Re: [Freesurfer] selxavg3 can't find image that exists

11 Apr 2011

      Scott Burns wrote:
...
Doug -
Thanks for the help. A few more questions...

Is it worth re-preprocessing with -sliceorder siemens?

depends. If you have an even number of slices, then your slice order is 
wrong, and you should delete the preprocessed data and start over. If 
you have an odd number, then you're ok.
...

Does mkanalysis-sess -fwhm 8 -stc siemens -surface fsaverage lh ... not do preprocessing but just uses those specs to build the string for the filename search? Or will it do preprocessing but not actually recompute anything because there's no update needed (assuming I've recently run preproc-sess)?

It will run the preprocessing (preproc-sess), but preproc-sess will not 
reanalyze anything unless an update is needed.
doug
...
scott
On Apr 10, 2011, at 10:40 PM, Douglas Greve wrote:
...
Hi Scott, the problem is that you specified the "funcstem" as a full filename with extension "-funcstem fmcpr.odd.sm8.fsaverage.lh.nii.gz" should be "-funcstem fmcpr.odd.sm8.fsaverage.lh" (the "stem" is a file name without the extension, so no .nii.gz). I don't think that you need to actually spec the funcstem explicitly. It looks like it will do the right thing if you just spec "-fwhm 8 -stc odd". Also, if you're using data from a Siemens scanner than it is probably better to use "-stc siemens" instead of "-stc odd". Using "-stc siemens" will properly handle interleaved slices regardless of whether you have an odd or even number of slices.
doug
On 4/10/11 7:20 PM, sburns@nmr.mgh.harvard.edu wrote:
...
Doug -- here's the output from the terminal....
kerryave:functionals $ selxavg3-sess -s ya24 -d
/cluster/kuperberg/SemPrMM/MRI/functionals/ -analysis ya.ATLLoc.spm.sm8.lh
-debug |&  tee debug.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 ( 1 == 0 ) then
goto check_params_return ;
goto check_params_return
set UniqueList = ( ) ;
set UniqueList = ( )
foreach d ( $SearchPathList )
foreach d ( /cluster/kuperberg/SemPrMM/MRI/functionals/ )
if ( ! -e $d ) then
if ( ! -e /cluster/kuperberg/SemPrMM/MRI/functionals/ ) then
set IsUnique = 1 ;
set IsUnique = 1
foreach u ( $UniqueList )
foreach u ( )
if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ;
if ( 1 ) set UniqueList = ( /cluster/kuperberg/SemPrMM/MRI/functionals/ )
set UniqueList = ( /cluster/kuperberg/SemPrMM/MRI/functionals/ )
end
end
set SearchPathList = ( $UniqueList ) ;
set SearchPathList = ( /cluster/kuperberg/SemPrMM/MRI/functionals/ )
set errs = 0 ;
set errs = 0
set SessPath = ( ) ;
set SessPath = ( )
foreach sess ( $SessList )
foreach sess ( ya24 )
set tmp = ( ) ;
set tmp = ( )
foreach d ( $SearchPathList )
foreach d ( /cluster/kuperberg/SemPrMM/MRI/functionals/ )
set stst = $d/$sess
set stst = /cluster/kuperberg/SemPrMM/MRI/functionals//ya24
if ( -d $stst ) then
if ( -d /cluster/kuperberg/SemPrMM/MRI/functionals//ya24 ) then
if ( ! -r $stst ) then
if ( ! -r /cluster/kuperberg/SemPrMM/MRI/functionals//ya24 ) then
pushd $stst>  /dev/null ;
pushd /cluster/kuperberg/SemPrMM/MRI/functionals//ya24
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/kuperberg/SemPrMM/MRI/functionals/ya24 )
end
end
set UniqueList = ( ) ;
set UniqueList = ( )
foreach s ( $SessPath )
foreach s ( /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24 )
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/kuperberg/SemPrMM/MRI/functionals/ya24 )
endif
endif
end
end
echo $SessPath
echo /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24
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 ya.ATLLoc.spm.sm8.lh ) then
if ( ! -e $analysis/analysis.info ) then
if ( ! -e ya.ATLLoc.spm.sm8.lh/analysis.info ) then
endif
endif
if ( $#flacfile != 0 ) then
if ( 0 != 0 ) then
if ( $perrun&&  $jkrun ) then
if ( 0&&  0 ) then
if ( $UseOctave ) then
if ( 0 ) then
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 = ya.ATLLoc.spm.sm8.lh
set fsd = `getana -a $analysis -t fsd` ;
set fsd = `getana -a $analysis -t fsd`
getana -a ya.ATLLoc.spm.sm8.lh -t fsd
set IsNative = `getana -a $analysis -t IsNative`
set IsNative = `getana -a $analysis -t IsNative`
getana -a ya.ATLLoc.spm.sm8.lh -t IsNative
set IsSurface = `getana -a $analysis -t IsSurface`
set IsSurface = `getana -a $analysis -t IsSurface`
getana -a ya.ATLLoc.spm.sm8.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 ya.ATLLoc.spm.sm8.lh -t subject
set hemi = `getana -a $analysis -t hemi`
set hemi = `getana -a $analysis -t hemi`
getana -a ya.ATLLoc.spm.sm8.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 ya.ATLLoc.spm.sm8.lh -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 ya.ATLLoc.spm.sm8.lh -t contrasts
if ( $#contrasts == 0&&  $RequireContrasts ) then
if ( 7 == 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/kuperberg/SemPrMM/MRI/functionals/log
if ( ! -e $logdir ) then
if ( ! -e /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log ) then
set LF = $logdir/selxavg3-sess-$fsd-$analysis-$DateStr.log
set LF =
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log
if ( -e $LF ) mv $LF $LF.old
if ( -e
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log
) mv
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log.old
endif
endif
endif
endif
endif
endif
echo "--------------------------------------------------------------"
echo --------------------------------------------------------------

