Hi Doug, Below this email is the email thread. I was wondering whether I could rename the preproc-sess output volume (fmcpr.nii.gz) to fmcpr.sm5.nii.gz in order to run the command. Given preproc-sess at -fwhm 5, this volume should be smoothed at 5 and should be the input for analysis, correct?
Thanks, Anais From: [email protected] [[email protected]] on behalf of Rodriguez-Thompson, Anais [[email protected]] 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: [email protected] [[email protected]] on behalf of Douglas N Greve [[email protected]] Sent: Thursday, July 30, 2015 4:29 PM To: [email protected] 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: [email protected] > [[email protected]] on behalf of Douglas N Greve > [[email protected]] > Sent: Thursday, July 30, 2015 12:19 PM > To: [email protected] > 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: [email protected] >> [[email protected]] on behalf of Douglas N Greve >> [[email protected]] >> Sent: Thursday, July 30, 2015 12:02 PM >> To: [email protected] >> 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 ________________________________________ From: [email protected] [[email protected]] on behalf of Douglas N Greve [[email protected]] Sent: Tuesday, August 04, 2015 3:22 PM To: [email protected] Subject: Re: [Freesurfer] Dimension mismatch between mask and run sorry, I don't remember what that thread is. Can you repost with the thread in the email? On 08/04/2015 03:20 PM, Rodriguez-Thompson, Anais wrote: > Hi Doug, > > I deleted all of the template.nii files, and now the command works. Thank you > for your advice! > > In regards to my other thread (selxavg3-sess error), where selxavg3 looks for > a file that doesn't exist (fmcpr.sm5.nii.gz), could I rename the preproc-sess > output volume (fmcpr.nii.gz) to fmcpr.sm5.nii.gz in order to run the command? > Given preproc-sess at -fwhm 5, this volume should be smoothed at 5 and should > be the input for analysis, correct? > > Thanks, > Anais > ________________________________________ > From: [email protected] > [[email protected]] on behalf of Douglas N Greve > [[email protected]] > Sent: Tuesday, August 04, 2015 3:08 PM > To: [email protected] > Subject: Re: [Freesurfer] Dimension mismatch between mask and run > > There is still a warning about "multiple formats". This means you have > not deleted all the offending files. > > On 08/04/2015 12:19 PM, Rodriguez-Thompson, Anais wrote: >> Hi Doug, >> >> Thanks for getting back to me. I tried deleting those files, and got the >> same error, although the terminal output looked slightly different towards >> the end (in terms of the compensation values). >> >> Here it is below: >> -------------------------------------------------------------- >> selxavg3-sess logfile is >> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_050514-150804121216.log >> -------------------------------------------------------------- >> preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a >> SIRP_LoadRegression_Stable5_050514 -nolog >> -------------------------------------------------------------- >> 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 GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a >> SIRP_LoadRegression_Stable5_050514 -nolog >> Tue Aug 4 12:12:17 EDT 2015 >> instem f >> mc 1 f fmcpr >> stc 0 fmcpr >> sm 0 fmcpr >> mask 1 brain >> GDDA098 Template ----------------------------- >> mktemplate-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun >> -fsd bold -rlf runlistfile -nolog -update >> >> Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 >> ---------------- >> Tue Aug 4 12:12:17 EDT 2015 >> Detected input format at nii >> GDDA098 Update not needed >> Run: 015 ---------------- >> Tue Aug 4 12:12:17 EDT 2015 >> GDDA098 015 Update not needed >> Run: 016 ---------------- >> Tue Aug 4 12:12:17 EDT 2015 >> GDDA098 016 Update not needed >> Run: 017 ---------------- >> Tue Aug 4 12:12:17 EDT 2015 >> GDDA098 017 Update not needed >> Tue Aug 4 12:12:17 EDT 2015 >> mktemplate-sess completed >> GDDA098 Mask ------------------------ >> mkbrainmask-sess -maskstem brain -fsd bold -s GDDA098 -d >> /autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistfile -nolog -update >> ------------------------------------------------ >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 >> Tue Aug 4 12:12:17 EDT 2015 >> WARNING: multiple formats found for template >> USING: template.nii.gz >> GDDA098 Update not needed for session-level mask >> WARNING: multiple formats found for 015/template >> USING: 015/template.nii.gz >> GDDA098 Update not needed for run 015 mask >> GDDA098 Update not needed for run 015 meanval >> WARNING: multiple formats found for 016/template >> USING: 016/template.nii.gz >> GDDA098 Update not needed for run 016 mask >> GDDA098 Update not needed for run 016 meanval >> WARNING: multiple formats found for 017/template >> USING: 017/template.nii.gz >> GDDA098 Update not needed for run 017 mask >> GDDA098 Update not needed for run 017 meanval >> Tue Aug 4 12:12:18 EDT 2015 >> mkbrainmask-sess done >> GDDA098 Registration ----------------------------- >> register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun >> -fsd bold -dof 6 -rlf runlistfile -per-run -nolog -update >> -------------------------------------------------------------- >> register-sess logfile is /dev/null >> -------------------------------------------------------------- >> Tue Aug 4 12:12:18 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 GDDA098 -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/GDDA098 >> ---------------- >> Tue Aug 4 12:12:18 EDT 2015 >> Run: 015 ---------------- >> Tue Aug 4 12:12:18 EDT 2015 >> WARNING: multiple formats found for bold/015/template >> USING: bold/015/template.nii.gz >> Update not needed >> Run: 016 ---------------- >> Tue Aug 4 12:12:18 EDT 2015 >> WARNING: multiple formats found for bold/016/template >> USING: bold/016/template.nii.gz >> Update not needed >> Run: 017 ---------------- >> Tue Aug 4 12:12:18 EDT 2015 >> WARNING: multiple formats found for bold/017/template >> USING: bold/017/template.nii.gz >> Update not needed >> Tue Aug 4 12:12:18 EDT 2015 >> register-sess completed >> GDDA098 MC ----------------------------- >> mc-sess -fstem f -fmcstem fmcpr -s GDDA098 -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/GDDA098 >> RunList: 015 016 017 >> WARNING: multiple formats found for 015/template >> USING: 015/template.nii.gz >> GDDA098 015 Update not needed >> WARNING: multiple formats found for 016/template >> USING: 016/template.nii.gz >> GDDA098 016 Update not needed >> WARNING: multiple formats found for 017/template >> USING: 017/template.nii.gz >> GDDA098 017 Update not needed >> >> >> Tue Aug 4 12:12:18 EDT 2015 >> mc-sess completed SUCCESSFULLY >> ---------------------------------------- >> Started at Tue Aug 4 12:12:17 EDT 2015 >> Ended at Tue Aug 4 12:12:18 EDT 2015 >> preproc-sess done >> ------------------------------------------- >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 >> Tue Aug 4 12:12:19 EDT 2015 >> anadir = >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514 >> DoGLMFit = 1 >> DoContrasts = 1 >> UpdateNeeded = 1 >> ------------------------------------------ >> ------- matlab output -------------------- >> No window system found. Java option 'MWT' ignored. >> Warning: Unable to open display 'iconic'. You will not be able to display >> graphics on the screen. >> Warning: No window system found. Java option 'MWT' ignored. >> >> < M A T L A B (R) > >> Copyright 1984-2013 The MathWorks, Inc. >> R2013b (8.2.0.701) 64-bit (glnxa64) >> August 13, 2013 >> >> >> To get started, type one of these: helpwin, helpdesk, or demo. >> For product information, visit www.mathworks.com. >> >> sxa3pwd = >> >> /autofs/cluster/roffman/users/Stable5_PerRun >> >> sxa3cmd = >> >> /usr/local/freesurfer/stable5_3_0/fsfast/bin/selxavg3-sess -s GDDA098 >> -analysis SIRP_LoadRegression_Stable5_050514 >> >>>> /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_selxavg3.m >> #@# GDDA098 ############################### >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 >> ------------------------- >> $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ >> /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_selxavg3.m >> /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_ldanaflac.m >> /usr/local/freesurfer/stable5_3_0/matlab/MRIread.m >> ------------------------- >> outtop = /autofs/cluster/roffman/users/Stable5_PerRun >> Extension format = nii.gz >> 1 Cond2vFix.mat >> Excluding 0 points >> nruns = 3 >> autostimdur = >> >> >> outanadir = >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514 >> Excluding 0 points >> Excluding 0 points >> Excluding 0 points >> Found 49193/143360 (34.3) voxels in mask >> Creating Design Matrix >> ... creation time = 0.011 sec >> DoMCFit = 1 >> ntptot = 705, nX = 18, DOF = 687 >> Saving X matrix to >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514/Xtmp.mat >> XCond = 35.9364 (normalized) >> Computing compensation for resdual AR1 bias >> 1 -0.5 -0.507451 (t=0.046548) >> 2 -0.25 -0.264 (t=0.105696) >> 3 0 -0.0235997 (t=0.137308) >> 4 0.25 0.211292 (t=0.189719) >> 5 0.5 0.434363 (t=0.217673) >> AR1 Correction M: 0.031657 1.0595 >> Computing contrast matrices >> OLS Beta Pass >> run 1 t= 0.0 >> ERROR: dimension mismatch between mask and 1th run >>>> ------------------------------------------ >> ERROR: fast_selxavg3() failed\n >> >> ________________________________________ >> From: [email protected] >> [[email protected]] on behalf of Douglas N Greve >> [[email protected]] >> Sent: Tuesday, August 04, 2015 11:39 AM >> To: [email protected] >> Subject: Re: [Freesurfer] Dimension mismatch between mask and run >> >> I'm not sure, but it may be that there are some files that are nii and >> others that are nii.gz. Eg, >> >> ls -tl /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/015/masks/ >> total 1248 >> -rw-rw---- 1 arodthom roffmagp 3579 Aug 3 18:06 brain.e3.nii.gz >> -rw-rw---- 1 arodthom roffmagp 5383 Aug 3 18:06 brain.nii.gz >> -rw-rw---- 1 arodthom roffmagp 606560 Mar 16 11:02 brain.e3.nii >> -rw-rw---- 1 arodthom roffmagp 606560 Mar 16 11:02 brain.nii >> >> The nii.gz are newer but I think selxavg3-sess will use the nii files, >> which have probably not been updated. Try deleting the same-named nii files >> >> >> On 08/03/2015 06:32 PM, Rodriguez-Thompson, Anais wrote: >>> Hi Freesurfer experts, >>> >>> For a data set of n=100, selxavg3 is erroring out on 10 subjects (GDDA086, >>> 88, 89, 91, 93, 94, 95, 96, 97, and 98). It says ERROR: dimension mismatch >>> between mask and 1th run. Do you know why freesurfer is having trouble with >>> these subjects in particular, and how I can avoid this error? >>> >>> Thanks for your help, >>> Anais >>> >>> Below is the terminal window output: >>> -------------------------------------------------------------- >>> selxavg3-sess logfile is >>> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_050514-150803173934.log >>> -------------------------------------------------------------- >>> preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a >>> SIRP_LoadRegression_Stable5_050514 -nolog >>> -------------------------------------------------------------- >>> 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 GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a >>> SIRP_LoadRegression_Stable5_050514 -nolog >>> Mon Aug 3 17:39:35 EDT 2015 >>> instem f >>> mc 1 f fmcpr >>> stc 0 fmcpr >>> sm 0 fmcpr >>> mask 1 brain >>> GDDA098 Template ----------------------------- >>> mktemplate-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun >>> -fsd bold -rlf runlistfile -nolog -update >>> >>> Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 >>> ---------------- >>> Mon Aug 3 17:39:36 EDT 2015 >>> Detected input format at nii >>> GDDA098 Update not needed >>> Run: 015 ---------------- >>> Mon Aug 3 17:39:36 EDT 2015 >>> GDDA098 015 Update not needed >>> Run: 016 ---------------- >>> Mon Aug 3 17:39:36 EDT 2015 >>> GDDA098 016 Update not needed >>> Run: 017 ---------------- >>> Mon Aug 3 17:39:36 EDT 2015 >>> GDDA098 017 Update not needed >>> Mon Aug 3 17:39:36 EDT 2015 >>> mktemplate-sess completed >>> GDDA098 Mask ------------------------ >>> mkbrainmask-sess -maskstem brain -fsd bold -s GDDA098 -d >>> /autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistfile -nolog -update >>> ------------------------------------------------ >>> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 >>> Mon Aug 3 17:39:36 EDT 2015 >>> WARNING: multiple formats found for template >>> USING: template.nii.gz >>> GDDA098 Update not needed for session-level mask >>> WARNING: multiple formats found for 015/template >>> USING: 015/template.nii.gz >>> GDDA098 Update not needed for run 015 mask >>> GDDA098 Update not needed for run 015 meanval >>> WARNING: multiple formats found for 016/template >>> USING: 016/template.nii.gz >>> GDDA098 Update not needed for run 016 mask >>> GDDA098 Update not needed for run 016 meanval >>> WARNING: multiple formats found for 017/template >>> USING: 017/template.nii.gz >>> GDDA098 Update not needed for run 017 mask >>> GDDA098 Update not needed for run 017 meanval >>> Mon Aug 3 17:39:37 EDT 2015 >>> mkbrainmask-sess done >>> GDDA098 Registration ----------------------------- >>> register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun >>> -fsd bold -dof 6 -rlf runlistfile -per-run -nolog -update >>> -------------------------------------------------------------- >>> register-sess logfile is /dev/null >>> -------------------------------------------------------------- >>> Mon Aug 3 