hi everyone

           i want just to inform you that it is ok with my problem of the huge pathnames generated by our cluster

thank you very much


--- En date de : Sam 7.1.12, Nick Schmansky <nicks@nmr.mgh.harvard.edu> a écrit :

De: Nick Schmansky <nicks@nmr.mgh.harvard.edu>
Objet: Re: [Freesurfer] Fw : Re: get_4dfp_dimoe problem
À: "LAOUCHEDI MAKHLOUF" <laoumakhl@yahoo.fr>
Cc: Freesurfer@nmr.mgh.harvard.edu
Date: Samedi 7 janvier 2012, 21h28

laouchedi,

the file 'endianio.c' is not a module that can be installed by the
end-user. it is source code. did you install the files that i referred
to in my prior email to the list? those were rebuilt using endianio.c,
and are found here:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64

and are named *4dfp. copy those files to your $FREESURFER_HOME/bin.

n.

On Fri, 2012-01-06 at 14:29 +0000, LAOUCHEDI MAKHLOUF wrote:
>
>
> --- En date de : Ven 6.1.12, LAOUCHEDI MAKHLOUF <laoumakhl@yahoo.fr> a
> écrit :
>
>    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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>    >is
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