Is the command line like this: yum install libXp.so.6.x86_64 because I did run yum install libXp.so.6 before and it did not work.
2015-07-01 11:28 GMT+07:00 Z K <zkauf...@nmr.mgh.harvard.edu>: > Yes, and when it is done installing, determine exactly what directory the > libXp.so.6 file was installed into. That is the directory you want to add > to your LD_LIBRARY_PATH environment variable. > > -Zeke > > > On Jun 30, 2015, at 11:39 PM, Thục Trinh <thuctrinh...@gmail.com> wrote: > > 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 > > > _______________________________________________ > 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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