It appears nu_estimate_np_and_em crashes only when processing the data when it resides on a mounted drive. And runs to completion when the subjects dir is on the same file system as the virtual machine. That is an mni tool and I can not fully explain that behavior. It might be worth posting a question to the minc support list:
http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users -Zeke > On Jun 14, 2015, at 3:20 PM, chenhf_uestc <chenhf_ue...@163.com> wrote: > > Hi Zeke, > > When I enter the commands > $> cd /media/sf_E_DRIVE/output/nv001/mri > $> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale > --i orig.mgz --o orig_nu.mgz > > The output is in the attached file 1.txt. However, if I keep the subjects_dir > (/usr/local/freesurfer/subjects) as default, there is no error information > (attached file 2. log). The attached file 3.log is the file I changed the > subjects_dir to /media/sf_E_DRIVE/output. > > This problem confused me several days. I also used other computers (install > VirtualboxXubuntu 12.04stable v5.3.015 Aug > 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G ) and > came across the same problem. > > If you need further information, please do not hesitate to contact me. > > Best, > Feng > > 发件人：zkauf...@nmr.mgh.harvard.edu > 发送时间：2015-06-15 04:58 > 主题：Re: [Freesurfer] freesurfer problem report > 收件人："Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu> > 抄送： > > Hello Feng Liu, > > What is the terminal output when you enter the following commands: > > $> cd /media/sf_E_DRIVE/output/nv001/mri > $> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale > --i orig.mgz --o orig_nu.mgz > > -Zeke > > > Dear freesurfer experts, > > > > I came across a problem when I run freesurfer. I just download the > > freesurfer software ( VirtualboxXubuntu 12.04stable v5.3.015 Aug > > 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G > > ). I install the software and configuration, and I changed subjects_dir as > > /media/sf_E_DRIVE. When I executed the command recon-all -s nv001 -all, > > there is error in the command window. > > > > The information of freesurfer problem are as follows: > > FREESURFER_HOME: /usr/local/freesurfer > > > > Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 > > > > Debian version: wheezy/sid > > > > Kernel info: Linux 3.2.0-23-generic i686 > > > > --------------------------------------------------------------------- > > Please include the following additional information in your report: > > > > 1) subject name > > nv001 > > 2) the entire command-line executed > > recon-all -s nv001 -all > > 3) the error message generated > > INFO: extension is mgz > > #-------------------------------------------- > > #@# Talairach Sun Jun 14 12:25:31 EDT 2015 > > /media/sf_E_DRIVE/output/nv001/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 i686 i386 GNU/Linux > > > > recon-all -s nv001 -all exited with ERRORS at Sun Jun 14 12:25:42 EDT > > 2015 > > > > For more details, see the log file > > /media/sf_E_DRIVE/output/nv001/scripts/recon-all.log > > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > 4) optionally include the subject's /script/recon-all.log > > Attached > > > > However, if I am not change the subjects_dir (usr the default: > > /usr/local/freesurfer/subjects), there is no error information. > > > > I do not know where I am wrong. > > Would greatly appreciate any form of help! > > > > 2015-06-15 > > > > > > > > Feng Liu, Ph.D. > > Department of Radiology, > > Tianjin Medical University General Hospital, > > No. 154, Anshan Road, Heping District, Tianjin > > 300052._______________________________________________ > > 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. > > <file 1.txt> > <file 2.log> > <file 3.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.
