Thanks Douglas,
I definitely appreciate your help.
Here is what it Spit out,
Rémy Wahnoun, PhD
Biomedical Research Group Manager
Barrow Neurological Institute at Phoenix Children's Hospital
Adjunct Faculty, Arizona State University
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 11 != 0 )
set flag = $argv[1] ; shift ;
set flag = --n
shift
switch ( $flag )
switch ( --n )
if ( $#argv == 0 ) goto arg1err ;
if ( 10 == 0 ) goto arg1err
set nIters = $argv[1] ; shift ;
set nIters = 1
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 9 != 0 )
set flag = $argv[1] ; shift ;
set flag = --proto-iters
shift
switch ( $flag )
switch ( --proto-iters )
if ( $#argv == 0 ) goto arg1err ;
if ( 8 == 0 ) goto arg1err
set nProtoIters = $argv[1] ; shift ;
set nProtoIters = 1000
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 7 != 0 )
set flag = $argv[1] ; shift ;
set flag = --distance
shift
switch ( $flag )
switch ( --distance )
if ( $#argv == 0 ) goto arg1err ;
if ( 6 == 0 ) goto arg1err
set Distance = $argv[1] ; shift ;
set Distance = 50
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 5 != 0 )
set flag = $argv[1] ; shift ;
set flag = --no-rescale
shift
switch ( $flag )
switch ( --no-rescale )
set DoRescale = 0 ;
set DoRescale = 0
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 4 != 0 )
set flag = $argv[1] ; shift ;
set flag = --i
shift
switch ( $flag )
switch ( --i )
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set InVol = $argv[1] ; shift ;
set InVol = orig.mgz
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = --o
shift
switch ( $flag )
switch ( --o )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set OutVol = $argv[1] ; shift ;
set OutVol = orig_nu.mgz
shift
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 ( $#InVol == 0 ) then
if ( 1 == 0 ) then
if ( ! -e $InVol ) then
if ( ! -e orig.mgz ) then
if ( $#OutVol == 0 ) then
if ( 1 == 0 ) then
goto check_params_return ;
goto check_params_return
set OutDir = `dirname $OutVol` ;
set OutDir = `dirname $OutVol`
dirname orig_nu.mgz
mkdir -p $OutDir ;
mkdir -p .
if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log
if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log
set LF = ./mri_nu_correct.mni.log
if ( -e $LF ) mv $LF $LF.bak
if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak
mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak
pwd | tee -a $LF
pwd
tee -a ./mri_nu_correct.mni.log
/media/sf_Imagery/FreeSurfer/xx/mri
which mri_nu_correct.mni | tee -a $LF
which mri_nu_correct.mni
tee -a ./mri_nu_correct.mni.log
/usr/local/freesurfer/bin/mri_nu_correct.mni
echo $cmdargs | tee -a $LF
echo --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
tee -a ./mri_nu_correct.mni.log
--debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
echo "nIters $nIters" | tee -a $LF
echo nIters 1
tee -a ./mri_nu_correct.mni.log
nIters 1
echo $VERSION | tee -a $LF
tee -a ./mri_nu_correct.mni.log
echo $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
uname -a | tee -a $LF
uname -a
tee -a ./mri_nu_correct.mni.log
Linux xubuntu-VirtualBox 3.2.0-64-generic #97-Ubuntu SMP Wed Jun 4 22:03:48 UTC 2014 i686 i686 i386 GNU/Linux
date | tee -a $LF
date
tee -a ./mri_nu_correct.mni.log
Mon Jun 23 15:32:45 EDT 2014
nu_correct -version | tee -a $LF
nu_correct -version
tee -a ./mri_nu_correct.mni.log
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13
if ( ! $#tmpdir ) set tmpdir = $OutDir/tmp.mri_nu_correct.mni.$$
if ( ! 0 ) set tmpdir = ./tmp.mri_nu_correct.mni.1745
set tmpdir = ./tmp.mri_nu_correct.mni.1745
mkdir -p $tmpdir
mkdir -p ./tmp.mri_nu_correct.mni.1745
echo "tmpdir is $tmpdir" | tee -a $LF
echo tmpdir is ./tmp.mri_nu_correct.mni.1745
tee -a ./mri_nu_correct.mni.log
tmpdir is ./tmp.mri_nu_correct.mni.1745
set cmd = ( mri_convert ${HiRes} $InVol $tmpdir/nu0.mnc )
set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc )
if ( $UseFloat ) set cmd = ( $cmd -odt float )
if ( 1 ) set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float )
set cmd = ( mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float )
pwd | & tee -a $LF
pwd
tee -a ./mri_nu_correct.mni.log
/media/sf_Imagery/FreeSurfer/xx/mri
echo $cmd | & tee -a $LF
echo mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
tee -a ./mri_nu_correct.mni.log
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
$cmd | & tee -a $LF
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
tee -a ./mri_nu_correct.mni.log
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1745/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=25.00, TE=5.36, TI=0.00, flip angle=30.00
i_ras = (-1, 1.49012e-08, 0)
j_ras = (0, 0, -1)
k_ras = (-1.30385e-08, 1, -5.96046e-08)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.1745/nu0.mnc...
