Does this file exist ? /Applications/freesurfer/subjects/fMRI/subj067_GROUP/001/masks/brain.e3.nii.gz
You can try deleting the /Applications/freesurfer/subjects/fMRI/subj067_GROUP/001/masks folder and re-running.
On 5/16/17 11:53 AM, stdp82@virgilio.it wrote:
selxavg3-sess -s subj067_GROUP -a fc.lamgseed.surf.lh -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 ( subj067_GROUP ) set tmp = ( ) ; set tmp = ( ) foreach d ( $SearchPathList ) foreach d ( . ) set stst = $d/$sess set stst = ./subj067_GROUP if ( -d $stst ) then if ( -d ./subj067_GROUP ) then if ( ! -r $stst ) then if ( ! -r ./subj067_GROUP ) then pushd $stst > /dev/null ; pushd ./subj067_GROUP 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 = ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP ) end end
set UniqueList = ( ) ; set UniqueList = ( ) foreach s ( $SessPath ) foreach s ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP ) 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 = ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP ) endif endif end end
echo $SessPath echo /Applications/freesurfer/subjects/fMRI/subj067_GROUP
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 ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#analysis == 0 && $flacfile == 0 ) then if ( 1 == 0 && == 0 ) then if ( $#analysis != 0 ) then if ( 1 != 0 ) then if ( ! -d $analysis ) then if ( ! -d fc.lamgseed.surf.lh ) then if ( ! -e $analysis/analysis.info ) then if ( ! -e fc.lamgseed.surf.lh/analysis.info ) then endif endif if ( $#flacfile != 0 ) then if ( 0 != 0 ) then if ( $perrun && $jkrun ) then if ( 0 && 0 ) then
if ( $UseOctave ) then if ( 0 ) then
if ( $#DoneFile ) then if ( 0 ) then
goto check_params_return ; goto check_params_return
set StudyDir = `pwd` ; set StudyDir = `pwd` pwd
if ( $#analysis ) then if ( 1 ) then
set analysisname = $analysis set analysisname = fc.lamgseed.surf.lh set fsd = `getana -a $analysis -t fsd` ; set fsd = `getana -a $analysis -t fsd` getana -a fc.lamgseed.surf.lh -t fsd set PerSession = `getana -a $analysis -t IsPerSession` set PerSession = `getana -a $analysis -t IsPerSession` getana -a fc.lamgseed.surf.lh -t IsPerSession set IsNative = `getana -a $analysis -t IsNative` set IsNative = `getana -a $analysis -t IsNative` getana -a fc.lamgseed.surf.lh -t IsNative set IsSurface = `getana -a $analysis -t IsSurface` set IsSurface = `getana -a $analysis -t IsSurface` getana -a fc.lamgseed.surf.lh -t IsSurface if ( $IsSurface ) then if ( 1 ) then set subject = `getana -a $analysis -t subject` set subject = `getana -a $analysis -t subject` getana -a fc.lamgseed.surf.lh -t subject set hemi = `getana -a $analysis -t hemi` set hemi = `getana -a $analysis -t hemi` getana -a fc.lamgseed.surf.lh -t hemi echo "Surface data $subject $hemi" echo Surface data fsaverage lh Surface data fsaverage lh endif endif set dt = `getana -a $analysis -t designtype` set dt = `getana -a $analysis -t designtype` getana -a fc.lamgseed.surf.lh -t designtype if ( $dt == "abblocked" ) set RequireContrasts = 0 ; if ( notask == abblocked ) set RequireContrasts = 0 if ( $dt == "retinotopy" ) set RequireContrasts = 0 ; if ( notask == retinotopy ) set RequireContrasts = 0 set contrasts = `getana -a $analysis -t contrasts` set contrasts = `getana -a $analysis -t contrasts` getana -a fc.lamgseed.surf.lh -t contrasts if ( $#contrasts == 0 && $RequireContrasts ) then if ( 1 == 0 && 1 ) then endif endif
if ( $#LF == 0 ) then if ( 0 == 0 ) then if ( $nolog ) then if ( 0 ) then
if ( $#OutParent == 0 ) then if ( 0 == 0 ) then set logdir = `pwd`/log ; set logdir = `pwd`/log pwd else else mkdir -p $logdir mkdir -p /Applications/freesurfer/subjects/fMRI/log if ( ! -e $logdir ) then if ( ! -e /Applications/freesurfer/subjects/fMRI/log ) then
set LF = $logdir/selxavg3-sess-$fsd-$analysis-$DateStr.log set LF = /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log if ( -e $LF ) mv $LF $LF.old if ( -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.old endif endif endif endif endif endif echo "--------------------------------------------------------------" 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.log selxavg3-sess logfile is /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo "--------------------------------------------------------------" echo --------------------------------------------------------------
echo "selxavg3-sess log file" | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo selxavg3-sess log file selxavg3-sess log file echo $0 | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo /Applications/freesurfer/fsfast/bin/selxavg3-sess /Applications/freesurfer/fsfast/bin/selxavg3-sess echo $inputargs | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo -s subj067_GROUP -a fc.lamgseed.surf.lh -debug -s subj067_GROUP -a fc.lamgseed.surf.lh -debug echo $VERSION | tee -a $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo $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 $LF id tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log uid=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 $LF pwd tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log /Applications/freesurfer/subjects/fMRI uname -a | tee -a $LF uname -a tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log Darwin 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 date | tee -a $LF date tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log Tue 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-specified if ( $funcstemspec ) set DoPreProc = 0 ; if ( 0 ) set DoPreProc = 0
if ( $DoPreProc ) then if ( 1 ) then foreach sess ( $SessList ) foreach sess ( /Applications/freesurfer/subjects/fMRI/subj067_GROUP ) set sessbase = `basename $sess` ; set sessbase = `basename $sess` basename /Applications/freesurfer/subjects/fMRI/subj067_GROUP set sessdir = `dirname $sess` ; set sessdir = `dirname $sess` dirname /Applications/freesurfer/subjects/fMRI/subj067_GROUP set 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 $LF tee -a /Applications/freesurfer/subjects/fMRI/log/selxavg3-sess-rest-fc.lamgseed.surf.lh-170516175117.log echo preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog $cmd | tee -a $LF preproc-sess -s subj067_GROUP -d /Applications/freesurfer/subjects/fMRI -a fc.lamgseed.surf.lh -nolog tee -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 $ Stefano setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova Darwin 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 -nolog Tue May 16 17:51:20 CEST 2017 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain subj067_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 2017 Detected input format at nii subj067_GROUP Update not needed Run: 001 ---------------- Tue May 16 17:51:20 CEST 2017 subj067_GROUP 001 Update not needed Tue May 16 17:51:20 CEST 2017 mktemplate-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_prova cd /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-v6.0.0-2beb96c Darwin 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 2017 Update not needed Tue May 16 17:51:21 CEST 2017 register-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 2017 subj067_GROUP Update not needed for session-level mask subj067_GROUP Update not needed for run 001 mask 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 if ( $status ) exit 1 ; if ( 1 ) exit 1 exit 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer