Hello, This is a recently discovered bug either mni related or virtual box related. The issue is that the "mri_nu_correct.mni" command will fail when executed in the VirtualBox environment on a subject whose data exists on a shared folder between the host and the virtual machine.
Currently the only known solution is to import the subject data folder into the VirtualBox environment, and then run recon-all. -Zeke On 08/03/2015 11:54 PM, Li, Zhihao wrote: > Hi FS experts, > > I was trying to run "recon-all" within the VirtualBox of NeuroDebian 8.0 > on a WIN8 host. The program stopped immaturely at the step of > "mri_nu_correct.mni". I went into the folder of "mri" and ran > "mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale > --i orig.mgz --o orig_nu.mgz" with the output pasted below. Could you > please help me to fix this problem? Thank you very much! > > > ----------------------------------- > > brain:mri$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 > --no-rescale --i orig.mgz --o orig_nu.mgz > /media/sf_host/SZU_ZL_3WAY/test/T1/FrSrfr_Recon/mri > /usr/local/freesurfer/bin/mri_nu_correct.mni > --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o > orig_nu.mgz > nIters 1 > $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ > Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 > (2015-04-24) x86_64 GNU/Linux > Mon Aug 3 22:51:33 EDT 2015 > Program nu_correct, built from: > Package MNI N3, version 1.10, compiled by nicks@minerva > (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 > tmpdir is ./tmp.mri_nu_correct.mni.31236 > /media/sf_host/SZU_ZL_3WAY/test/T1/FrSrfr_Recon/mri > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31236/nu0.mnc -odt float > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31236/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=2530.00, TE=3.45, TI=1100.00, flip angle=7.00 > 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.31236/nu0.mnc... > > -------------------------------------------------------- > Iteration 1 Mon Aug 3 22:51:38 EDT 2015 > nu_correct -clobber ./tmp.mri_nu_correct.mni.31236/nu0.mnc > ./tmp.mri_nu_correct.mni.31236/nu1.mnc -tmpdir > ./tmp.mri_nu_correct.mni.31236/0/ -iterations 1000 -distance 50 > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. > (Maybe you should just omit the defined()?) > defined(@array) is deprecated at > /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. > (Maybe you should just omit the defined()?) > [brain@neurodebian:/media/sf_host/SZU_ZL_3WAY/test/T1/FrSrfr_Recon/mri/] > [2015-08-03 22:51:38] 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.31236/0/ > ./tmp.mri_nu_correct.mni.31236/nu0.mnc > ./tmp.mri_nu_correct.mni.31236/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 > > > > _______________________________________________ > 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. 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