[Freesurfer] recon-all -s FrSrfr_Recon exited with ERRORS
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 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/comp
Re: [Freesurfer] recon-all -s FrSrfr_Recon exited with ERRORS
Hello, What is the contents of the $FREESURFER_HOME/build-stamp.txt file? -Zele On 08/03/2015 11:54 PM, Li, Zhihao wrote: > Hi FS experts, > > I was trying to run "recon-all" within the VirtualBox of NeuroDebian 8.0 > on a WIN8 host. The program stopped immaturely at the step of > "mri_nu_correct.mni". I went into the folder of "mri" and ran > "mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale > --i orig.mgz --o orig_nu.mgz" with the output pasted below. Could you > please help me to fix this problem? Thank you very much! > > > --- > > brain:mri$ 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
Re: [Freesurfer] recon-all -s FrSrfr_Recon exited with ERRORS
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 t
Re: [Freesurfer] recon-all -s FrSrfr_Recon exited with ERRORS
I had the same problem too, using VBox and running the .vdi version of FreeSurfer with no modifications. When the "recon-all" reach to the talairach phase, the program stops with this error: # > #@# Talairach Thu Oct 8 20:16:43 EDT 2015 > /media/sf_NEURO/freesurfer_em/subject001/mri > mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale > --i orig.mgz --o orig_nu.mgz > Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 > 20:41:14 UTC 2012 i686 athlon i386 GNU/Linux > recon-all -s subject001 exited with ERRORS at Thu Oct 8 20:16:51 EDT 2015 > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting The problem is not about mri_nu_correct (as some people say in previous answers to this question). For some reason, this error appears when you are trying to run the reconstruction on files stored on virtualbox shared folders (/media/sf_host/). I don't understand why sometimes it works perfectly, and sometimes the error appears. SOLUTION: The only solution is to copy the subjects to a local folder of the virtual enviroment (for example: the desktop, /home/fsuser/desktop), and then run the recon-all. After reconstruction, you can move the files back to the shared folder. 2015-08-04 5:54 GMT+02:00 Li, Zhihao : > 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_estim
