--- 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 È­¿äÀÏ ¿ÀÀü 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 ¿ù¿äÀÏ ¿ÀÀü 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
-------------------------------------------------------------------------------------------

 

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