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 ------------------------------ This transmission, including any attachments, is for the sole use of the intended recipient (s) and may contain information that is confidential, proprietary, legally privileged, or otherwise protected by law from disclosure. 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