Hi, I am trying to use mri_nu_correct.mni function in freesurfer on theXUbuntu system installed on the VirtualBox on a Windows 7 machine. I converted Siemens IMA into analyze format .img (with function;mri_convert -i input_file_name.IMA -ot analyze -ooutput_file_name.img), then when I called the function mri_nu_correctfor the inhomogeneity correction, it gave me an error message (seebelow). What is wrong? Cheers,Baris FreeSurfer:~/Documents/EEGLAB/NFT/MPRAGE/7031> mri_nu_correct.mni --iS1.img --o S1inh.img --n2/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031/home/virtualuser/freesurfer/bin/mri_nu_correct.mni--iS1.img --o S1inh.img --n 2nIters 2$Id: mri_nu_correct.mni,v 1.182011/03/02 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/LinuxMon Nov 2110:53:06 EST 2011Program nu_correct, built from:Package MNI N3,version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on2010-02-20 at 20:19:13tmpdir is./tmp.mri_nu_correct.mni.3086/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031mri_convertS1.img ./tmp.mri_nu_correct.mni.3086/nu0.mnc -odt floatmri_convertS1.img ./tmp.mri_nu_correct.mni.3086/nu0.mnc -odt float $Id:mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $reading fromS1.img...TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00i_ras =(-0.0286335, -0.999213, 0.0274527)j_ras = (-0.00717244, -0.0272578,-0.999603)k_ras = (-0.999564, 0.028819, 0.00638633)changing data typefrom short to float (noscale = 0)...writing to./tmp.mri_nu_correct.mni.3086/nu0.mnc...--------------------------------------------------------Iteration 1Mon Nov 21 10:53:10 EST 2011nu_correct -clobber./tmp.mri_nu_correct.mni.3086/nu0.mnc./tmp.mri_nu_correct.mni.3086/nu1.mnc -tmpdir./tmp.mri_nu_correct.mni.3086/0/[virtualuser@FreeSurfer:/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031/][2011-11-21 10:53:11] 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.3086/0/./tmp.mri_nu_correct.mni.3086/nu0.mnc./tmp.mri_nu_correct.mni.3086/nu1.impAssertion failed at line 827 in filetemplates/CachedArray.ccnu_estimate_np_and_em: crashed while runningvolume_stats (termination status=256)nu_correct: crashed while runningnu_estimate_np_and_em (termination status=256)ERROR: nu_correct
hmmm, I'm not sure. It looks like an nu_correct problem, in which case you should probably ask the MNI people. Nick: any ideas?
Bruce On Wed, 23 Nov 2011, Baris Demiral wrote:
Hi, I am trying to use mri_nu_correct.mni function in freesurfer on theXUbuntu system installed on the VirtualBox on a Windows 7 machine. I converted Siemens IMA into analyze format .img (with function;mri_convert -i input_file_name.IMA -ot analyze -ooutput_file_name.img), then when I called the function mri_nu_correctfor the inhomogeneity correction, it gave me an error message (seebelow). What is wrong? Cheers,Baris FreeSurfer:~/Documents/EEGLAB/NFT/MPRAGE/7031> mri_nu_correct.mni --iS1.img --o S1inh.img --n2/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031/home/virtualuser/freesurfer/bin/mri_nu_correct.mni--iS1.img --o S1inh.img --n 2nIters 2$Id: mri_nu_correct.mni,v 1.182011/03/02 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/LinuxMon Nov 2110:53:06 EST 2011Program nu_correct, built from:Package MNI N3,version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on2010-02-20 at 20:19:13tmpdir is./tmp.mri_nu_correct.mni.3086/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031mri_convertS1.img ./tmp.mri_nu_correct.mni.3086/nu0.mnc -odt floatmri_convertS1.img ./tmp.mri_nu_correct.mni.3086/nu0.mnc -odt float $Id:mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $reading fromS1.img...TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00i_ras =(-0.0286335, -0.999213, 0.0274527)j_ras = (-0.00717244, -0.0272578,-0.999603)k_ras = (-0.999564, 0.028819, 0.00638633)changing data typefrom short to float (noscale = 0)...writing to./tmp.mri_nu_correct.mni.3086/nu0.mnc...--------------------------------------------------------Iteration 1Mon Nov 21 10:53:10 EST 2011nu_correct -clobber./tmp.mri_nu_correct.mni.3086/nu0.mnc./tmp.mri_nu_correct.mni.3086/nu1.mnc -tmpdir./tmp.mri_nu_correct.mni.3086/0/[virtualuser@FreeSurfer:/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031/][2011-11-21 10:53:11] 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.3086/0/./tmp.mri_nu_correct.mni.3086/nu0.mnc./tmp.mri_nu_correct.mni.3086/nu1.impAssertion failed at line 827 in filetemplates/CachedArray.ccnu_estimate_np_and_em: crashed while runningvolume_stats (termination status=256)nu_correct: crashed while runningnu_estimate_np_and_em (termination status=256)ERROR: nu_correct
i dont have an ideas either. this is new territory for me as well, as its working on a siemans ima file converted to analyze.
hmmm, I'm not sure. It looks like an nu_correct problem, in which case you should probably ask the MNI people. Nick: any ideas?
Bruce On Wed, 23 Nov 2011, Baris Demiral wrote:
Hi, I am trying to use mri_nu_correct.mni function in freesurfer on theXUbuntu system installed on the VirtualBox on a Windows 7 machine. I converted Siemens IMA into analyze format .img (with function;mri_convert -i input_file_name.IMA -ot analyze -ooutput_file_name.img), then when I called the function mri_nu_correctfor the inhomogeneity correction, it gave me an error message (seebelow). What is wrong? Cheers,Baris FreeSurfer:~/Documents/EEGLAB/NFT/MPRAGE/7031> mri_nu_correct.mni --iS1.img --o S1inh.img --n2/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031/home/virtualuser/freesurfer/bin/mri_nu_correct.mni--iS1.img --o S1inh.img --n 2nIters 2$Id: mri_nu_correct.mni,v 1.182011/03/02 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/LinuxMon Nov 2110:53:06 EST 2011Program nu_correct, built from:Package MNI N3,version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on2010-02-20 at 20:19:13tmpdir is./tmp.mri_nu_correct.mni.3086/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031mri_convertS1.img ./tmp.mri_nu_correct.mni.3086/nu0.mnc -odt floatmri_convertS1.img ./tmp.mri_nu_correct.mni.3086/nu0.mnc -odt float $Id:mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $reading fromS1.img...TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00i_ras =(-0.0286335, -0.999213, 0.0274527)j_ras = (-0.00717244, -0.0272578,-0.999603)k_ras = (-0.999564, 0.028819, 0.00638633)changing data typefrom short to float (noscale = 0)...writing to./tmp.mri_nu_correct.mni.3086/nu0.mnc...--------------------------------------------------------Iteration 1Mon Nov 21 10:53:10 EST 2011nu_correct -clobber./tmp.mri_nu_correct.mni.3086/nu0.mnc./tmp.mri_nu_correct.mni.3086/nu1.mnc -tmpdir./tmp.mri_nu_correct.mni.3086/0/[virtualuser@FreeSurfer:/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031/][2011-11-21 10:53:11] 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.3086/0/./tmp.mri_nu_correct.mni.3086/nu0.mnc./tmp.mri_nu_correct.mni.3086/nu1.impAssertion failed at line 827 in filetemplates/CachedArray.ccnu_estimate_np_and_em: crashed while runningvolume_stats (termination status=256)nu_correct: crashed while runningnu_estimate_np_and_em (termination status=256)ERROR: nu_correct
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