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 >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list 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.