if ( $status ) then
if ( 0 ) then
@ nthIter = 1 ;
@ nthIter = 1
while ( $nthIter < = $nIters )
while ( 1 < = 1 )
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
echo "--------------------------------------------------------" | & tee -a $LF
echo --------------------------------------------------------
tee -a ./mri_nu_correct.mni.log
--------------------------------------------------------
echo "Iteration $nthIter `date`" | & tee -a $LF
echo Iteration 1 `date`
tee -a ./mri_nu_correct.mni.log
date
Iteration 1 Mon Jun 23 15:32:49 EDT 2014
@ m = $nthIter - 1
@ m = 1 - 1
set cmd = ( nu_correct -clobber $tmpdir/nu${m}.mnc $tmpdir/nu${nthIter}.mnc )
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc )
set cmd = ( $cmd -tmpdir ${tmpdir}/${m}/ ) ;
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ )
if ( $#nProtoIters ) set cmd = ( $cmd -iterations $nProtoIters ) ;
if ( 1 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 )
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 )
if ( $#StopThresh ) set cmd = ( $cmd -stop $StopThresh ) ;
if ( 0 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -stop )
if ( $#Distance ) set cmd = ( $cmd -distance $Distance ) ;
if ( 1 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 )
set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 )
if ( $#FWHM ) set cmd = ( $cmd -fwhm $FWHM ) ;
if ( 0 ) set cmd = ( nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50 -fwhm )
echo $cmd | & tee -a $LF
echo nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
tee -a ./mri_nu_correct.mni.log
nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
$cmd | & tee -a $LF
nu_correct -clobber ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ -iterations 1000 -distance 50
tee -a ./mri_nu_correct.mni.log
[fsuser@xubuntu-VirtualBox:/media/sf_Imagery/FreeSurfer/xx/mri/] [2014-06-23 15:32:49] running:
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1745/0/ ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu1.imp
Assertion failed at line 827 in file templates/CachedArray.cc
nu_estimate_np_and_em: crashed while running volume_stats (termination status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)
if ( $status ) then
if ( 0 ) then
rm -f $tmpdir/nu${m}.mnc $tmpdir/nu${m}.imp
rm -f ./tmp.mri_nu_correct.mni.1745/nu0.mnc ./tmp.mri_nu_correct.mni.1745/nu0.imp
@ nthIter = $nthIter + 1 ;
@ nthIter = 1 + 1
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
end
end
while ( $nthIter < = $nIters )
while ( 2 < = 1 )
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
echo " " | & tee -a $LF
echo
tee -a ./mri_nu_correct.mni.log
set numnc = $tmpdir/nu$nIters.mnc
set numnc = ./tmp.mri_nu_correct.mni.1745/nu1.mnc
if ( $DoRescale ) then
if ( 0 ) then
if ( ! -e $numnc ) then
if ( ! -e ./tmp.mri_nu_correct.mni.1745/nu1.mnc ) then
echo "ERROR: file $numnc does not exist!" | & tee -a $LF
echo ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist!
tee -a ./mri_nu_correct.mni.log
ERROR: file ./tmp.mri_nu_correct.mni.1745/nu1.mnc does not exist!
exit 1 ;
exit 1
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