Hi EK
looks like an N3 problem. You might want to ask on the appropriate MNI list.
cheers Bruce On Wed, 15 Feb 2012, EK Kim wrote:
Hello, Freesurfers, I got an error message when I trying to use recon-all function in freesurfer on the XUbuntu system installed on the VirtualBox on a Windows 7 machine. I searched the e-mailing list but I can't find any answers. My problem is related to the nu_correct and nu_estimate_np_and_em. However, nu_correct and nu_estimate_np_and_em were located to exact path (/home/virtualuser/freesurfer/mni/bin). echo $MNI_DATAPATH, echo $MNI_PERL5LIB showed exact path. In addition, I already tried to use fixup_mni_paths. Could anyone give me an advice for fixing up this problem? Thanks in advance. Cheers,
EK error message! -------------------------------------------------------------------------------------------- #@# Nu Intensity Correction Wed Feb 15 01:23:24 EST 2012 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/virtualuser/Desktop/DATA/30664304/mri /home/virtualuser/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux Wed Feb 15 01:23:25 EST 2012 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 tmpdir is ./tmp.mri_nu_correct.mni.17682 /home/virtualuser/Desktop/DATA/30664304/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17682/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17682/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.17682/nu0.mnc...
Iteration 1 Wed Feb 15 01:23:37 EST 2012 nu_correct -clobber ./tmp.mri_nu_correct.mni.17682/nu0.mnc ./tmp.mri_nu_correct.mni.17682/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17682/0/ [virtualuser@FreeSurfer:/home/virtualuser/Desktop/DATA/30664304/mri/] [2012-02-15 01:23:37] running: /home/virtualuser/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17682/0/ ./tmp.mri_nu_correct.mni.17682/nu0.mnc ./tmp.mri_nu_correct.mni.17682/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)
ERROR: nu_correct Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux