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 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.
