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 >> >> >> >>
>
> >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.
>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'm glad it worked out Bruce On Thu, 19 Jan 2012, LAOUCHEDI MAKHLOUF wrote:
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-ff 81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/aver age/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/d9 24f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesu rfer/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_2falbalo nga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff 81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/aver age/711-2C_as_mni_average_305/var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalo nga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff 81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/aver age/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.i e/h > >>>>tt > >>>> ps_3a_2f_2fwms01. > >>>> > >>>> > >>>>ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-599 4-4 > >>>>7e > >>>> 5- > >>>> > >>>> > >>>>ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/avera ge/ > >>>>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/h ttp > >>>>s_ > >>>> 3a_2f_2fwms01. > >>>> > >>>> > >>>>ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-599 4-4 > >>>>7e > >>>> 5- > >>>> > >>>> > >>>>ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/avera ge/ > >>>>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/ws1 515 > >>>>8/ > >>>> .t > >>>> > >>>> > >>>>mp/8d3aa62d-5994-47e5-ba6d-031806ec9ffb/systemExecTask82018837771114 467 > >>>>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. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-
Bruce Fischl -
LAOUCHEDI MAKHLOUF