Fw : Re: get_4dfp_dimoe problem - Freesurfer

6 Jan 2012

    De: LAOUCHEDI MAKHLOUF <laoumakhl@yahoo.fr>
    Objet: Re: [Freesurfer] get_4dfp_dimoe problem
    À: "AviSnyder" <avi@npg.wustl.edu>
    Date: Vendredi 6 janvier 2012, 15h28

    hi everyone
                     i just remind you of my problem of the file
    name which was too long on our cloud; you advised us to
    download the endianio.c module, we did this and we installed
    it then we've run recon-all but we still have an error
    message :

    $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $
    Getifh: /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mnone.4dfp.ifh read error, imgfile='/var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mnone.4dfp.img'
    Segmentation fault
    ERROR:
    'imgreg_4dfp /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2C_as_mni_average_305 /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=139
    ERROR: mpr2mni305 execution aborted

    i've attached the recon-all.log contained in the scripts dir
    and the log file contained in mri/transforms dir


    thank you very much


    --- En date de : Mer 4.1.12, Snyder, Avi <avi@npg.wustl.edu> a
    écrit :

            De: Snyder, Avi <avi@npg.wustl.edu>
            Objet: Re: [Freesurfer] get_4dfp_dimoe problem
            À: "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>
            Cc: "LAOUCHEDI MAKHLOUF" <laoumakhl@yahoo.fr>,
            "Freesurfer@nmr.mgh.harvard.edu"
            <Freesurfer@nmr.mgh.harvard.edu>
            Date: Mercredi 4 janvier 2012, 1h31

            I don't think there are any special env variables.
            It may be that the environment in which FreeSurfer is
            being run simply
            generates huge pathnames.
            A few months ago I revised the module containing
            get_4dfp_dimoe() to
            double the size of filename buffers.
            This module (endianio.c) is attached. Theoretically,
            compiling with this
            revised source could fix the problem.

            Avi
            -----------------------------
            On 1/3/12 6:04 PM, "Bruce Fischl"
            <fischl@nmr.mgh.harvard.edu> wrote:

            >Hi Avi
            >
            >just running recon-all I think. Is there an env
            variable you use to
            >specify 
            >a tmp dir or something?
            >
            >thanks
            >Bruce
            >
            >On Tue, 3 Jan 2012, Snyder, Avi wrote:
            >
            >> It looks like both the command (imgreg_4dfp) and
            argument
            >> (.../711-2B_as_mni_average_305_mask.4dfp.img)
            fields are garbled.
            >> Evidently, operating system paths have not been
            correctly set.
            >> The 4dfp suite of tools is available and probably
            could be installed but
            >> I'm not sure that is what is wanted.
            >> I don't understand what LAOUCHEDI MAKHLOUF is
            trying to do.
            >>
            >> AZS
            >>
            -----------------------------------------------------
            >> On 1/3/12 10:40 AM, "Bruce Fischl"
            <fischl@nmr.mgh.harvard.edu> wrote:
            >>
            >>> this is actually not part of FreeSurfer proper,
            but rather something
            >>>that
            >>> Avi Synder (ccd) was kind enough to contribute.
            Avi: can you comment?
            >>>
            >>> thanks
            >>> Bruce
            >>> On
            >>> Tue, 3 Jan 2012, LAOUCHEDI MAKHLOUF wrote:
            >>>
            >>>> hi everyone
            >>>> we run recon-all on a cloud and we obtained this
            error:
            >>>>
            >>>> mpr2mni305 failed, see
            transforms/talairach_avi.log
            >>>>
            >>>> The log says the file name is too long perhaps
            because of the tmp dir
            >>>> file
            >>>> names:
            >>>>
            >>>>
            >>>> 
            >>>>get_4dfp_dimoe:/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/h
            >>>>tt
            >>>> ps_3a_2f_2fwms01.
            >>>>
            >>>> 
            >>>>ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-4
            >>>>7e
            >>>> 5-
            >>>>
            >>>> 
            >>>>ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/
            >>>>71
            >>>> 1-
            >>>> 2B_as_mni_average_305_mask.4dfp.img filename too
            long
            >>>> ERROR:
            >>>> 
            >>>>'imgreg_4dfp/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/http
            >>>>s_
            >>>> 3a_2f_2fwms01.
            >>>>
            >>>> 
            >>>>ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-4
            >>>>7e
            >>>> 5-
            >>>>
            >>>> 
            >>>>ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/
            >>>>71
            >>>> 1-
            >>>> 2C_as_mni_average_305
            >>>> /var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.i
            >>>>
            >>>> 
            >>>>e/https_3a_2f_2fwms01.ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws1515
            >>>>8/
            >>>> .t
            >>>>
            >>>> 
            >>>>mp/8d3aa62d-5994-47e5-ba6d-031806ec9ffb/systemExecTask82018837771114467
            >>>>75
            >>>> /f
            >>>>
            reesurfer/average/711-2B_as_mni_average_305_masktalsrcimg_g11 none
            >>>> talsrcimg_to_711-2C_as_mni_average_305_t4 4355'
            failed! status=255
            >>>>
            >>>>
            >>>> knowing that it is difficult for us to do things
            differently (to
            >>>>change
            >>>> the
            >>>> path); is it possible to do something in
            freesurfer to work with
            >>>>thesse
            >>>> filenames ?
            >>>>
            >>>> thanks for your help
            >>
            >>
            >>
            >>
            >
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