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.
