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* > Biomedical Research Group Manager > Barrow Neurological Institute at Phoenix Children's Hospital > Adjunct Faculty, Arizona State University > /www.NeuralControl.net <http://www.NeuralControl.net>/ > > > On Wed, Jun 25, 2014 at 7:40 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > 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> > <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. > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@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: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 . 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 gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
