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 >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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 >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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. 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 . 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.
