Re: Re: Re: [Freesurfer] path error on cluster super-computer

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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer