This is dying somewhere in the MNI nu_correct code. Look at the orig.mgz to see if that looks ok
On 06/23/2014 03:58 PM, Remy Wahnoun wrote:
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
/www.NeuralControl.net http://www.neuralcontrol.net//
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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