I thought this problem was fixed when you eliminated the multiple formats (?)
On 8/20/15 12:03 PM, Rodriguez-Thompson, Anais wrote: > Hi Doug, > > I sent a message a while back about a problem I was having running selxavg3 > (I've attached the thread below this email). Selxavg3 is looking for a file > that was not generated during preprocessing (fmcpr.sm5.nii.gz). > > The commands I was using were > preproc-sess -s (subject) -d $SUBJECTS_DIR -fsd bold -fwhm 5 -per-run > mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_072915 -TR 2 -paradigm > slopepar -event-related -fsd bold -runlistfile runlistfile -tpef > tpef_1.5mm.txt -native -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 > 1.25 -refeventdur 2 -fwhm 5 -per-run > > I sent you a couple of logs, but did not hear back about how I can generate > the fmcpr.sm5.nii file. In the meantime I haven't been able to run any first > level analyses on my subjects. Is there any update to this issue? > > Any insight into the problem would be greatly appreciated! > > Thanks, > Anais > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rodriguez-Thompson, > Anais [arodriguez-thomp...@mgh.harvard.edu] > Sent: Thursday, July 30, 2015 6:34 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] selxavg3-sess error > > Hi Doug, > > Attached is doug2.log. > > Thanks, > Anais > ________________________________________ > 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: Thursday, July 30, 2015 4:29 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] selxavg3-sess error > > ok, still not sure what is happening. Can you try > > preproc-sess -debug -s GDDA001 -d > /autofs/cluster/roffman/users/Stable5_PerRun -a > SIRP_LoadRegression_Stable5_072915 |& tee doug2.log > > and send me doug2.log > > > On 07/30/2015 12:54 PM, Rodriguez-Thompson, Anais wrote: >> Hi Doug, >> >> Below are the contents of doug.log: >> >> 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 ( GDDA001 ) >> set tmp = ( ) ; >> set tmp = ( ) >> foreach d ( $SearchPathList ) >> foreach d ( . ) >> set stst = $d/$sess >> set stst = ./GDDA001 >> if ( -d $stst ) then >> if ( -d ./GDDA001 ) then >> if ( ! -r $stst ) then >> if ( ! -r ./GDDA001 ) then >> pushd $stst > /dev/null ; >> pushd ./GDDA001 >> 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/roffman/users/Stable5_PerRun/GDDA001 ) >> end >> end >> >> >> set UniqueList = ( ) ; >> set UniqueList = ( ) >> foreach s ( $SessPath ) >> foreach s ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) >> 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/roffman/users/Stable5_PerRun/GDDA001 ) >> endif >> endif >> end >> end >> >> >> echo $SessPath >> echo /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 >> >> 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 SIRP_LoadRegression_Stable5_072915 ) then >> if ( ! -e $analysis/analysis.info ) then >> if ( ! -e SIRP_LoadRegression_Stable5_072915/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 >> >> 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 = SIRP_LoadRegression_Stable5_072915 >> set fsd = `getana -a $analysis -t fsd` ; >> set fsd = `getana -a $analysis -t fsd` >> getana -a SIRP_LoadRegression_Stable5_072915 -t fsd >> set PerSession = `getana -a $analysis -t IsPerSession` >> set PerSession = `getana -a $analysis -t IsPerSession` >> getana -a SIRP_LoadRegression_Stable5_072915 -t IsPerSession >> set IsNative = `getana -a $analysis -t IsNative` >> set IsNative = `getana -a $analysis -t IsNative` >> getana -a SIRP_LoadRegression_Stable5_072915 -t IsNative >> set IsSurface = `getana -a $analysis -t IsSurface` >> set IsSurface = `getana -a $analysis -t IsSurface` >> getana -a SIRP_LoadRegression_Stable5_072915 -t IsSurface >> if ( $IsSurface ) then >> if ( 0 ) then >> set dt = `getana -a $analysis -t