R: Re: R: Re: selxavg3-sess error - Freesurfer

16 May 2017


      Yes, the file exists.Additionally, please take in account that I have run other FC analysis on this subj using other seed as ROI.
----Messaggio originale----
Da: "Douglas Greve" greve@nmr.mgh.harvard.edu
Data: 16-mag-2017 18.21
A: freesurfer@nmr.mgh.harvard.edu
Ogg: Re: [Freesurfer] R: Re: selxavg3-sess error
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 &amp;&amp; ! $AllowRedundant ) then
      if ( ! 1 &amp;&amp; ! 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 &amp;&amp; $flacfile == 0 ) then
      if ( 1 == 0 &amp;&amp; == 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 &amp;&amp; $jkrun ) then
      if ( 0 &amp;&amp; 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 &amp;&amp; $RequireContrasts ) then
      if ( 1 == 0 &amp;&amp; 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
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