17:39:37 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 GDDA098 -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/GDDA098 >>> ---------------- >>> Mon Aug 3 17:39:37 EDT 2015 >>> Run: 015 ---------------- >>> Mon Aug 3 17:39:37 EDT 2015 >>> WARNING: multiple formats found for bold/015/template >>> USING: bold/015/template.nii.gz >>> Update not needed >>> Run: 016 ---------------- >>> Mon Aug 3 17:39:37 EDT 2015 >>> WARNING: multiple formats found for bold/016/template >>> USING: bold/016/template.nii.gz >>> Update not needed >>> Run: 017 ---------------- >>> Mon Aug 3 17:39:37 EDT 2015 >>> WARNING: multiple formats found for bold/017/template >>> USING: bold/017/template.nii.gz >>> Update not needed >>> Mon Aug 3 17:39:37 EDT 2015 >>> register-sess completed >>> GDDA098 MC ----------------------------- >>> mc-sess -fstem f -fmcstem fmcpr -s GDDA098 -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/GDDA098 >>> RunList: 015 016 017 >>> WARNING: multiple formats found for 015/template >>> USING: 015/template.nii.gz >>> GDDA098 015 Update not needed >>> WARNING: multiple formats found for 016/template >>> USING: 016/template.nii.gz >>> GDDA098 016 Update not needed >>> WARNING: multiple formats found for 017/template >>> USING: 017/template.nii.gz >>> GDDA098 017 Update not needed >>> >>> >>> Mon Aug 3 17:39:38 EDT 2015 >>> mc-sess completed SUCCESSFULLY >>> ---------------------------------------- >>> Started at Mon Aug 3 17:39:35 EDT 2015 >>> Ended at Mon Aug 3 17:39:38 EDT 2015 >>> preproc-sess done >>> ------------------------------------------- >>> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 >>> Mon Aug 3 17:39:38 EDT 2015 >>> anadir = >>> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514 >>> DoGLMFit = 1 >>> DoContrasts = 1 >>> UpdateNeeded = 1 >>> ------------------------------------------ >>> ------- matlab output -------------------- >>> Warning: Unable to open display 'iconic'. You will not be able to display >>> graphics on the screen. >>> Warning: No window system found. Java option 'MWT' ignored. >>> >>> < M A T L A B (R) > >>> Copyright 1984-2013 The MathWorks, Inc. >>> R2013b (8.2.0.701) 64-bit (glnxa64) >>> August 13, 2013 >>> >>> No window system found. Java option 'MWT' ignored. >>> >>> To get started, type one of these: helpwin, helpdesk, or demo. >>> For product information, visit www.mathworks.com. >>> >>> sxa3pwd = >>> >>> /autofs/cluster/roffman/users/Stable5_PerRun >>> >>> sxa3cmd = >>> >>> /usr/local/freesurfer/stable5_3_0/fsfast/bin/selxavg3-sess -s GDDA098 >>> -analysis SIRP_LoadRegression_Stable5_050514 >>> >>>>> /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_selxavg3.m >>> #@# GDDA098 ############################### >>> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 >>> ------------------------- >>> $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ >>> /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_selxavg3.m >>> /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_ldanaflac.m >>> /usr/local/freesurfer/stable5_3_0/matlab/MRIread.m >>> ------------------------- >>> outtop = /autofs/cluster/roffman/users/Stable5_PerRun >>> Extension format = nii.gz >>> 1 Cond2vFix.mat >>> Excluding 0 points >>> nruns = 3 >>> autostimdur = >>> >>> >>> outanadir = >>> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514 >>> Excluding 0 points >>> Excluding 0 points >>> Excluding 0 points >>> Found 49193/143360 (34.3) voxels in mask >>> Creating Design Matrix >>> ... creation time = 0.011 sec >>> DoMCFit = 1 >>> ntptot = 705, nX = 18, DOF = 687 >>> Saving X matrix to >>> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514/Xtmp.mat >>> XCond = 35.9364 (normalized) >>> Computing compensation for resdual AR1 bias >>> 1 -0.5 -0.507451 (t=0.033876) >>> 2 -0.25 -0.264 (t=0.081305) >>> 3 0 -0.0235997 (t=0.100205) >>> 4 0.25 0.211292 (t=0.143646) >>> 5 0.5 0.434363 (t=0.160328) >>> AR1 Correction M: 0.031657 1.0595 >>> Computing contrast matrices >>> OLS Beta Pass >>> run 1 t= 0.4 >>> ERROR: dimension mismatch between mask and 1th run >>>>> ------------------------------------------ >>> ERROR: fast_selxavg3() failed\n >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> [email protected] >> 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 >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > 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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] 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 . 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