designtype` >> set dt = `getana -a $analysis -t designtype` >> getana -a SIRP_LoadRegression_Stable5_072915 -t designtype >> if ( $dt == "abblocked" ) set RequireContrasts = 0 ; >> if ( event-related == abblocked ) set RequireContrasts = 0 >> if ( $dt == "retinotopy" ) set RequireContrasts = 0 ; >> if ( event-related == retinotopy ) set RequireContrasts = 0 >> set contrasts = `getana -a $analysis -t contrasts` >> set contrasts = `getana -a $analysis -t contrasts` >> getana -a SIRP_LoadRegression_Stable5_072915 -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 /autofs/cluster/roffman/users/Stable5_PerRun/log >> if ( ! -e $logdir ) then >> if ( ! -e /autofs/cluster/roffman/users/Stable5_PerRun/log ) then >> >> set LF = $logdir/selxavg3-sess-$fsd-$analysis-$DateStr.log >> set LF = >> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log >> if ( -e $LF ) mv $LF $LF.old >> if ( -e >> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log >> ) mv >> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log >> >> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log.old >> endif >> endif >> endif >> endif >> endif >> endif >> echo "--------------------------------------------------------------" >> echo -------------------------------------------------------------- >> -------------------------------------------------------------- >> echo "selxavg3-sess logfile is $LF" >> echo selxavg3-sess logfile is >> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log >> selxavg3-sess logfile is >> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log >> echo "--------------------------------------------------------------" >> echo -------------------------------------------------------------- >> -------------------------------------------------------------- >> >> echo "selxavg3-sess log file" >> $LF >> echo selxavg3-sess log file >> echo $0 >> $LF >> echo /usr/local/freesurfer/stable5_3_0/fsfast/bin/selxavg3-sess >> echo $inputargs >> $LF >> echo -s GDDA001 -a SIRP_LoadRegression_Stable5_072915 -debug >> echo $VERSION >> $LF >> echo $Id: selxavg3-sess,v 1.57.2.1 2011/12/09 20:06:47 greve Exp $ >> id >> $LF >> id >> pwd >> $LF >> pwd >> uname -a >> $LF >> uname -a >> date >> $LF >> date >> >> 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 SIRP_LoadRegression_Stable5_072915 -t funcstem-specified >> if ( $funcstemspec ) set DoPreProc = 0 ; >> if ( 0 ) set DoPreProc = 0 >> >> >> if ( $DoPreProc ) then >> if ( 1 ) then >> foreach sess ( $SessList ) >> foreach sess ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) >> set sessbase = `basename $sess` ; >> set sessbase = `basename $sess` >> basename /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 >> set sessdir = `dirname $sess` ; >> set sessdir = `dirname $sess` >> dirname /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 >> set cmd = ( preproc-sess -s $sessbase -d $sessdir -a $analysis -nolog ) ; >> set cmd = ( preproc-sess -s GDDA001 -d >> /autofs/cluster/roffman/users/Stable5_PerRun -a >> SIRP_LoadRegression_Stable5_072915 -nolog ) >> >> echo $cmd | tee -a $LF >> echo preproc-sess -s GDDA001 -d /autofs/cluster/roffman/users/Stable5_PerRun >> -a SIRP_LoadRegression_Stable5_072915 -nolog >> tee -a >> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log >> preproc-sess -s GDDA001 -d /autofs/cluster/roffman/users/Stable5_PerRun -a >> SIRP_LoadRegression_Stable5_072915 -nolog >> $cmd | tee -a $LF >> preproc-sess -s GDDA001 -d /autofs/cluster/roffman/users/Stable5_PerRun -a >> SIRP_LoadRegression_Stable5_072915 -nolog >> tee -a >> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log >> -------------------------------------------------------------- >> preproc-sess logfile is /dev/null >> -------------------------------------------------------------- >> $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ >> arodthom >> setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 >> setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun >> Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC >> 2014 x86_64 x86_64 x86_64 GNU/Linux >> /autofs/cluster/roffman/users/Stable5_PerRun >> /usr/local/freesurfer/stable5_3_0/fsfast/bin/preproc-sess >> -s GDDA001 -d /autofs/cluster/roffman/users/Stable5_PerRun -a >> SIRP_LoadRegression_Stable5_072915 -nolog >> Thu Jul 30 12:52:18 EDT 2015 >> instem f >> mc 1 f fmcpr >> stc 0 fmcpr >> sm 0 fmcpr >> mask 1 brain >> GDDA001 Template ----------------------------- >> mktemplate-sess -s GDDA001 -d /autofs/cluster/roffman/users/Stable5_PerRun >> -fsd bold -rlf runlistfile -nolog -update >> >> Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 >> ---------------- >> Thu Jul 30 12:52:18 EDT 2015 >> Detected input format at nii >> GDDA001 Update not needed >> Run: 016 ---------------- >> Thu Jul 30 12:52:18 EDT 2015 >> GDDA001 016 Update not needed >> Run: 017 ---------------- >> Thu Jul 30 12:52:18 EDT 2015 >> GDDA001 017 Update not needed >> Run: 018 ---------------- >> Thu Jul 30 12:52:18 EDT 2015 >> GDDA001 018 Update not needed >> Thu Jul 30 12:52:18 EDT 2015 >> mktemplate-sess completed >> GDDA001 Mask ------------------------ >> mkbrainmask-sess -maskstem brain -fsd bold -s GDDA001 -d >> /autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistfile -nolog -update >> ------------------------------------------------ >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 >> Thu Jul 30 12:52:18 EDT 2015 >> WARNING: multiple formats found for template >> USING: template.nii.gz >> GDDA001 Update not needed for session-level mask >> WARNING: multiple formats found for 016/template >> USING: 016/template.nii.gz >> GDDA001 Update not needed for run 016 mask >> GDDA001 Update not needed for run 016 meanval >> WARNING: multiple formats found for 017/template >> USING: 017/template.nii.gz >> GDDA001 Update not needed for run 017 mask >> GDDA001 Update not needed for run 017 meanval >> WARNING: multiple formats found for 018/template >> USING: 018/template.nii.gz >> GDDA001 Update not needed for run 018 mask >> GDDA001 Update not needed for run 018 meanval >> Thu Jul 30 12:52:19 EDT 2015 >> mkbrainmask-sess done >> GDDA001 Registration ----------------------------- >> register-sess -s GDDA001 -d /autofs/cluster/roffman/users/Stable5_PerRun >> -fsd bold -dof 6 -rlf runlistfile -per-run -nolog -update >> -------------------------------------------------------------- >> register-sess logfile is /dev/null >> -------------------------------------------------------------- >> Thu Jul 30 12:52:19 EDT 2015 >> >> setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun >> cd /autofs/cluster/roffman/users/Stable5_PerRun >> /usr/local/freesurfer/stable5_3_0/fsfast/bin/register-sess -s GDDA001 -d >> /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf >> runlistfile -per-run -nolog -update >> >> cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or >> directory >> Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC >> 2014 x86_64 x86_64 x86_64 GNU/Linux >> >> Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 >> ---------------- >> Thu Jul 30 12:52:19 EDT 2015 >> Run: 016 ---------------- >> Thu Jul 30 12:52:19 EDT 2015 >> WARNING: multiple formats found for bold/016/template >> USING: bold/016/template.nii.gz >> Update not needed >> Run: 017 ---------------- >> Thu Jul 30 12:52:19 EDT 2015 >> WARNING: multiple formats found for bold/017/template >> USING: bold/017/template.nii.gz >> Update not needed >> Run: 018 ---------------- >> Thu Jul 30 12:52:19 EDT 2015 >> WARNING: multiple formats found for bold/018/template >> USING: bold/018/template.nii.gz >> Update not needed >> Thu