Thanks Pedro! I've updated mri_nu_correct.mni to use a tmpdir in SUBJECTS_DIR/subjid/mri space, rather than nu_correct's default /usr/tmp, which, as Woo-Suk discovered, is not always user writable. This will appear in the next version of freesurfer.
Nick On Tue, 2008-07-08 at 10:00 +0900, Woo-Suk, Tae wrote: > Thanks Pedro Paulo de Magalh?es Oliveira Junior! > > My error corrected after modifying 'tmpdir in bin/mri_nu_correct.mni'. > > > Best regard! > > > > Woo-Suk, Tae > Chuncheon, Korea > > > --- Original Message --- > From : "Pedro Paulo de Magalh?es Oliveira > Junior"<[EMAIL PROTECTED]> > To : "Woo-Suk, Tae"<[EMAIL PROTECTED]> > Date : 2008/07/08 화요일 오전 1:12:44 > Subject : Re: Re: [Freesurfer] path error on cluster super- > computer > > I think you can change > > tmpdir in bin/mri_nu_correct.mni > > But first check if you are setting the variables correctly: > FREESURFER_HOME and executing source SetUpFreeSurfer.sh > > > 2008/7/7 Woo-Suk, Tae <[EMAIL PROTECTED]>: > The super-user of super-computer did not give me the > writing permission for /usr/tmp, > > so I should modify the source script of FreeSurfer. > > How can I do it? > > > > Woo-Suk, Tae > Chuncheon, Korea > > > > > --- Original Message --- > From : "Pedro Paulo de Magalh?es Oliveira > Junior"<[EMAIL PROTECTED]> > To : "Woo-Suk, Tae"<[EMAIL PROTECTED]> > Date : 2008/07/07 월요일 오전 9:28:29 > Subject : Re: [Freesurfer] path error on > cluster super-computer > > I would try: > > chmod -R 777 /usr/tmp > > > 2008/7/6 Woo-Suk, Tae <[EMAIL PROTECTED]>: > > Dear FreeSurfer experts! > > I had a error message when I ran a > subjects on cluter super-computer. > It seemed that the error was caused > by permission on "/usr" directory. > How can I correct this problem? > > Woo-Suk, Tae > Chuncheon, Korea > > > > > ------------------------------------------------------------------------------------------- > Iteration 1 Mon Jul 7 08:51:03 KST > 2008 > nu_correct - > clobber > ./tmp.mri_nu_correct.mni.25070/nu0.mnc ./tmp.mri_nu_correct.mni.25070/nu1.mnc > couldn't create > "/usr/tmp/nu_correct_25115/": > Permission denied > [EMAIL > PROTECTED]:/home01/a174tws/freesurfer/subjects/001/mri/] [2008-07-07 > 08:51:04] running: > > /home01/a174tws/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 > /usr/tmp/nu_correct_25115/ ./tmp.mri_nu_correct..mni.25070/nu0.mnc > ./tmp.mri_nu_correct.mni.25070/nu1.imp > > nccreate: filename > "/usr/tmp/nu_correct_25115/nu0.mnc": > No such file or directory > micreate: MINC package entry point > nu_estimate_np_and_em: crashed while > running mincresample (termination > status=768) > nu_correct: crashed while running > nu_estimate_np_and_em (termination > status=768) > ERROR: nu_correct > Linux tachyond 2.6.9-67.0.4.ELsmp #1 > SMP Wed Mar 19 15:45:32 KST 2008 > x86_64 x86_64 x86_64 GNU/Linux > > recon-all exited with ERRORS at Mon > Jul 7 08:51:05 KST 2008 > > ------------------------------------------------------------------------------------------- > > > > > > _______________________________________________ > 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 > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