echo "selxavg3-sess logfile is $LF"
echo selxavg3-sess logfile is
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log
selxavg3-sess logfile is
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log
echo "--------------------------------------------------------------"
echo --------------------------------------------------------------

echo "selxavg3-sess log file">>  $LF
echo selxavg3-sess log file
echo $0>>  $LF
echo /usr/local/freesurfer/stable5_0_0/fsfast/bin/selxavg3-sess
echo $inputargs>>  $LF
echo -s ya24 -d /cluster/kuperberg/SemPrMM/MRI/functionals/ -analysis
ya.ATLLoc.spm.sm8.lh -debug
echo $VERSION>>  $LF
echo $Id: selxavg3-sess,v 1.52.2.5 2010/08/25 19:07:37 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 ya.ATLLoc.spm.sm8.lh -t funcstem-specified
if ( $funcstemspec ) set DoPreProc = 0 ;
if ( 1 ) set DoPreProc = 0
set DoPreProc = 0
if ( $DoPreProc ) then
if ( 0 ) then
if ( $#MLF == 0 ) set MLF = /tmp/selxavg3-sess-$$.m
if ( 0 == 0 ) set MLF = /tmp/selxavg3-sess-1405.m
set MLF = /tmp/selxavg3-sess-1405.m
rm -f $MLF
rm -f /tmp/selxavg3-sess-1405.m
echo "% `date`  ">>  $MLF
echo % `date`
date
echo "% `pwd`  ">>  $MLF
echo % `pwd`
pwd
echo "% $flacfile $analysis  ">>  $MLF
echo %  ya.ATLLoc.spm.sm8.lh
echo "  ">>  $MLF
echo
echo "  ">>  $MLF
echo
set okfile = /tmp/selxavg3-sess-$$.ok
set okfile = /tmp/selxavg3-sess-1405.ok
rm -f $okfile
rm -f /tmp/selxavg3-sess-1405.ok
set parname = `getana -a $analysis -t parname`
set parname = `getana -a $analysis -t parname`
getana -a ya.ATLLoc.spm.sm8.lh -t parname
set funcstem = `getana -a $analysis -t funcstem`
set funcstem = `getana -a $analysis -t funcstem`
getana -a ya.ATLLoc.spm.sm8.lh -t funcstem
set rlf = `getana -a $analysis -t runlistfile`
set rlf = `getana -a $analysis -t runlistfile`
getana -a ya.ATLLoc.spm.sm8.lh -t runlistfile
set ConList = `getana -a $analysis -t contrasts`
set ConList = `getana -a $analysis -t contrasts`
getana -a ya.ATLLoc.spm.sm8.lh -t contrasts
@ nthsess = 0 ;
@ nthsess = 0
@ nprocs = 0 ;
@ nprocs = 0
foreach sess ( $SessList )
foreach sess ( /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24 )
@ nthsess = $nthsess + 1 ;
@ nthsess = 0 + 1
set sessbase = `basename $sess` ;
set sessbase = `basename $sess`
basename /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24
set sessdir = `dirname  $sess` ;
set sessdir = `dirname  $sess`
dirname /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24
echo "-------------------------------------------" |&  tee -a $LF
echo -------------------------------------------
tee -a
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log

