[Freesurfer] nu_correct: crashed while running nu_estimate_np_and_em (termination status=512)
External Email - Use Caution Hi all, This post is a follow-up to a question I asked a long time ago. I finally figured out a way around my problem, and wanted to share it with anyone else who is getting this error. I was reading this thread, which referred to problems people were having using virtual machines: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45472.html Though not using a virtual machine, I was trying to run freesurfer on data that were housed on a different computer via a mounted partition. The above thread gave me the idea to try copying my data from the mounted partition to the local machine, and when I did that everything ran just fine. Sally ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] nu_correct: crashed while running nu_estimate_np_and_em (termination status=512)
External Email - Use Caution Dear freesurfer team, I have been having a problem running freesurfer on one computer. The same commands and data work fine on other machines. The error message is: nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) Looking through the message board, others have had a similar problem. I have tried many of the suggestions offered without success. Note that I have the problem using freesurfer-6.0.0 as well as freesurfer-5.3.3-HCP Information on the error messages, OS and some of the things I have tried are described below. I have seen a few inquiries of this type never resolved as far as I can tell: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-April/056844.html https://neurostars.org/t/fmriprep-crashing-during-freesurfer-nu-correct/2108 Anything you can suggest would be appreciated. Thanks, Sally I did make sure it is not a space problem:https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-February/050008.html I successfully tried the minc commands which used /opt/minc/1.9.16/bin - the files were created: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-February/050030.html mri_convert.bin orig.mgz orig.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig.nii... Using s-form transform: -1., 0., 0., 127., 0., 0., 1., -145.1500, 0., -1., 0., 147., 0., 0., 0., 1., name | start | step| cosines yspace | -145.1500 | 1. | 0. 1. 0. zspace | 147. | -1. | -0. -0. 1. xspace | 127. | -1. | 1. -0. -0. mri_convert.bin junk.mnc junk.mgh $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from junk.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, -1) writing to junk.mgh... Here's the OS info: CentOS Linux release 7.4.1708 (Core) Here's the contents of recon-all.error: -- SUBJECT FS_TEST DATE Tue Jan 22 17:07:30 GMT 2019 USER me HOST mycomputer PROCESSOR x86_64 OS Linux Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ /usr/local/freesurfer-6.0.0/bin/recon-all PWD /FS_TEST/mri CMD mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 Here's the contents of FS_TEST/mri/mri_nu_correct.mni.log -- /FS_TEST/mri /usr/local/freesurfer-6.0.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Tue Jan 22 17:07:26 GMT 2019 Program nu_correct, built from: N3 1.12.00 tmpdir is ./tmp.mri_nu_correct.mni.81524 /FS_TEST/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.81524/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.81524/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 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.81524/nu0.mnc... Iteration 1 Tue Jan 22 17:07:29 GMT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.81524/nu0.mnc ./tmp.mri_nu_correct.mni.81524/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.81524/0/ -iterations 1000 -distance 50 Cannot read input file: ./tmp.mri_nu_correct.mni.81524/nu0.mnc [me@mycomputer:/FS_TEST/mri/] [2019-01-22 17:07:29] running: /opt/minc/1.9.16/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 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.81524/0/
[Freesurfer] nu_correct crashed
Hi everyone, I just installed the latest version of Ubuntu (Ubuntu 16.04 LTS) and I reinstalled FreeSurfer (centos4). When I computed recon-all it exited with errors (nu_correct crashed). I have attached the .log files. I have already used FreeSurfer with older versions of Ubuntu and I have never had this error. Do you have any idea what needs to be done? Thanks a lot - Fanny Munsch PhD in Neurosciences Engineer in MRI post-processing mri_nu_correct.mni.log Description: mri_nu_correct.mni.log orig_nu.log Description: orig_nu.log ___ 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.
[Freesurfer] nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280)
Hi Freesurfers, I am running recon-all -autorecon1 and I have an error like this: /libdisk/tmp_EMM/subj/mri /libdisk/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 neuron1 3.3.8-gcg-201303011431 #1 SMP Fri Mar 1 14:34:57 PST 2013 x86_64 x86_64 x86_64 GNU/Linux Wed Sep 4 14:45:46 UTC 2013 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.28384 /libdisk/tmp_EMM/subj/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28384/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.28384/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=10.02, TE=4.56, TI=600.00, flip angle=12.00 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.28384/nu0.mnc... Iteration 1 Wed Sep 4 14:45:49 UTC 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.28384/nu0.mnc ./tmp.mri_nu_correct.mni.28384/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.28384/0/ -iterations 1000 -distance 50 [Elena@neuron1:/libdisk/tmp_EMM/subj/mri/] [2013-09-04 14:45:49] running: /libdisk/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.28384/0/ ./tmp.mri_nu_correct.mni.28384/nu0.mnc ./tmp.mri_nu_correct.mni.28384/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /libdisk/freesurfer/mni/bin/sharpen_volume line 153. Processing:.Done nu_estimate_np_and_em: crashed while running spline_smooth (termination status=11) nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) Does anyone have any idea how I can fix this? Thanks in advance Regards, Elena ___ 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.
