7 Jan
2012
7 Jan
'12
3:28 p.m.
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 >> >> >> >> > > >The information in this e-mail is intended only for the person to whom it >is >addressed. If you believe this e-mail was sent to you in error and the >e-mail >contains patient information, please contact the Partners Compliance >HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in >error >but does not contain patient information, please contact the sender and >properly >dispose of the e-mail. >
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