tue May 16 17:51:20 CEST 2017 subj067_GROUP 001 Update not neededTue May 16 17:51:20 CEST 2017mktemplate-sess completed subj067_GROUP Registration -----------------------------register-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -fsd rest -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg--------------------------------------------------------------register-sess logfile is /dev/null--------------------------------------------------------------Tue May 16 17:51:21 CEST 2017 setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_provacd /Applications/freesurfer/subjects/fMRI/Applications/freesurfer/fsfast/bin/register-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -fsd rest -delete-dat -dof 6 -bold -per-run -nolog -update -init-coreg freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96cDarwin iMac-di-Stefano.local 16.5.0 Darwin Kernel Version 16.5.0: Fri Mar 3 16:52:33 PST 2017; root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64 Session: /Applications/freesurfer/subjects/fMRI/subj067_GROUP ----------------Tue May 16 17:51:21 CEST 2017/Applications/freesurfer/subjects/fMRI/subj067_GROUP Run: 001 ----------------Tue May 16 17:51:21 CEST 2017Update not neededTue May 16 17:51:21 CEST 2017register-sess completed subj067_GROUP Mask ------------------------mkbrainmask-sess -maskstem brain -fsd rest -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -per-run -nolog -update------------------------------------------------/Applications/freesurfer/subjects/fMRI/subj067_GROUP Tue May 16 17:51:21 CEST 2017subj067_GROUP Update not needed for session-level masksubj067_GROUP Update not needed for run 001 maskmeanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz nii nii.gz bhdr img w, then returns stem.fmt. See also stem2fmt, fname2stem The file needs to exist on disk. --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.datERROR: cannot find stem2fnameif ( $status ) exit 1 ;if ( 1 ) exit 1exit 1 Thanks
----Messaggio originale----
Da: "Douglas Greve" greve@nmr.mgh.harvard.edu
Data: 16-mag-2017 17.21
A: freesurfer@nmr.mgh.harvard.edu
Ogg: Re: [Freesurfer] selxavg3-sess error
not sure what is going on. Is the script stem2fname in your path? If so, run selxavg3-sess with -debug as the first option and send the terminal output
On 5/16/17 3:08 AM, stdp82@virgilio.it wrote:
Hi list, this error occurs during selxavg3-sess in FS-FAST fcMRI
meanval --i stem2fname stem Looks for stem.fmt where fmt is mgh mgz nii nii.gz bhdr img w, then returns stem.fmt. See also stem2fmt, fname2stem The file needs to exist on disk. --m 001/masks/brain.e3.nii.gz --o 001/global.meanval.dat --avgwf 001/global.waveform.dat ERROR: cannot find stem2fname
I have already run for this folder other seed. The error occurs only on it (amygdala).
Thanks
Stefano
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer