Yes, and when it is done installing, determine exactly what directory the libXp.so.6 file was installed into. That is the directory you want to add to your LD_LIBRARY_PATH environment variable.
-Zeke > On Jun 30, 2015, at 11:39 PM, Thục Trinh <thuctrinh...@gmail.com> wrote: > > Hi, > I did exactly what you said, and the error still remain: 3dvolreg.afni: error > while loading shared libraries: libXp.so.6: cannot open shared object file: > No such file or directory > I cannot find any folder name libXp.so.6,should I re-download libXp.so.6 64 > bits ? > > > 2015-06-29 18:15 GMT+07:00 Jalmar Teeuw <jal...@me.com>: >> Sorry, I didn't have access to my CentOS machine, the 32-bit libraries use >> the suffix i686 instead of i386, so try >> >> sudo yum remove libXp.i686 >> >> By removing the 32-bit version you essential ensure only the 64-bit version >> is available when the application tries to load libXp. Hope that works. My >> machine only has the 64-bit version installed. Although technically, it >> should not matter if you have both installed on the system as it should >> automatically pick the correction version. >> >> If it doesn't work, you could try to run >> >> find / -type f -iname "libXp.so*" -print >> >> to check if the libXp libraries might be installed somewhere else. It may >> take some time to scan the entire system and any mounted volumes. You can >> use the `file <file>` command to check if the library is 32 or 64-bit, and >> remove any 32-bit or even 64-bit version outside /usr/lib64 (BEWARE: >> removing libraries is at risk of breaking functioning of other application >> that depend on that particular library. If necessary, you can always run >> `sudo yum install libXp.i686` to install the 32-bit version again) >> >> >>> On Jun 29, 2015, at 08:10 AM, Thục Trinh <thuctrinh...@gmail.com> wrote: >>> >> >>> Hi, >>> "yum remove libXp.i386" command returns with >>> No Packages marked for removal >>> This is my output for:'file $FREESURFER_HOME/bin/3dvolreg.afni' >>> /usr/local/freesurfer/bin/3dvolreg.afni: ELF 64-bit LSB executable, x86-64, >>> version 1 (GNU/Linux), statically linked, stripped >>> >>> >>> 2015-06-26 16:19 GMT+07:00 Jalmar Teeuw <jal...@me.com>: >>>> >>>> Have you tried removing the 32-bit version of the libraries? >>>> >>>> I believe it is >>>> >>>> yum remove libXp.i386 >>>> >>>> >>>> What is the output of >>>> >>>> file $FREESURFER_HOME/bin/3dvolreg.afni >>>> >>>> Maybe you could try locate all the libXp.so on your system and see if >>>> there is a local 32-bit copy >>>> >>>> find / -type f -iname "libXp.so*" >>>> >>>> >>>>> On 25 Jun 2015, at 09:45, Thục Trinh <thuctrinh...@gmail.com> wrote: >>>>> >>>>> the lib files are now in /usr/lib64, the ERROR still the same after I set >>>>> a new path for shared lib with this command in .bashrc file >>>>> export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH >>>>> the Error still the same. >>>>> 3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong >>>>> ELF class: ELFCLASS32 >>>>> output of uname -a on my system is: >>>>> Linux localhost.localdomain 2.6.32-358.el6.x86_64 #1 SMP Fri Feb 22 >>>>> 00:31:26 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux >>>>> >>>>> 2015-06-25 14:15 GMT+07:00 Jalmar Teeuw <jal...@me.com>: >>>>>> Is still gives you the same error? I'm not certain about libXpm; I >>>>>> recall having to install certain libraries on a slimmed down version of >>>>>> Centos 6.5, libXp and libXpm were amongst those libraries. >>>>>> >>>>>> For me, the lib files are stored in /usr/lib64 >>>>>> >>>>>> Try >>>>>> >>>>>> find /usr/lib64 -type f -iname "libXp*" -print >>>>>> >>>>>> This will search for the files. >>>>>> >>>>>> >>>>>> What is the output >>>>>> >>>>>> uname -a >>>>>> >>>>>> On your system? >>>>>> >>>>>> >>>>>> On 25 Jun 2015, at 09:01, Thục Trinh <thuctrinh...@gmail.com> wrote: >>>>>> >>>>>>> Hi, >>>>>>> After complete install the suitable version of shared library as you >>>>>>> suggested, I cannot find any file name libXpm.x86_64 to set the new >>>>>>> path for shared library. >>>>>>> Ps: Is there any differences between libXpm.x86_64 and libXp.x86_64 >>>>>>> >>>>>>> 2015-06-24 16:03 GMT+07:00 Jalmar Teeuw <jal...@me.com>: >>>>>>>> That sounds more like you have only the 32-bit version of the libXp >>>>>>>> installed when 64-bit is required. Are you using the 64-bit version of >>>>>>>> Freesurfer 5.3.0 for CentOS 6 that is available on the downloads page? >>>>>>>> >>>>>>>> Have you tried >>>>>>>> >>>>>>>> sudo yum install libXp.x86_64 >>>>>>>> >>>>>>>> on the terminal? This should install the 64-bit libraries alongside >>>>>>>> the 32-bit libraries of libXp. >>>>>>>> >>>>>>>> If I recall correctly, you might also need the libXpm libraries, use >>>>>>>> >>>>>>>> sudo yum install libXpm.x86_64 >>>>>>>> >>>>>>>> >>>>>>>> > On 24 Jun 2015, at 04:49, Thục Trinh <thuctrinh...@gmail.com> wrote: >>>>>>>> > >>>>>>>> > I did that, and run the command 3dvolreg.afni on Terminal to check. >>>>>>>> > The Error still remain: 3dvolreg.afni: error while loading shared >>>>>>>> > libraries: libXp.so.6: wrong ELF class: ELFCLASS32 >>>>>>>> > >>>>>>>> > 2015-06-23 10:39 GMT+07:00 Z K <zkauf...@nmr.mgh.harvard.edu>: >>>>>>>> > From reading the email thread history, it appears you may have >>>>>>>> > downloaded the apple OS X version of 3rvolreg.afni and overwrote the >>>>>>>> > original, which is the cause of the error. Please extract the >>>>>>>> > original version of that binary from the original tarball. If you no >>>>>>>> > longer have it you can download it from this page: >>>>>>>> > >>>>>>>> > https://surfer.nmr.mgh.harvard.edu/fswiki/Download >>>>>>>> > >>>>>>>> > -Zeke >>>>>>>> > >>>>>>>> > >>>>>>>> > On Jun 22, 2015, at 11:29 PM, Thục Trinh <thuctrinh...@gmail.com> >>>>>>>> > wrote: >>>>>>>> > >>>>>>>> >> hello, >>>>>>>> >> I am using CentOS release 6.4 ( final) 64bit and Freesurfer v.5.3.0. >>>>>>>> >> I think that makes the confliction. >>>>>>>> >> >>>>>>>> >> 2015-06-23 8:26 GMT+07:00 Thục Trinh <thuctrinh...@gmail.com>: >>>>>>>> >> Hello Douglas and ZK, >>>>>>>> >> I set the path for shared library in my .basrch file, but it still >>>>>>>> >> does not work and comes up with this Error: >>>>>>>> >> 3dvolreg.afni: error while loading shared libraries: libXp.so.6: >>>>>>>> >> wrong ELF class: ELFCLASS32 >>>>>>>> >> ERROR: 3dvolreg.afni >>>>>>>> >> Invalid null command. >>>>>>>> >> >>>>>>>> >> Trinh >>>>>>>> >> >>>>>>>> >> 2015-06-23 3:03 GMT+07:00 Z K <zkauf...@nmr.mgh.harvard.edu>: >>>>>>>> >> Trinh, >>>>>>>> >> >>>>>>>> >> Attempt to determine where libXp.so.6 was installed on your system >>>>>>>> >> after >>>>>>>> >> you installed it using yum. For example, on my system libXp.so.6 >>>>>>>> >> exists >>>>>>>> >> in directory "/usr/lib64". Once you determine the location where the >>>>>>>> >> library resides, add that directory to your LD_LIBRARY_PATH after >>>>>>>> >> you >>>>>>>> >> source freesurfer. >>>>>>>> >> >>>>>>>> >> $> source $FREESURFER_HOME/SetUpFreeSurfer.sh >>>>>>>> >> $> export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH >>>>>>>> >> $> preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh >>>>>>>> >> -fwhm 5 -per-run >>>>>>>> >> >>>>>>>> >> -Zeke >>>>>>>> >> >>>>>>>> >> >>>>>>>> >> >>>>>>>> >> >>>>>>>> >> On 06/22/2015 02:40 PM, Douglas Greve wrote: >>>>>>>> >> > I'm not sure what to tell you. Zeke, do you have any ideas? >>>>>>>> >> > Alternatively, you can just install afni on your machine. Once you >>>>>>>> >> > verify that the installation works, copy 3dvolreg from the >>>>>>>> >> > installation. >>>>>>>> >> > >>>>>>>> >> > On 6/21/15 3:55 PM, Thục Trinh wrote: >>>>>>>> >> >> Hello Douglas, >>>>>>>> >> >> I already had *3dvolreg.afni* in */freesurfer/bin/*, but I still >>>>>>>> >> >> download the new one 3dvolreg.afni and replaced it in >>>>>>>> >> >> /freesurfer/bin. >>>>>>>> >> >> But the Error still remain the same. >>>>>>>> >> >> *3dvolreg.afni: error while loading shared libraries: libXp.so.6: >>>>>>>> >> >> cannot open shared object file: No such file or directory* >>>>>>>> >> >> *ERROR: 3dvolreg.afni* >>>>>>>> >> >> *Invalid null command.* >>>>>>>> >> >> >>>>>>>> >> >> >>>>>>>> >> >> 2015-06-19 16:04 GMT+07:00 Douglas Greve >>>>>>>> >> >> <gr...@nmr.mgh.harvard.edu >>>>>>>> >> >> <mailto:gr...@nmr.mgh.harvard.edu>>: >>>>>>>> >> >> >>>>>>>> >> >> >>>>>>>> >> >> See this thread >>>>>>>> >> >> >>>>>>>> >> >> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37764.html >>>>>>>> >> >> >>>>>>>> >> >> >>>>>>>> >> >> >>>>>>>> >> >> >>>>>>>> >> >> On 6/17/15 5:59 PM, Thục Trinh wrote: >>>>>>>> >> >>> Hi freesurfer experts, >>>>>>>> >> >>> I am practicing on the fsfast tutorial data that were given >>>>>>>> >> >>> at >>>>>>>> >> >>> Freesurfer website. >>>>>>>> >> >>> I run the command to do the pre-processing on the sess01 >>>>>>>> >> >>> <*noproc*>. >>>>>>>> >> >>> *preproc-sess -s sess01 -fsd bold -stc up -surface >>>>>>>> >> >>> fsaverage lhrh >>>>>>>> >> >>> -fwhm 5 -per-run* >>>>>>>> >> >>> it was unfinished and failed with the ERROR: >>>>>>>> >> >>> *3dvolreg.afni: error while loading shared libraries: >>>>>>>> >> >>> libXp.so.6: >>>>>>>> >> >>> cannot open shared object file: No such file or directory* >>>>>>>> >> >>> *ERROR: 3dvolreg.afni* >>>>>>>> >> >>> *Invalid null command.* >>>>>>>> >> >>> so I run the command to install libXp.so.6 under root >>>>>>>> >> >>> permission >>>>>>>> >> >>> *yum install libXp.so.6 *and completely installed. >>>>>>>> >> >>> I found the file *3dvolreg.afni *in the $FREESURFER_HOME/bin >>>>>>>> >> >>> But the ERROR still remained unfixed. >>>>>>>> >> >>> >>>>>>>> >> >>> Please help me with any suggestions to finish the >>>>>>>> >> >>> preproc-sesss >>>>>>>> >> >>> Thankyou and have a nice day. >>>>>>>> >> >>> Trinh Tran >>>>>>>> >> >>> >>>>>>>> >> >>> >>>>>>>> >> >>> _______________________________________________ >>>>>>>> >> >>> Freesurfer mailing list >>>>>>>> >> >>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> >> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> >> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >> >> >>>>>>>> >> >> >>>>>>>> >> >> _______________________________________________ >>>>>>>> >> >> Freesurfer mailing list >>>>>>>> >> >> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >> >> >>>>>>>> >> >> >>>>>>>> >> >> 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 >>>>>>>> >> >>>>>>>> >> >>>>>>>> >> _______________________________________________ >>>>>>>> >> 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 >>>>>>>> > >>>>>>>> > >>>>>>>> > 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 >>>>>>>> > >>>>>>>> > >>>>>>>> > 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 >>>>>>> >>>>>>> >>>>>>> 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 >>>>>> >>>>>> >>>>>> 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 >>>>> >>>>> >>>>> 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 >>>> >>>> >>>> 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 >>> >>> >>> 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 >> >> >> 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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