--- 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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