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
