Yay !!! It works finally. So the problem in the first place is: I got the wrong version of shared library :) Thank you so much.
2015-07-01 14:58 GMT+07:00 Jalmar Teeuw <jal...@me.com>: > Yes, the sudo prefix is optional, but may be required otherwise you get a > 'not authorized' message (i.e. you need administrative privileges to > install software and libraries); note 'libXp' is case-sensitive! > > sudo yum install libXp.x86_64 > > The library will be installed at /usr/lib64/libXp.so.6, a symbolic link to > /usr/lib64/libXp.so.6.2.0 > > And try Zeke's advice as well, just to be sure > > export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH > > You would have to run that command at every new terminal you open, or add > it to the configuration file of your terminal. > > P.S. I removed libXp on my machine, and yes, 3dvolreg.afni complains about > missing libXp.so.6. After installing it again with the first command, it > works again. > > On Jul 01, 2015, at 06:47 AM, Thục Trinh <thuctrinh...@gmail.com> wrote: > > 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. >> >> > _______________________________________________ > 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. > >
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