The problem is probably that your slice thickness is 5.2mm. This will
certainly never work for getting surfaces, though I don't quite
understand why nu is failing
doug
On 06/30/2014 03:51 PM, Remy Wahnoun wrote:
> Thanks Douglas,
> orig.mgz looks fine to me. Do you know if there is any detailed log i
> could look into? Or maybe process tasks one after the other?
>
>
> *Rémy Wahnoun, PhD*> /www.NeuralControl.net <http://www.NeuralControl.net>/
> Biomedical Research Group Manager
> Barrow Neurological Institute at Phoenix Children's Hospital
> Adjunct Faculty, Arizona State University
>
>
> On Wed, Jun 25, 2014 at 7:40 AM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:> > /www.NeuralControl.net <http://www.NeuralControl.net>
>
>
> 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
> >
> <mailto:Freesurfer@nmr.mgh.harvard.edu>> <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. Any unauthorized review, use, copying,
> > disclosure, or distribution is prohibited. If you are not the
> intended
> > recipient, or the person responsible for delivering this to an
> > addressee, you should notify the sender immediately by telephone
> or by
> > reply e-mail, and destroy all copies of the original message.
> >
> >
> >
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> > 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 <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing:> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
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>
>
> The information in this e-mail is intended only for the person to
> whom it is
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> the e-mail
> contains patient information, please contact the Partners
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--
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: 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/
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