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.
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