echo "$sess " |&  tee -a $LF
echo /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24
tee -a
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24
date |&  tee -a $LF
date
tee -a
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log
Sun Apr 10 19:19:09 EDT 2011
if ( ! -d $sess ) then
if ( ! -d /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24 ) then
set funcdir = $sess/$fsd
set funcdir = /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc
set anadir = $sess/$fsd/$analysisname
set anadir =
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/ya.ATLLoc.spm.sm8.lh
if ( $#OutParent == 0 ) then
if ( 0 == 0 ) then
set anadir = $sess/$fsd/$analysisname
set anadir =
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/ya.ATLLoc.spm.sm8.lh
else
else
echo anadir = $anadir | tee -a $LF
echo anadir =
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/ya.ATLLoc.spm.sm8.lh
tee -a
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/log/selxavg3-sess-ATLLoc-ya.ATLLoc.spm.sm8.lh-110410191908.log
anadir =
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/ya.ATLLoc.spm.sm8.lh
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/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/ya.ATLLoc.spm.sm8.lh/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 = ( ya.ATLLoc.spm.sm8.lh/analysis.info )
set RunList = ( `getrunlist $sess/$fsd $rlf` ) ;
set RunList = ( `getrunlist $sess/$fsd $rlf` )
getrunlist /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc rlf
set funclist = ( )
set funclist = ( )
foreach Run ( $RunList )
foreach Run ( 007 )
set funcstempath = $sess/$fsd/$Run/$funcstem ;
set funcstempath =
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz
set func = `stem2fname $funcstempath` ;
set func = `stem2fname $funcstempath`
stem2fname
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz
if ( $status ) then
if ( 1 ) then
echo "ERROR: cannot find $funcstempath"
echo ERROR: cannot find
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz
ERROR: cannot find
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz
exit 1 ;
exit 1
...
Scott, can you run
selxavg3-sess -analysis ya.ATLLoc.spm.sm8.lh -s ya24 -d
/cluster/kuperberg/SemPrMM/MRI/functionals/ -debug |&  tee debug.log
and send me debug.log?
doug
Scott Burns wrote:
...
Freesurfers --
Here's the output of my terminal...
kerryave:functionals $ cd /cluster/kuperberg/SemPrMM/MRI/functionals/
kerryave:functionals $ rm
/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/scripts/atlloc_fs-stats.log
kerryave:functionals $ selxavg3-sess -analysis ya.ATLLoc.spm.sm8.lh -s
ya24 -d /cluster/kuperberg/SemPrMM/MRI/functionals/ -svres -nolog
Surface data fsaverage lh
selxavg3-sess logfile is /dev/null

/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24
Fri Apr  8 16:47:17 EDT 2011
anadir =
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/ya.ATLLoc.spm.sm8.lh
ERROR: cannot find
/autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz
kerryave:functionals $ ls -l
ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz
-rw-rw-r-- 1 sburns lingua 83660305 Apr  7 07:56
ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz
Does anyone know what's going on? Here's my analysis.info
http://analysis.info  for that analysis...
kerryave:functionals $ cd ya.ATLLoc.spm.sm8.lh/
kerryave:ya.ATLLoc.spm.sm8.lh $ cat analysis.infohttp://analysis.info
# FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319
# MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve
Exp $
# MKACMD /usr/local/freesurfer/stable5_0_0/fsfast/bin/mkanalysis-sess
-analysis ya.ATLLoc.spm.sm8.lh -fsd ATLLoc -rlf rlf -p atlloc.par
-spmhrf 0 -refeventdur 2 -event-related -TR 2 -nconditions 4 -mcextreg
-hpf 128 -funcstem fmcpr.odd.sm8.fsaverage.lh.nii.gz -surface
fsaverage lh -force
# DATE Fri Apr  8 08:31:01 EDT 2011
analysis ya.ATLLoc.spm.sm8.lh
mcstem fmcpr
funcstem fmcpr.odd.sm8.fsaverage.lh.nii.gz
fsd ATLLoc
runlistfile rlf
TR 2
RegDOF 6
RawSpace surface fsaverage lh
mask brain
RawFWHM 0
RawSTC none
inorm 100
acfbins 30
fixacf  1
acffwhm 20
acfsvd  0
designtype event-related
nskip 0
polyfit 2
HPFCutoffHz 128
nconditions 4
parname atlloc.par
RefEventDur 2
timewindow 40.000000
prestim 0
TER 0.050000
spmhrf 0
stimulusdelay 0
Condition 1 Condition01
Condition 2 Condition02
Condition 3 Condition03
Condition 4 Condition04
nuisreg mcprextreg 3
Thanks for the help.
Scott Burns
Kuperberg Lab
Martinos Center for Biomedical Imaging
sburns@nmr.mgh.harvard.edumailto:sburns@nmr.mgh.harvard.edu
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
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.

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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Re: [Freesurfer] selxavg3 can't find image that exists

Surface data fsaverage lh

selxavg3-sess logfile is /dev/null