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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