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.