Jul 30 12:52:19 EDT 2015 >> register-sess completed >> GDDA001 MC ----------------------------- >> mc-sess -fstem f -fmcstem fmcpr -s GDDA001 -d >> /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistfile >> -per-run -nolog -update >> Logfile is /dev/null >> ------------------------------------------- >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 >> RunList: 016 017 018 >> WARNING: multiple formats found for 016/template >> USING: 016/template.nii.gz >> GDDA001 016 Update not needed >> WARNING: multiple formats found for 017/template >> USING: 017/template.nii.gz >> GDDA001 017 Update not needed >> WARNING: multiple formats found for 018/template >> USING: 018/template.nii.gz >> GDDA001 018 Update not needed >> >> >> Thu Jul 30 12:52:19 EDT 2015 >> mc-sess completed SUCCESSFULLY >> ---------------------------------------- >> Started at Thu Jul 30 12:52:18 EDT 2015 >> Ended at Thu Jul 30 12:52:19 EDT 2015 >> preproc-sess done >> if ( $status ) exit 1 ; >> if ( 0 ) exit 1 >> end >> end >> endif >> endif >> >> if ( $#MLF == 0 ) set MLF = /tmp/selxavg3-sess-$$.m >> if ( 0 == 0 ) set MLF = /tmp/selxavg3-sess-30587.m >> set MLF = /tmp/selxavg3-sess-30587.m >> rm -f $MLF >> rm -f /tmp/selxavg3-sess-30587.m >> echo "% `date` " >> $MLF >> echo % `date` >> date >> echo "% `pwd` " >> $MLF >> echo % `pwd` >> pwd >> echo "% $flacfile $analysis " >> $MLF >> echo % SIRP_LoadRegression_Stable5_072915 >> echo " " >> $MLF >> echo >> echo " " >> $MLF >> echo >> >> set okfile = /tmp/selxavg3-sess-$$.ok >> set okfile = /tmp/selxavg3-sess-30587.ok >> rm -f $okfile >> rm -f /tmp/selxavg3-sess-30587.ok >> >> set parname = `getana -a $analysis -t parname` >> set parname = `getana -a $analysis -t parname` >> getana -a SIRP_LoadRegression_Stable5_072915 -t parname >> set funcstem = `getana -a $analysis -t funcstem` >> set funcstem = `getana -a $analysis -t funcstem` >> getana -a SIRP_LoadRegression_Stable5_072915 -t funcstem >> set rlf = `getana -a $analysis -t runlistfile` >> set rlf = `getana -a $analysis -t runlistfile` >> getana -a SIRP_LoadRegression_Stable5_072915 -t runlistfile >> set ConList = `getana -a $analysis -t contrasts` >> set ConList = `getana -a $analysis -t contrasts` >> getana -a SIRP_LoadRegression_Stable5_072915 -t contrasts >> >> >> @ nthsess = 0 ; >> @ nthsess = 0 >> @ nprocs = 0 ; >> @ nprocs = 0 >> foreach sess ( $SessList ) >> foreach sess ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) >> @ nthsess = $nthsess + 1 ; >> @ nthsess = 0 + 1 >> set sessbase = `basename $sess` ; >> set sessbase = `basename $sess` >> basename /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 >> set sessdir = `dirname $sess` ; >> set sessdir = `dirname $sess` >> dirname /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 >> >> echo "-------------------------------------------" | & tee -a $LF >> echo ------------------------------------------- >> tee -a >> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log >> ------------------------------------------- >> echo "$sess " | & tee -a $LF >> echo /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 >> tee -a >> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 >> date | & tee -a $LF >> date >> tee -a >> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log >> Thu Jul 30 12:52:20 EDT 2015 >> >> if ( ! -d $sess ) then >> if ( ! -d /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) then >> >> set funcdir = $sess/$fsd >> set funcdir = /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold >> set anadir = $sess/$fsd/$analysisname >> set anadir = >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915 >> if ( $#OutParent == 0 ) then >> if ( 0 == 0 ) then >> set anadir = $sess/$fsd/$analysisname >> set anadir = >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915 >> else >> else >> echo anadir = $anadir | tee -a $LF >> echo anadir = >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915 >> tee -a >> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_072915-150730125217.log >> anadir = >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915 >> >> set DoGLMFit = 0 ; >> set DoGLMFit = 0 >> if ( $Overwrite || $perrun ) set DoGLMFit = 1 ; >> if ( 0 || 0 ) set DoGLMFit = 1 >> set beta = `stem2fname $anadir/beta` >> set beta = `stem2fname $anadir/beta` >> stem2fname >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/SIRP_LoadRegression_Stable5_072915/beta >> if ( $status ) set DoGLMFit = 1 ; >> if ( 0 ) set DoGLMFit = 1 >> if ( $DoGLMFit == 0 ) then >> if ( 0 == 0 ) then >> >> set deplist = ( $analysis/analysis.info ) ; >> set deplist = ( SIRP_LoadRegression_Stable5_072915/analysis.info ) >> set RunList = ( `getrunlist $sess/$fsd $rlf` ) ; >> set RunList = ( `getrunlist $sess/$fsd $rlf` ) >> getrunlist /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold >> runlistfile >> set funclist = ( ) >> set funclist = ( ) >> foreach Run ( $RunList ) >> foreach Run ( 016 017 018 ) >> set funcstempath = $sess/$fsd/$Run/$funcstem ; >> set funcstempath = >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/016/fmcpr.sm5 >> set func = `stem2fname $funcstempath` ; >> set func = `stem2fname $funcstempath` >> stem2fname >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/016/fmcpr.sm5 >> if ( $status ) then >> if ( 1 ) then >> echo "ERROR: cannot find $funcstempath" >> echo ERROR: cannot find >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/016/fmcpr.sm5 >> ERROR: cannot find >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001/bold/016/fmcpr.sm5 >> exit 1 ; >> exit 1 >> >> >> >> Thanks, >> Anais >> ________________________________________ >> 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: Thursday, July 30, 2015 12:19 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] selxavg3-sess error >> >> those look ok. Can you run your selxavg3-sess command with -debug and >> capture the output in a log file? Eg, >> >> selxavg3-sess -s sess -a SIRP_LoadRegression_Stable5_072915 -debug |& >> tee doug.log >> >> and send me doug.log >> >> >> >> On 07/30/2015 12:09 PM, Rodriguez-Thompson, Anais wrote: >>> My preproc-sess command is preproc-sess -s (subject) -d $SUBJECTS_DIR -fsd >>> bold -fwhm 5 -per-run >>> >>> My mkanalysis command is mkanalysis-sess -analysis >>> SIRP_LoadRegression_Stable5_072915 -TR 2 -paradigm slopepar -event-related >>> -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt -native -timewindow >>> 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 -fwhm 5 -per-run >>> >>> Thanks, >>> Anais >>> ________________________________________ >>> 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: Thursday, July 30, 2015 12:02 PM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] selxavg3-sess error >>> >>> What is your preproc-sess command and your mkanalysis-sess command? >>> >>> >>> On 07/30/2015 12:00 PM, Rodriguez-Thompson, Anais wrote: >>>> Hi Freesurfer experts, >>>> >>>> I'm having trouble running selxavg3-sess in 5.3 because it is looking for >>>> a file that does not exist (fmcpr.sm5.nii.gz). I read in another >>>> freesurfer mail thread that this issue can be fixed by preprocessing the >>>> subject. However, even after re-preprocessing my subjects at fwhm= 5, this >>>> file is still not generated. My subjects do have a fmcpr.nii.gz file. >>>> Should I remake my analysis with fwhm=0 so that it uses this file, or is >>>> there a way to generate fmcpr.sm5? >>>> >>>> Thanks for your help, >>>> Anais >>>> _______________________________________________ >>>> 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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