Hello everybody,
I am trying to use mri_nu_correct.mni function in freesurfer on the XUbuntu 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 -o output_file_name.img), then when I called the function mri_nu_correect for the inhomogeneity correction, it gave me an error message (see below). What is wrong?
Cheers, Baris
FreeSurfer:~/Documents/EEGLAB/NFT/MPRAGE/7031> mri_nu_correct.mni --i S1.img --o S1inh.img --n 2/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031/home/virtualuser/freesurfer/bin/mri_nu_correct.mni--i S1.img --o S1inh.img --n 2nIters 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/LinuxMon Nov 21 10:53:06 EST 2011Program nu_correct, built from:Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13tmpdir is ./tmp.mri_nu_correct.mni.3086/home/virtualuser/Documents/EEGLAB/NFT/MPRAGE/7031mri_convert S1.img ./tmp.mri_nu_correct.mni.3086/nu0.mnc -odt floatmri_convert S1.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 from S1.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 type from short to float (noscale = 0)...writing to ./tmp.mri_nu_correct.mni.3086/nu0.mnc... --------------------------------------------------------Iteration 1 Mon 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.imp Assertion failed at line 827 in file templates/CachedArray.ccnu_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