.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; }
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, TaeChuncheon, Korea-------------------------------------------------------------------------------------------Iteration 1 Mon Jul 7 08:51:03 KST 2008nu_correct -clobber ./tmp.mri_nu_correct.mni.25070/nu0.mnc ./tmp.mri_nu_correct.mni.25070/nu1.mnccouldn't create "/usr/tmp/nu_correct_25115/": Permission denied[a174tws@tachyond:/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 directorymicreate: MINC package entry pointnu_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_correctLinux 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-------------------------------------------------------------------------------------------
I would try:
chmod -R 777 /usr/tmp
2008/7/6 Woo-Suk, Tae wstae@kangwon.ac.kr:
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 [a174tws@tachyond:/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
.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } 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, TaeChuncheon, Korea--- Original Message ---From : "Pedro Paulo de Magalh?es Oliveira Junior"To : "Woo-Suk, Tae"Date : 2008/07/07 월요일 오전 9:28:29Subject : Re: [Freesurfer] path error on cluster super-computer I would try:
chmod -R 777 /usr/tmp 2008/7/6 Woo-Suk, Tae wstae@kangwon.ac.kr: 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, TaeChuncheon, Korea-------------------------------------------------------------------------------------------Iteration 1 Mon Jul 7 08:51:03 KST 2008nu_correct -clobber ./tmp.mri_nu_correct.mni.25070/nu0.mnc ./tmp.mri_nu_correct.mni.25070/nu1.mnccouldn't create "/usr/tmp/nu_correct_25115/": Permission denied[a174tws@tachyond:/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 directorymicreate: MINC package entry pointnu_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_correctLinux 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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
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 wstae@kangwon.ac.kr:
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"ppj@netfilter.com.br *To : *"Woo-Suk, Tae"wstae@kangwon.ac.kr *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 wstae@kangwon.ac.kr:
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 [a174tws@tachyond:/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/freesurferhttps://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
.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } 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"To : "Woo-Suk, Tae"Date : 2008/07/08 화요일 오전 1:12:44Subject : 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 wstae@kangwon.ac.kr: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, TaeChuncheon, Korea
--- Original Message ---From : "Pedro Paulo de Magalh?es Oliveira Junior"ppj@netfilter.com.brTo : "Woo-Suk, Tae"wstae@kangwon.ac.krDate : 2008/07/07 월요일 오전 9:28:29Subject : Re: [Freesurfer] path error on cluster super-computer I would try:
chmod -R 777 /usr/tmp 2008/7/6 Woo-Suk, Tae wstae@kangwon.ac.kr: 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, TaeChuncheon, Korea-------------------------------------------------------------------------------------------Iteration 1 Mon Jul 7 08:51:03 KST 2008nu_correct -clobber ./tmp.mri_nu_correct.mni.25070/nu0.mnc ./tmp.mri_nu_correct.mni.25070/nu1.mnccouldn't create "/usr/tmp/nu_correct_25115/": Permission denied[a174tws@tachyond:/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 directorymicreate: MINC package entry pointnu_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_correctLinux 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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
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"<ppj@netfilter.com.br> To : "Woo-Suk, Tae"<wstae@kangwon.ac.kr> 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 <wstae@kangwon.ac.kr>: 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"<ppj@netfilter.com.br> To : "Woo-Suk, Tae"<wstae@kangwon.ac.kr> 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 <wstae@kangwon.ac.kr>: 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 [a174tws@tachyond:/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
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freesurfer@nmr.mgh.harvard.edu
-
Nick Schmansky -
Pedro Paulo de Magalhães Oliveira Junior -
Woo-Suk, Tae